apraga/org - Change EXXDISQ3I67ZY3JZP7BFBDXLHLL5YIPQMXYMN4IPTNYJFOFPLOPAC

Merging aura tasks (meeting etc) in a single org-file

Created by Alexis Praga on July 24, 2024

EXXDISQ3I67ZY3JZP7BFBDXLHLL5YIPQMXYMN4IPTNYJFOFPLOPAC

Dependencies

In channels

main

Change contents

File deletion: todo.org, projects.org
BF:BFD[3.2] → [4.1:33]
BF:BFD[4.33] → [5.1:1]
BFD:BFD[3.2] → [5.150:186]
BF:BFD[5.186] → [5.1:1]
B:BD[5.1] → [6.1:15]
```
#+title: Todo
```

File addition: reunions.org_archive (----------)

[3.2]

#    -*- mode: org -*-
Archived entries from file /home/alexis/org/reunions.org
* DONE Regarder génome IOP [4/4]
SCHEDULED: <2024-05-22 mer.> DEADLINE: <2024-05-24 ven.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-05-29 mer. 13:35
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
:LOGBOOK:
CLOCK: [2024-05-22 mer. 14:59]--[2024-05-22 mer. 15:13] =>  0:14
CLOCK: [2024-05-22 mer. 14:08]--[2024-05-22 mer. 14:10] =>  0:02
CLOCK: [2024-05-22 mer. 11:35]--[2024-05-22 mer. 13:46] =>  2:11
:END:
- [X] MR-2304725 : négatif ?
  Aurapport
  - GALT: récessif et variant htz, pas de clinique de galactosémie ? (plutôt à la naissance)
  - GJB2: non compatible clinique
  Seqone :
  - intronique NR5A1 : difficile d'en conclure quelque chose...
  SV : évènement complexe chr9:138145330 (9q34.3) chr10:79064 (10p15.3)  mais ségrège
- [X] MR-2101776
  2 variants MCM8 : un touchant épissage et un tronquant mais gène pLI= 1. Clinique en faveur...
  Pas grand chose sur decipher
  SNV: inv 7q touchant RBM28 [[https://omim.org/clinicalSynopsis/table?mimNumber=612079][OMIM]]  mais hérité père asympto
- [X] MR-2305313 : neg ?
  - 2 variants HSPG2 écartés sur clinique (gènes récessif)
- [X] MR-2304151 : neg ?
  ERCC6 VOUS- ? (seqone) regarder dans decipher
/Créé le/ [2024-05-17 ven. 17:12]
* DONE RVI IOP [[https://univ-grenoble-alpes-fr.zoom.us/j/94124867955?pwd=WGg2ZDRnZU45U29oQUdla2NRaDFJZz09][lien zoom]]
DEADLINE: <2024-05-24 ven. 08:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-05-29 mer. 13:35
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
/Créé le/ [2024-05-17 ven. 17:13]
* DONE Revoir variants loupé CHD3
CLOSED: [2024-05-17 ven. 18:01] SCHEDULED: <2024-05-17 ven.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-05-29 mer. 13:35
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
/Créé le/ [2024-05-17 ven. 18:00]
* DONE Préparer axes 3
SCHEDULED: <2024-05-29 mer.> DEADLINE: <2024-05-30 jeu.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
/Créé le/ [2024-05-16 jeu. 17:30]
- Image vue d'ensemble pipeline
* DONE 22q11
SCHEDULED: <2024-05-24 ven. 13:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-24 ven. 09:51]
* DONE Réunion biologistes Lyon
SCHEDULED: <2024-05-24 ven. 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-24 ven. 17:03]
* DONE Réunion Julien interprétation génome
SCHEDULED: <2024-05-29 mer. 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-28 mar. 09:33]
* DONE Regarder à nouveau dossiers réunion Jérémie [3/3]
DEADLINE: <2024-05-31 ven. 17:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
:LOGBOOK:
CLOCK: [2024-05-29 mer. 11:01]--[2024-05-29 mer. 11:39] =>  0:38
CLOCK: [2024-05-29 mer. 09:49]--[2024-05-29 mer. 10:15] =>  0:26
:END:
  /Entered on/  [2024-05-29 mer. 09:30]
- [X] MR-2301991 : rien vu expliquant tout le phénotype (juste obésité)
- [X] MR-2304917 : SLC25A24 convaincant mais jumeau sain porteur donc non (vu avec Julien)
- [X] MR-2303537
  OTX2 échappe NMD fin de gène, ok super pour clinique ophtalmo (microphtalmie +  rétinopathie et clinvar patho sur ce phénotype) mais n'explique pas le reste
 SLC26A5 : htz compositie pour surdité ? sur score bioinfo
* DONE Interprétation avec Wiam
SCHEDULED: <2024-05-30 jeu. 17:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-29 mer. 10:05]
* DONE Interprétation 3 génomes avec Jérémy et Julien
SCHEDULED: <2024-05-31 ven. 17:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-05-29 mer. 17:22]
* DONE Axe 3
SCHEDULED: <2024-05-30 jeu. 09:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-03 lun. 10:08
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-05-30 jeu. 10:19]
* DONE Regarder génome IOP [4/4]
SCHEDULED: <2024-05-22 mer.> DEADLINE: <2024-05-24 ven.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-06 jeu. 17:37
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
:LOGBOOK:
CLOCK: [2024-05-22 mer. 14:59]--[2024-05-22 mer. 15:13] =>  0:14
CLOCK: [2024-05-22 mer. 14:08]--[2024-05-22 mer. 14:10] =>  0:02
CLOCK: [2024-05-22 mer. 11:35]--[2024-05-22 mer. 13:46] =>  2:11
:END:
- [X] MR-2304725 : négatif ?
  Aurapport
  - GALT: récessif et variant htz, pas de clinique de galactosémie ? (plutôt à la naissance)
  - GJB2: non compatible clinique
  Seqone :
  - intronique NR5A1 : difficile d'en conclure quelque chose...
  SV : évènement complexe chr9:138145330 (9q34.3) chr10:79064 (10p15.3)  mais ségrège
- [X] MR-2101776
  2 variants MCM8 : un touchant épissage et un tronquant mais gène pLI= 1. Clinique en faveur...
  Pas grand chose sur decipher
  SNV: inv 7q touchant RBM28 [[https://omim.org/clinicalSynopsis/table?mimNumber=612079][OMIM]]  mais hérité père asympto
- [X] MR-2305313 : neg ?
  - 2 variants HSPG2 écartés sur clinique (gènes récessif)
- [X] MR-2304151 : neg ?
  ERCC6 VOUS- ? (seqone) regarder dans decipher
/Créé le/ [2024-05-17 ven. 17:12]
* DONE RVI IOP [[https://univ-grenoble-alpes-fr.zoom.us/j/94124867955?pwd=WGg2ZDRnZU45U29oQUdla2NRaDFJZz09][lien zoom]]
DEADLINE: <2024-05-24 ven. 08:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-06 jeu. 17:37
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
/Créé le/ [2024-05-17 ven. 17:13]
* DONE Revoir variants loupé CHD3
CLOSED: [2024-05-17 ven. 18:01] SCHEDULED: <2024-05-17 ven.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-06 jeu. 17:37
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
/Créé le/ [2024-05-17 ven. 18:00]
* DONE Diapos clinique [7/7]
DEADLINE: <2024-05-31 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-06 jeu. 17:37
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: rvi
:END:
  /Entered on/  [2024-05-28 mar. 09:15]
    - [X] MR-2401132 à compléter avec CR génétique ? non trouvé
    - [X] MR-2401482
    - [X] MR-2401357 manque CR génétique
    - [X] MR-2400284 discuté 14 juin
    - [X] MR-2404788 à récupérer sur hygen mais plus d'accès ??
    - [X] MR-2400248 idem
    - [X] MR-2400955 idem
* DONE Regarder dossiers Jérémie [5/5]
CLOSED: [2024-06-07 ven. 15:36] SCHEDULED: <2024-06-07 ven. 16:00> DEADLINE: <2024-06-07 ven. 16:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-11 mar. 15:27
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-31 ven. 19:21]
** DONE MR-2001133 rien
CLOSED: [2024-06-06 jeu. 12:59]
** DONE MR-2303288 VOUS dup NCKAP1 rendue VOUS
CLOSED: [2024-06-07 ven. 11:41]
- VOUS KMT2D : score patho, mélange faux-sens mais hérité du père et la mère a une DI + retard. Kabuki : versions sans dysmorphie typique ni malfo ?
- VOUS- sur GSPG2 ? Clinique colle mais gène peu connu
- ARID2: clinique ne colle pas ? DI 7 petite taille + di seule, pas dysmorphie coffin siris
  CNV :
  - dup PIK3R1 = fausse ?
  - dup NCKAP1 = rapéporté dans la DI mais pert de fonmciton (pHalpo 0.56)
** DONE MR-2303537 OTX2
CLOSED: [2024-06-07 ven. 11:57]
SLC26A5 2 VOUS- (?) pour surdité
** DONE MR-2301275 rien
CLOSED: [2024-06-07 ven. 15:06]
PUF60 : VOUS avec VAF 20%, clinique peu spécifique, score bioinfo peu spécifique, début gène,, peu connu, de novo
KIAA1109: un VOUS mais autre variant non convaincant
NMNAT1: récessif, 2 clinvarpatho pour amarose de Leber -> pas d'examen ophtalmique
Seqone pdzd7 : clinique ne colle pas
** DONE MR-2401268 rien
CLOSED: [2024-06-07 ven. 15:36]
seqone non fait
* DONE Point Jérémie 5 dossier
CLOSED: [2024-06-07 ven. 17:37] SCHEDULED: <2024-06-07 ven. 16:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-11 mar. 15:27
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-31 ven. 19:21]
* DONE Visio interCHU Biomnis
CLOSED: [2024-06-07 ven. 11:25] SCHEDULED: <2024-06-07 ven. 10:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-11 mar. 15:27
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-06 jeu. 10:08]
* DONE Lire génomes [4/4]
DEADLINE: <2024-05-31 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-11 mar. 15:27
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
  /Entered on/  [2024-05-28 mar. 09:16]
  - [X] MR-2401132 diag loupé ? rien vu mais après discussion avec virgine TPR53K -> revoir
    clinvar 4 sur acide aminé, clinvar 5 sur l'acide aminé adjacent )
    Clinique différentes mais manque d'info
    homozygote hérité de chaque parent
    - curagenv2
      - SCN2A : hérité père asympto, non compatible https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9005871/
      - CACNA1A . hérité mère asympo
      - DEPDC5
      - VARS (en fait, VARS1) : clinique compatible mais AR sans 2e hit flagrant (2 intronique profond)
    - seqone
      - RANBP2 : VOUS  et clinique non en faveur (pas d'infection ?). En début de gène, faux-sens avec plutôt faux-sens rapportées mais score bioinfo peu en faveur
  - [X] MR-2401482 rien revoir
    aurapport : rien
    seqone : NEK8 récessif sans 2e variant
  - [X] MR-2401357 : VOUS sur DPP6 forme mild. Clingen : rôle dans neurodev "disputed", milieu de gène
    - TANC2 VOUS- sur forme mild ? 1% cohorte, légère modification épissage, début de gène
    - TRAPP9 récessif, bof, faux-sens fin de gène
    - dup 1mb de 1q41 : bof, 2 gènes récessifs, 3 copies hérité mère clinique peu en faveur. RAB3GAP2 ptriplo 0.44
  - [X] MR-2400284 VOUS sur DEAF1: qq scores en faveur, milieu de gène
* DONE RVI
SCHEDULED: <2024-05-31 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-11 mar. 15:27
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
  /Entered on/  [2024-05-28 mar. 09:16]
* DONE Formation VDM
CLOSED: [2024-06-06 jeu. 16:29] SCHEDULED: <2024-06-06 jeu. 09:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-11 mar. 15:27
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-05-29 mer. 11:05]
* DONE Vérifier diapos cliniques complètes :rvi:
CLOSED: [2024-06-12 mer. 17:14] DEADLINE: <2024-06-14 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble
:END:
Entered on [2024-06-03 lun. 11:24]
* DONE Lire génomes [9/9]
CLOSED: [2024-06-14 ven. 16:43] DEADLINE: <2024-06-14 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
Entered on [2024-06-03 lun. 11:21]
** DONE MR-2304788 déjà rendu
CLOSED: [2024-06-14 ven. 09:05]
** DONE MR-2400248 :
CLOSED: [2024-06-14 ven. 10:17]
- FRMPD4 : VOUS car faux-sens fin de gène, score bioinfo bénin, peu fréquent gnomad, hémizygote
- TRIP12 : idem FRMPD4... hérité de la mère
- KCNN3 : idem que les 2 autres mais qq score bioinfo en faveur (hérité mère)
- SYNGAP : VOUS- ? faux-sens gène perte de fonction, clinique non en faveur (forme mild ??)
 CNV:
 - Xq42  RN113A: évènement complexe ? (del + inv ?)
** DONE MR-2400955 rien
CLOSED: [2024-06-14 ven. 14:25]
- RNF2 gène peu connu, score bioinfo peu en faveur, hérité père atteint. VOUS ?
- SEDT1B bof
 vérif MAD      D
** DONE MR-2300720 rien
CLOSED: [2024-06-05 mer. 15:04]
- DPH1 non clinvar conflicting, les rares patho sont faux-sens mais récessif sans 2e variant
- FGFR1 non score bioinfo
- POLR3A non score binfo
- WDR81 idem
- KI26A : 2 faux-sens pour maladie récessive mais score non en faveur (1 repêché dans seqone)
** DONE MR-2400707 suspicion marfan patho FBN1 oc
CLOSED: [2024-06-05 mer. 11:22]
** DONE MR-2401534 : 2 VOUS
CLOSED: [2024-06-05 mer. 11:55]
- NEK8 non récessif -> regarder seqone: pas de 2e hit
même faux sens  clinvar patho mais 0 étoile, score bioinfo en faveur
zone bien conservée
- HNRNPU VOUS : hérité, atteinte épissage, pli à 1 mais zone LOF gnomad. Clinique correspond partiellement DI+épileptic encéphalotpatie
  Genereviews
  - Cardiac abnormalities	30% (Septal defects are the most common)
  - Renal anomalies	<10%
  - Hyperventilation & apnea	Rare
- HK1 VOUS, hérité, gène peu connu, score patho mais n'explique as les malformations
omim "A few patients had scoliosis, hip dislocation, foot deformities, laryngotracheomalacia (the sibs), and/or mild nonspecific"
- dup SYT1 non : triplo 0.68 clinique ne colle pas, problème sur les bornes ?, dans la cohorte
** DONE MR-2401755 : 1 VOUS
CLOSED: [2024-06-05 mer. 15:50]
DEAF1 faux-sens patho decipher mais exclu bioinfo
NIBPL exclut cohorte
PCNT exclu clinique
DCHS1 récessif sans second variant
curagen v2: PRKAR1A intronique proche, score bioinfo, acrydysoses -> VOUS
** DONE MR-2401840 class 4 NUS1
CLOSED: [2024-06-05 mer. 16:21]
scarb2 AR non 1 seul varant
NUS1 : de novo, clinique colle, score bioinfo, non vu gnomad. Variant faux-sens déjà rapporté path
** DONE MR-2401868 rien
CLOSED: [2024-06-05 mer. 17:02]
* DONE RVI
CLOSED: [2024-06-14 ven. 16:43] SCHEDULED: <2024-06-14 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
Entered on [2024-06-03 lun. 11:21]
* DONE MR-2301514 CFTR htz
CLOSED: [2024-06-19 mer. 18:05] DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
:LOGBOOK:
CLOCK: [2024-06-18 mar. 10:04]--[2024-06-18 mar. 10:12] =>  0:08
:END:
- NIPBL: non vu gnomad, score bioinfo peu en faveur, plutôt tronquant alors que faux-sens, hérité mère asympto, clinique ne colle pas (juste fente)... -> VOUS-
- CFTR
- DOCK6 : score bleu, plutôt missense patho decipher mais légère atteinte épissage, récessif -> non
- DCHS1: valve mitrale, pas el phénotype et non décrit syndrome cimeter
- FOXC1 vous moins ? qq score bionfo, peu présent gnomad, gène plutôt LOF, clinique ophtalmo + cardio mais pas exactement ça (- Atrial septal defect - Valvular defects - Patent ductus arteriosus)
  CNV
  - del HNRPNPC, article 2023: trouble neurodvev seul don non
* DONE MR-2401889
CLOSED: [2024-06-20 jeu. 12:03] SCHEDULED: <2024-06-20 jeu. 10:00> DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
- SCN5A 3* UTR et l'autre intronique profond
- TLR4 non connu, faux-sens fin de gène
- *CRELD1* clinvar patho pour défaut septum ventriculair (fauxsens). Expliquerait cardio ? Gène peu connu decipher mais plusieurs faux-sens patho. Malaide domainter avec pénétrance imcomplète. Hérité mère. Classe 4? Article (paywall): retard de dev, épilepsie, hypotonie, infection. *ceux avec missens on diminution protinque dimimunée" mais "diminushed ability to induce craniofacial defect" https://pubmed.ncbi.nlm.nih.gov/37947183/
   baz1b non connu score
- LRRK1 : anomalie splice mais récessif sans 2e allèle
  CNV
  - *question* dup 34kb 2p12: touche quelque éléments encode -> on ne fait rien ?
   Seqone
   - RERE = insertion en phase. trouble neurodev + malfo mais seul cardio pourrait coller à priori. Clinvar benin
   - HEPHL1 VOUS-  récesif, 2 variant avec bon scores, clini non en faveur, gène peu connu. Régurgitation mitral/tricsuspide pulmonaire colle pas. Mais en cis
* KILL MR-2304879
CLOSED: [2024-06-21 ven. 14:26] SCHEDULED: <2024-06-20 jeu. 11:00> DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: grenoble rvi
:END:
- /SYNGAP1/ 3x gnomad, score bioinfo peu en faveur, hérité, rare faux-sens patho decipher, clinique colle (microcéphalie)
- FBXO11 clinvar bénin
- KAT5 non présent gnomad, neurobdev, score bionifo bof, gène peu connu faux-sens patho
- IQSEC1 idem
  seqone non fait
  cnv, snv rien
* KILL MR-2401943
CLOSED: [2024-06-21 ven. 16:47] DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: grenoble rvi
:END:
* DONE MR-2402030 inv CHD7
CLOSED: [2024-06-18 mar. 14:49] DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
Vu avec Véronique: diag = inversion CHD7
- VOUS mosaïque CHD7 retrouvé mais moins intéressant
* KILL MR-2401267
CLOSED: [2024-06-21 ven. 16:47] DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: grenoble rvi
:END:
* DONE Diapos cliniques
CLOSED: [2024-06-17 lun. 16:10] DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
  /Entered on/  [2024-06-14 ven. 17:43]
* DONE Vérifier Diapos cliniques
CLOSED: [2024-06-21 ven. 11:45] SCHEDULED: <2024-07-14 dim. 09:00> DEADLINE: <2024-06-21 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Grenoble
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: grenoble rvi
:END:
  /Entered on/  [2024-06-14 ven. 17:43]
* DONE Slack Julien pour delinv (?) MR-20231276 chr12:99192348
CLOSED: [2024-06-11 mar. 15:31] SCHEDULED: <2024-06-11 mar.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-11 mar. 15:16]
* DONE Mail pour se présenter
CLOSED: [2024-06-12 mer. 14:59] SCHEDULED: <2024-06-12 mer.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-12 mer. 11:15]
* DONE Voir avec Jérémie dossier du 6 juin
CLOSED: [2024-06-12 mer. 16:03] SCHEDULED: <2024-06-12 mer.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-12 mer. 14:59]
** DONE MR-2001133 rien: revoir clinique épilepsie ? ségrégation ne colle pas
CLOSED: [2024-06-12 mer. 15:43]
Julien : ras de probant, del CSFR2A max VIS, seqone DEPDC5
** DONE MR-2303288 VOUS dup NCKAP1 rendue VOUS: validé
CLOSED: [2024-06-12 mer. 15:08]
** DONE MR-2303537 OTX2
CLOSED: [2024-06-12 mer. 16:02]
SLC26A5 2 VOUS- (?) pour surdité
** DONE MR-2301275 discuté, staffé négativ, prélèvement père ?
CLOSED: [2024-06-12 mer. 16:03]
** DONE MR-2401268 rien
CLOSED: [2024-06-07 ven. 15:36]
* DONE 3 génomes Jérémie 2e lecture [3/3]
CLOSED: [2024-06-14 ven. 14:02] SCHEDULED: <2024-06-13 jeu.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-13 jeu. 10:09]
** DONE MR-2301276
CLOSED: [2024-06-14 ven. 12:34]
rien si ce n'est la delinv (?) ANKSB1 https://www.nature.com/articles/s41467-019-11437-w
peut coller sur clinique (partiellement) et démonré sur cellulaire
** KILL MR-2301483
CLOSED: [2024-06-14 ven. 12:34]
** KILL MR-2302630 del connue
CLOSED: [2024-06-14 ven. 12:34]
* DONE Regarder rapidement génomes à discuter [7/7]
CLOSED: [2024-06-14 ven. 17:35] DEADLINE: <2024-07-12 ven. 11:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
Liens
** DONE MR-2201152
CLOSED: [2024-06-13 jeu. 17:27]
MECP2 pour coller avec DI liée à l'X #30026eer
IRM, EEG normales
inst1 peu convaincant ?
DLG3 : VOUS ?
** DONE MR-2001133 rien
CLOSED: [2024-06-13 jeu. 17:17]
rien
DEPDC5, il n'y a pas de trace d'épilepsie dans les documents sur Hygen. D'après une review récente, c'est plutôt de l'épilepsie focale sans DI ( https://www.sciencedirect.com/science/article/abs/pii/S1525505022001275 ). Veux-tu en discuter en RVI ? Sinon ça parlait de Silver-Russell dans les courriers mais je n'ai rien vu en faveur.  Après, c'est hérité de la mère et c'est le père qui a de l'épilepsi
** DONE MR-2303537
CLOSED: [2024-06-13 jeu. 17:17]
SLC26A5 2 VOUS- (?) pour surdité
** DONE MR-2301275 déjà staffé ras
CLOSED: [2024-06-13 jeu. 17:19]
** DONE MR-2303166
CLOSED: [2024-06-13 jeu. 17:31]
dup chrX:54449198-54460505 Xp11.22 = diag ? FGD1 - sd Aarskgo-scott
SOX1 VOUS ?
Ccl à discuter avec prescripteur
** DONE MR-2301994 non fait
CLOSED: [2024-06-14 ven. 17:35]
** DONE MR-2401268 non fait
CLOSED: [2024-06-14 ven. 17:35]
* DONE RVI
CLOSED: [2024-06-14 ven. 16:43] SCHEDULED: <2024-06-14 ven. 14:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
Entered on [2024-06-14 ven. 14:01]
* DONE MR-2302630
CLOSED: [2024-06-19 mer. 14:44] DEADLINE: <2024-06-19 mer. 16:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
- FLBN non : avec overlap phénotype mais 6/7 probablement bénin dans clinvar, score bioinfo peu en faveur, hérité mère... VOUS dans courrieur ? Plutôt perte de fonction
- ATP6V1 : explique aplasie ongle, acide amine consèvre , à 6 AA de 2 fauxsense clinvar patho, score bioinfo mitigé, clinvar mitigé, 9 fois gnomad  -> VOUS
- ACVR1 molécuraiment intéressant mais clinique non
Ccl  à discuter de principe en staff. À signaler dans courrier
* DONE MR-2301158
CLOSED: [2024-06-19 mer. 17:13] DEADLINE: <2024-06-19 mer. 16:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
SEDT1: 4x gnomad, gène plutôt perte de fonction ?, qq score bioinfo en faveur, retard de dev seul, hérité de la mère. VOUS- ?
seqone : insertion POUF3 frameshift en début de protéine, codon stop prématurée, pli=1, de novo, clinique neurodepv
revue : https://onlinelibrary.wiley.com/doi/10.1111/cge.14353 pas de clinique qui colle avec le reste -> non retrouvé igv car faux positif
discuter POU3F3 non vu IGV -> faux positif à rendre
Envoyé vers hygen
* KILL Interprétation avec Jérémie + Julien
CLOSED: [2024-06-19 mer. 11:00] SCHEDULED: <2024-06-19 mer. 16:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: KILL
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-18 mar. 09:54]
* DONE MR-2304637
CLOSED: [2024-06-21 ven. 11:43] DEADLINE: <2024-06-20 jeu. 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-20 jeu. 11:45]
  - *KANSL1 VOUS-*, score bénin, hérité mère, faux-sens gene plutôt LOF. On reste en vous dans la classification
  - FIPBP pas 2 allel
  - /CRKL/ de novo a prioir, VOUS, cardio seul amis ne colle pas au phénotype (impliqué dans les value atrioventriculaire "targeted deletion of Crk and Crkl impeded the remodeling of endocardial cushions at the atrioventricular canal into the atrioventricular valves."
https://www.ahajournals.org/doi/full/10.1161/JAHA.123.029683?rfr_dat=cr_pub++0pubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org
- /CACNA1A/ faux sens score binfo en faveur, gène plutôt faux-sens patho. Clinique ne colle pas (retard de dev semble constant chez faux-sens selon revue 2021 https://www.sciencedirect.com/science/article/pii/S109836002105142X?via%3Dihub, phénotype cardiaque rare)
    )
  a priori de novo
  CNV: dup PRKAR1B phénotype intéressant mais intronique sans promoteur
  SV: transloc (?) chr8 et 18avec présidspoition autisme mais intronique
  autre interchromomique pas mais de gène d'intérêt
  Ccl VOUS CACNA1C à discuter
* DONE Diapos décomposition BLAT MR-2402030 : échec conclusion
CLOSED: [2024-06-21 ven. 13:59] DEADLINE: <2024-06-21 ven. 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-21 ven. 10:37]
* DONE Vérifier MR-2301158 vers hygen (négatif)
CLOSED: [2024-06-24 lun. 11:09] SCHEDULED: <2024-06-24 lun. 12:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-06-24 lun. 11:47
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-21 ven. 11:43]
  Bug lors de l'envoi : message d'erreur, présent couchdb puis non envoyé
* DONE Mettre dans org-mode tous dossiers interprétés
CLOSED: [2024-07-01 lun. 13:37] SCHEDULED: <2024-06-28 ven.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-01 lun. 14:23
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: RVI Montpellier
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: montpellier rvi
:END:
  /Entered on/  [2024-06-28 ven. 15:17]
* DONE Prise en main outils d'interprétation
CLOSED: [2024-06-11 mar. 10:33] SCHEDULED: <2024-06-11 mar. 09:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
  /Entered on/  [2024-05-28 mar. 15:25]
* DONE Présentation nushell axe 3
CLOSED: [2024-06-12 mer. 10:43] DEADLINE: <2024-06-13 jeu. 9h>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
:LOGBOOK:
CLOCK: [2024-06-12 mer. 16:56]--[2024-06-12 mer. 17:20] =>  0:24
CLOCK: [2024-06-12 mer. 09:56]--[2024-06-12 mer. 10:43] =>  0:47
CLOCK: [2024-06-10 lun. 11:55]--[2024-06-10 lun. 12:29] =>  0:34
:END:
  /Entered on/  [2024-05-29 mer. 17:53]
  XML
  JSON
  VCF ?
* DONE Bioinformatique
CLOSED: [2024-06-27 jeu. 14:39] SCHEDULED: <2024-06-27 jeu. 11:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-11 mar. 10:29]
* DONE Réunion Jérémie et Lucas
CLOSED: [2024-06-14 ven. 13:57] SCHEDULED: <2024-06-14 ven. 11:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-13 jeu. 17:14]
* DONE Amis de la cytogénétique
CLOSED: [2024-06-21 ven. 10:38] SCHEDULED: <2024-06-20 jeu. 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-14 ven. 17:02]
* DONE API hour
CLOSED: [2024-06-19 mer. 13:49] SCHEDULED: <2024-06-19 mer. 13:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-14 ven. 17:32]
* DONE Véronique pour revoir présentation ACRAA
CLOSED: [2024-06-19 mer. 18:05] SCHEDULED: <2024-06-19 mer. 16:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-02 mar. 11:44
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-19 mer. 11:01]
* DONE Bioinformatique
CLOSED: [2024-06-27 jeu. 14:39] SCHEDULED: <2024-06-27 jeu. 11:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-11 mar. 10:29]
* PROJ Visite labo Lyon
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: PROJ
:END:
  /Entered on/  [2024-06-11 mar. 10:59]
* DONE Réunion Jérémie et Lucas
CLOSED: [2024-06-14 ven. 13:57] SCHEDULED: <2024-06-14 ven. 11:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-13 jeu. 17:14]
* DONE API Hour Julien Gagneur
SCHEDULED: <2024-07-03 mer. 13:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-06-19 mer. 13:48]
* DONE Discussion Charles CHD7
CLOSED: [2024-07-02 mar. 13:50] SCHEDULED: <2024-07-02 mar. 13:15>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-07-02 mar. 11:09]
* DONE Répétition CHD7 Charles + Véroniques
CLOSED: [2024-07-04 jeu. 16:41] SCHEDULED: <2024-07-04 jeu. 13:15>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:END:
Entered on [2024-07-02 mar. 13:50]
* DONE Curagen v2 et mise à jour Aurapport :bio:
CLOSED: [2024-06-13 jeu. 16:43] SCHEDULED: <2024-06-13 jeu. 11:30>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: Réunion biologistes Auragen
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: auragen
:END:
Entered on [2024-06-11 mar. 10:28]
** DONE [[file:slides/reunion_bio_20240613.org][Slides mise à jour aurapport]]
CLOSED: [2024-06-12 mer. 12:00] DEADLINE: <2024-06-13 jeu. 11:30> SCHEDULED: <2024-06-11 mar.>
:LOGBOOK:
CLOCK: [2024-06-11 mar. 15:58]--[2024-06-11 mar. 18:16] =>  2:18
:END:
  /Entered on/  [2024-06-11 mar. 10:28]
** DONE Capture d'écran mise à jour gnomad et transcript (Maelle)
CLOSED: [2024-06-12 mer. 10:44] SCHEDULED: <2024-06-11 mar.>
  /Entered on/  [2024-06-11 mar. 15:16]
  http://172.25.219.87:8081/aurapport/app/#/variant/snv/14906-chr14_g.50723590G_A?case=MR-2304175  :aurapport:  :montpellier:
** DONE Exemple de Julien avec dossier mercredid pour variant sans transcrit mane
CLOSED: [2024-06-12 mer. 16:56] SCHEDULED: <2024-06-11 mar.>
  /Entered on/  [2024-06-11 mar. 18:15]
** DONE Compléter IGV
CLOSED: [2024-06-12 mer. 11:15] SCHEDULED: <2024-06-11 mar.>
  /Entered on/  [2024-06-11 mar. 18:15]
** DONE Compléter popup avec annotation de variants
CLOSED: [2024-06-12 mer. 11:15] SCHEDULED: <2024-06-11 mar.>
  /Entered on/  [2024-06-11 mar. 18:16]
* DONE Corrections virginie
CLOSED: [2024-06-12 mer. 14:44] DEADLINE: <2024-06-12 mer. 18:00> SCHEDULED: <2024-06-12 mer.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-16 mar. 09:53
:ARCHIVE_FILE: ~/org/reunions.org
:ARCHIVE_OLPATH: Réunion biologistes Auragen
:ARCHIVE_CATEGORY: reunions
:ARCHIVE_TODO: DONE
:ARCHIVE_ITAGS: bio auragen
:END:
  /Entered on/  [2024-06-12 mer. 12:00]

File addition: reunion_bio_20240613.org (----------)

[3.2]

#+title: Reunion_bio_20240613
- Introduire la notion bluegreen
- IGV avec le CI en 1ère position pour tout dossier: il y a eu des couacs, réglé pour tous les dossiers si mail bioinfo. Rapidement.
- Gestion des arbres pour les dossiers bluegreen & les réanalyses. Contexte : il n'y avait pas les arbres pour les réanalyses
Affichage des samplot / STR pour tous les dossiers non "classiques" comme les -r ou -t. Idem. Message clé "tout doit fonctionner"
- Si 1 dossié est poussé vers Hygen, blocage des 2 dossiers blue & green : Message clé : rassurer les bio (on n'écrase pas les dossiers)
  ex: MR-2304917
***
TOUTES VERSIONS
- Rappel des informations "structure familiale" via le "+" en bas de page à gauche pour toutes les pages de variants
-> projection avoir les HPO
- Ajout lien gnomAD même si 0 occ annoncée (MM) : déployée mercredi 10
- Ajout lien vers pubmed pour les gènes non OMIM pour tout dossier: on pointait vers clingen avant
- Affichage d'un lien direct MobiDetails
- Lien Decipher fonctionnel ciblé sur le gène (contexte : il y avait un bug)
 > projection vers ta proposition
VERSIONS 7.0 et +
- Mise à disposition de la qualité des CNV manta (contexte : variant manqué donc on relâche un peu les filtres)
- Mise à disposition des pLI > 0.9 pour les CNV & SV - si < 0.9 rien n'est affiché: démo
VERSIONS 8.0 et +
Mise à jour des transcrits MANE & affichage si non dispo
MANE / LRG / longest (gencode 32?)
à voir avec Maelle = les sans MANE gris

Replacement in biblio/auragen.org at line 1 [2.197864]
B:BD[2.197864] → [2.197865:197882]
```
#+title: Auragen
```
[2.197864]
[2.197882]
```
#+title: Main
#+COLUMNS: %25ITEM %YEAR %TAGS %TODO
```

Insertion in biblio/auragen.org at line 4 [2.197864]

[2.197883]

* Général
** TODO Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome
:PROPERTIES:
:TITLE:    Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome
:BTYPE:    article
:CUSTOM_ID: collins2017
:AUTHOR:   Ryan L. Collins and Harrison Brand and Claire E. Redin and Carrie Hanscom and Caroline Antolik and Matthew R. Stone and Joseph T. Glessner and Tamara Mason and Giulia Pregno and Naghmeh Dorrani and Giorgia Mandrile and Daniela Giachino and Danielle Perrin and Cole Walsh and Michelle Cipicchio and Maura Costello and Alexei Stortchevoi and Joon-Yong An and Benjamin B. Currall and Catarina M. Seabra and Ashok Ragavendran and Lauren Margolin and Julian A. Martinez-Agosto and Diane Lucente and Brynn Levy and Stephan J. Sanders and Ronald J. Wapner and Fabiola Quintero-Rivera and Wigard Kloosterman and Michael E. Talkowski
:JOURNAL:  Genome Biology
:YEAR:     2017
:VOLUME:   18
:NUMBER:   1
:PAGES:    36
:DOI:      10.1186/s13059-017-1158-6
:URL:      http://dx.doi.org/10.1186/s13059-017-1158-6
:END:
Défini des SV complexes avec illustrations ([[https://link.springer.com/article/10.1186/s13059-017-1158-6/figures/2][figure]] )

Replacement in biblio/auragen.org at line 54 [2.197864]
B:BD[2.198980] → [2.198980:198993]
```
*** Software
```
[2.198980]
[2.198993]
```
*** KILL Identification pseudogene: pas le scope
CLOSED: [2024-07-22 Mon 17:07]
```
Replacement in biblio/auragen.org at line 79 [2.197864]
B:BD[2.200358] → [2.200358:200394]
```
:CUSTOM_ID: abrahamsson22ppsifinder
```
[2.200358]
[2.200394]
```
:CUSTOM_ID: abrahamsson2022ppsifinder
```
Replacement in biblio/auragen.org at line 95 [2.197864]
B:BD[2.200949] → [2.200949:200981]
```
:CUSTOM_ID: syber2022pseudopipe
```
[2.200949]
[2.200981]
```
:CUSTOM_ID: syber2022pseudofinder
```

Insertion in biblio/auragen.org at line 105 [2.197864]

[2.201291]

**** DONE Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
CLOSED: [2024-07-17 Wed 16:39] SCHEDULED: <2024-07-15 lun.>
:PROPERTIES:
:TITLE:    Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution
:BTYPE:    article
:CUSTOM_ID: zheng2007pseudogenes
:AUTHOR:   Zheng, Deyou and Frankish, Adam and Baertsch, Robert and Kapranov, Philipp and Reymond, Alexandre and Choo, Siew Woh and Lu, Yontao and Denoeud, France and Antonarakis, Stylianos E and Snyder, Michael and others
:JOURNAL:  Genome research
:VOLUME:   17
:NUMBER:   6
:PAGES:    839--851
:YEAR:     2007
:PUBLISHER: Cold Spring Harbor Lab
:END:

Replacement in biblio/auragen.org at line 157 [2.197864]
B:BD[2.202647] → [2.202647:202673]
```
:CUSTOM_ID: Baertsch_2008
```
[2.202647]
[2.202673]
```
:CUSTOM_ID: baertsch2008retrofinder
```

Replacement in biblio/auragen.org at line 201 [2.197864]

B:BD[2.204373] → [2.204373:204467]

**** TODO Pseudogenes and Their Genome-Wide Prediction in Plants
SCHEDULED: <2024-07-09 mar.>

[2.204373]

[2.204467]

**** DONE Pseudogenes and Their Genome-Wide Prediction in Plants
CLOSED: [2024-07-17 mer. 12:08] SCHEDULED: <2024-07-15 lun.>

Insertion in biblio/auragen.org at line 218 [2.197864]

[2.206227]

:END:
**** DONE Automatic annotation of eukaryotic genes, pseudogenes and promoters
CLOSED: [2024-07-17 Wed 15:00] SCHEDULED: <2024-07-17 mer.>
:PROPERTIES:
:TITLE:    Automatic annotation of eukaryotic genes, pseudogenes and promoters
:BTYPE:    article
:CUSTOM_ID: solovyev2006automatic
:AUTHOR:   Solovyev, Victor and Kosarev, Peter and Seledsov, Igor and Vorobyev, Denis
:URL:  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2006-7-s1-s10
:JOURNAL:  Genome biology
:VOLUME:   7
:PAGES:    1--12
:YEAR:     2006
:URL: https://link.springer.com/article/10.1186/Gb-2006-7-S1-S10
:PUBLISHER: Springer

Insertion in biblio/auragen.org at line 234 [2.197864]

[2.206233]

**** DONE The GENCODE pseudogene resource
CLOSED: [2024-07-17 Wed 15:15] SCHEDULED: <2024-07-17 Wed>
:PROPERTIES:
:TITLE:    The GENCODE pseudogene resource
:BTYPE:    article
:CUSTOM_ID: pei2012gencode
:AUTHOR:   Pei, Baikang and Sisu, Cristina and Frankish, Adam and Howald, C{\'e}dric and Habegger, Lukas and Mu, Xinmeng Jasmine and Harte, Rachel and Balasubramanian, Suganthi and Tanzer, Andrea and Diekhans, Mark and others
:JOURNAL:  Genome biology
:VOLUME:   13
:PAGES:    1--26
:YEAR:     2012
:PUBLISHER: Springer
:URL:      https://link.springer.com/article/10.1186/gb-2012-13-9-r51
:END:
**** DONE Discovery of non-reference processed pseudogenes in the Swedish population
CLOSED: [2024-07-17 Wed 16:03]
:PROPERTIES:
:TITLE:    Discovery of non-reference processed pseudogenes in the Swedish population
:BTYPE:    article
:CUSTOM_ID: boer2023processen
:AUTHOR:   Esmee Ten Berk de Boer and Kristine Bilgrav Saether and Jesper Eisfeldt
:JOURNAL:  Frontiers in Genetics
:YEAR:     2023
:VOLUME:   14
:NUMBER:   nil
:PAGES:    nil
:DOI:      10.3389/fgene.2023.1176626
:URL:      http://dx.doi.org/10.3389/fgene.2023.1176626
:END:
**** DONE Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance
CLOSED: [2024-07-17 Wed 16:40] SCHEDULED: <2024-07-17 Wed>
:PROPERTIES:
:TITLE:    Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance
:BTYPE:    article
:CUSTOM_ID: yang24loss
:AUTHOR:   Yi Yang and Pengzhi Wang and Samir El Qaidi and Philip R. Hardwidge and Jinlin Huang and Guoqiang Zhu
:JOURNAL:  Applied Microbiology and Biotechnology
:YEAR:     2024
:VOLUME:   108
:NUMBER:   1
:PAGES:    328
:DOI:      10.1007/s00253-023-12971-w
:URL:      http://dx.doi.org/10.1007/s00253-023-12971-w
:END:
**** DONE Re-recognition of pseudogenes: From molecular to clinical applications
CLOSED: [2024-07-17 Wed 17:06]
:PROPERTIES:
:TITLE:    Re-recognition of pseudogenes: From molecular to clinical applications
:BTYPE:    article
:CUSTOM_ID: chen2020rerecognition
:AUTHOR:   Xu Chen and Lin Wan and Wei Wang and Wen-Jin Xi and An-Gang Yang and Tao Wang
:JOURNAL:  Theranostics
:YEAR:     2020
:VOLUME:   10
:NUMBER:   4
:PAGES:    1479-1499
:DOI:      10.7150/thno.40659
:URL:      http://dx.doi.org/10.7150/thno.40659
:END:

Replacement in biblio/auragen.org at line 294 [2.197864]

B:BD[2.206234] → [2.206234:206494]

**** TODO Autres
SCHEDULED: <2024-07-14 dim.>
- annotation par GENCODE https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-9-r51/figures/1 utilise pseudopipe et retrofinder
- une étape parmi d'autre : https://github.com/hillerlab/GeneLossPipe

[2.206234]

[2.206494]

**** DONE Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice
CLOSED: [2024-07-17 Wed 17:18] SCHEDULED: <2024-07-17 mer.>
:PROPERTIES:
:TITLE:    Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice
:BTYPE:    article
:URL:    https://academic.oup.com/plphys/article/151/1/3/6108462
:CUSTOM_ID: zou2009evolutionary
:AUTHOR:   Zou, Cheng and Lehti-Shiu, Melissa D and Thibaud-Nissen, Fran{\c{c}}oise and Prakash, Tanmay and Buell, C Robin and Shiu, Shin-Han
:JOURNAL:  Plant physiology
:VOLUME:   151
:NUMBER:   1
:PAGES:    3--15
:YEAR:     2009
:PUBLISHER: American Society of Plant Biologists
:END:
**** DONE Identification of Pseudogenes in Brachypodium distachyon Chromosomes
CLOSED: [2024-07-17 Wed 17:34]
:PROPERTIES:
:TITLE:    Identification of Pseudogenes in Brachypodium distachyon Chromosomes
:BTYPE:    article
:CUSTOM_ID: camiolo2018identification
:AUTHOR:   Camiolo, Salvatore and Porceddu, Andrea
:JOURNAL:  Brachypodium Genomics: Methods and Protocols
:PAGES:    149--171
:YEAR:     2018
:PUBLISHER: Springer
:END:

Replacement in biblio/auragen.org at line 322 [2.197864]

B:BD[2.206495] → [2.206495:206649]

- https://github.com/topics/pseudogenes
**** TODO Structural characterization and duplication modes of pseudogenes in plants
SCHEDULED: <2024-07-10 mer.>

[2.206495]

[2.206649]

**** DONE Structural characterization and duplication modes of pseudogenes in plants
CLOSED: [2024-07-17 Wed 17:34] SCHEDULED: <2024-07-15 lun.>

Insertion in biblio/auragen.org at line 335 [2.197864]
[2.207027]
[2.207027]
```
:URL:      https://www.nature.com/articles/s41598-021-84778-6
```

Replacement in biblio/auragen.org at line 337 [2.197864]

B:BD[2.207033] → [2.207033:207141]

**** TODO Processed pseudogenes acquired somatically during cancer development
SCHEDULED: <2024-07-10 mer.>

[2.207033]

[2.207141]

**** DONE Processed pseudogenes acquired somatically during cancer development
CLOSED: [2024-07-17 Wed 17:36] SCHEDULED: <2024-07-15 lun.>

Insertion in biblio/auragen.org at line 350 [2.197864]

[2.207646]

:END:
*** TODO Appel de variant sur pseudogène connu
**** TODO [#A] Integrating gene annotation with orthology inference at scale
SCHEDULED: <2024-07-23 Tue>
:PROPERTIES:
:TITLE:    Integrating gene annotation with orthology inference at scale
:BTYPE:    article
:CUSTOM_ID: Kirilenko_2023
:VOLUME:   380
:ISSN:     1095-9203
:URL:      http://dx.doi.org/10.1126/science.abn3107
:DOI:      10.1126/science.abn3107
:NUMBER:   6643
:JOURNAL:  Science
:PUBLISHER: American Association for the Advancement of Science (AAAS)
:AUTHOR:   Kirilenko, Bogdan M. and Munegowda, Chetan and Osipova, Ekaterina and Jebb, David and Sharma, Virag and Blumer, Moritz and Morales, Ariadna E. and Ahmed, Alexis-Walid and Kontopoulos, Dimitrios-Georgios and Hilgers, Leon and Lindblad-Toh, Kerstin and Karlsson, Elinor K. and Hiller, Michael and Andrews, Gregory and Armstrong, Joel C. and Bianchi, Matteo and Birren, Bruce W. and Bredemeyer, Kevin R. and Breit, Ana M. and Christmas, Matthew J. and Clawson, Hiram and Damas, Joana and Di Palma, Federica and Diekhans, Mark and Dong, Michael X. and Eizirik, Eduardo and Fan, Kaili and Fanter, Cornelia and Foley, Nicole M. and Forsberg-Nilsson, Karin and Garcia, Carlos J. and Gatesy, John and Gazal, Steven and Genereux, Diane P. and Goodman, Linda and Grimshaw, Jenna and Halsey, Michaela K. and Harris, Andrew J. and Hickey, Glenn and Hiller, Michael and Hindle, Allyson G. and Hubley, Robert M. and Hughes, Graham M. and Johnson, Jeremy and Juan, David and Kaplow, Irene M. and Karlsson, Elinor K. and Keough, Kathleen C. and Kirilenko, Bogdan and Koepfli, Klaus-Peter and Korstian, Jennifer M. and Kowalczyk, Amanda and Kozyrev, Sergey V. and Lawler, Alyssa J. and Lawless, Colleen and Lehmann, Thomas and Levesque, Danielle L. and Lewin, Harris A. and Li, Xue and Lind, Abigail and Lindblad-Toh, Kerstin and Mackay-Smith, Ava and Marinescu, Voichita D. and Marques-Bonet, Tomas and Mason, Victor C. and Meadows, Jennifer R. S. and Meyer, Wynn K. and Moore, Jill E. and Moreira, Lucas R. and Moreno-Santillan, Diana D. and Morrill, Kathleen M. and Muntané, Gerard and Murphy, William J. and Navarro, Arcadi and Nweeia, Martin and Ortmann, Sylvia and Osmanski, Austin and Paten, Benedict and Paulat, Nicole S. and Pfenning, Andreas R. and Phan, BaDoi N.and Pollard, Katherine S. and Pratt, Henry E. and Ray, David A. and Reilly, Steven K. and Rosen, Jeb R. and Ruf, Irina and Ryan, Louise and Ryder, Oliver A. and Sabeti, Pardis C. and Schäffer, Daniel E. and Serres, Aitor and Shapiro, Beth and Smit, Arian F. A. and Springer, Mark and Srinivasan, Chaitanya and Steiner, Cynthia and Storer, Jessica M. and Sullivan, Kevin A. M. and Sullivan, Patrick F. and Sundström, Elisabeth and Supple, Megan A. and Swofford, Ross and Talbot, Joy-El and Teeling, Emma and Turner-Maier, Jason and Valenzuela, Alejandro and Wagner, Franziska and Wallerman, Ola and Wang, Chao and Wang, Juehan and Weng, Zhiping and Wilder, Aryn P. and Wirthlin, Morgan E. and Xue, James R. and Zhang, Xiaomeng
:YEAR:     2023
:MONTH:    apr
:END:
**** TODO Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation
SCHEDULED: <2024-07-23 Tue>
:PROPERTIES:
:TITLE:    Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation
:BTYPE:    article
:CUSTOM_ID: steyaert2023systematic
:AUTHOR:   Wouter Steyaert and Lonneke Haer-Wigman and Rolph Pfundt and Debby Hellebrekers and Marloes Steehouwer and Juliet Hampstead and Elke de Boer and Alexander Stegmann and Helger Yntema and Erik-Jan Kamsteeg and Han Brunner and Alexander Hoischen and Christian Gilissen
:JOURNAL:  Nature Communications
:YEAR:     2023
:VOLUME:   14
:NUMBER:   1
:PAGES:    6845
:DOI:      10.1038/s41467-023-42531-9
:URL:      http://dx.doi.org/10.1038/s41467-023-42531-9

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[2.207652]
[2.207652]

Replacement in biblio/auragen.org at line 398 [2.197864]

B:BD[2.207968] → [2.207968:208192]

A replacer "Utilisation de données HapMap + généalgique + données génotype et phénotype -> retrouve lignage par rapport lignée fondatrice"
** DONE Actionable genotypes and their association with life span in Iceland

[2.207968]

[2.208192]

A replacer "Utilisation de données HapMap + généalogique + données génotype et phénotype -> retrouve lignage par rapport lignée fondatrice"
** Bibliographie générale
*** DONE Actionable genotypes and their association with life span in Iceland

Replacement in biblio/auragen.org at line 415 [2.197864]

B:BD[2.208779] → [2.208779:208899]


** DONE Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks :identity_tracing:

[2.208779]

[2.208899]

*** DONE Addressing Beacon re-identification attacks: quantification and mitigation of privacy risks :identity_tracing:

Replacement in biblio/auragen.org at line 430 [2.197864]

B:BD[2.209458] → [2.209458:209549]

** DONE Addressing the concerns of the lacks family: quantification of kin genomic privacy

[2.209458]

[2.209549]

*** DONE Addressing the concerns of the lacks family: quantification of kin genomic privacy

Replacement in biblio/auragen.org at line 442 [2.197864]

B:BD[2.209977] → [2.209977:210084]

** DONE An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information

[2.209977]

[2.210084]

*** DONE An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information

Replacement in biblio/auragen.org at line 458 [2.197864]

B:BD[2.210627] → [2.210627:210720]

** DONE Assessing transcriptomic reidentification risks using discriminative sequence models

[2.210627]

[2.210720]

*** DONE Assessing transcriptomic reidentification risks using discriminative sequence models

Replacement in biblio/auragen.org at line 474 [2.197864]

B:BD[2.211228] → [2.211228:211314]

** DONE Bayesian method to predict individual SNP genotypes from gene expression data

[2.211228]

[2.211314]

*** DONE Bayesian method to predict individual SNP genotypes from gene expression data

Replacement in biblio/auragen.org at line 490 [2.197864]

B:BD[2.211746] → [2.211746:211812]

** KILL Data Sharing Under the General Data Protection Regulation

[2.211746]

[2.211812]

*** KILL Data Sharing Under the General Data Protection Regulation

Replacement in biblio/auragen.org at line 508 [2.197864]

B:BD[2.213124] → [2.213124:213189]

** DONE De-anonymizing genomic databases using phenotypic traits

[2.213124]

[2.213189]

*** DONE De-anonymizing genomic databases using phenotypic traits

Replacement in biblio/auragen.org at line 522 [2.197864]

B:BD[2.213709] → [2.213709:213794]

** DONE Detection of sharing by descent, long-range phasing and haplotype imputation

[2.213709]

[2.213794]

*** DONE Detection of sharing by descent, long-range phasing and haplotype imputation

Replacement in biblio/auragen.org at line 538 [2.197864]

B:BD[2.214499] → [2.214499:214601]

** DONE Deterministic identification of specific individuals from GWAS results :attribute_disclosure:

[2.214499]

[2.214601]

*** DONE Deterministic identification of specific individuals from GWAS results :attribute_disclosure:

Replacement in biblio/auragen.org at line 554 [2.197864]

B:BD[2.215090] → [2.215090:215169]

** DONE [#A] Ensuring privacy and security of genomic data and functionalities

[2.215090]

[2.215169]

*** DONE [#A] Ensuring privacy and security of genomic data and functionalities

Replacement in biblio/auragen.org at line 574 [2.197864]

B:BD[2.215680] → [2.215680:215766]

** DONE Epigenome data release: a participant-centered approach to privacy protection

[2.215680]

[2.215766]

*** DONE Epigenome data release: a participant-centered approach to privacy protection

Replacement in biblio/auragen.org at line 596 [2.197864]

B:BD[2.216786] → [2.216786:216886]

** DONE Estimating the success of re-identifications in incomplete datasets using generative models

[2.216786]

[2.216886]

*** DONE Estimating the success of re-identifications in incomplete datasets using generative models

Replacement in biblio/auragen.org at line 612 [2.197864]

B:BD[2.217360] → [2.217360:217440]

** DONE Ethical implications of epigenetics in the era of personalized medicine

[2.217360]

[2.217440]

*** DONE Ethical implications of epigenetics in the era of personalized medicine

Deletion in biblio/auragen.org at line 614 [2.197864]
B:BD[2.217472] → [2.217472:217501]
```
SCHEDULED: <2024-07-09 mar.>
```
Replacement in biblio/auragen.org at line 617 [2.197864]
B:BD[2.217616] → [2.217616:217646]
```
:CUSTOM_ID: santaló22:_ethic
```
[2.217616]
[2.217646]
```
:CUSTOM_ID: santalo2022ethic
```
Deletion in biblio/auragen.org at line 633 [2.197864]
B:BD[2.218180] → [2.218180:218184]
```
**
```

Replacement in biblio/auragen.org at line 634 [2.197864]

B:BD[2.218185] → [2.218185:218267]


** DONE Investigative genetic genealogy: Current methods, knowledge and practice

[2.218185]

[2.218267]

*** DONE Investigative genetic genealogy: Current methods, knowledge and practice

Replacement in biblio/auragen.org at line 649 [2.197864]

B:BD[2.218685] → [2.218685:218764]

** KILL Privacy challenges and research opportunities for genomic data sharing

[2.218685]

[2.218764]

*** DONE Privacy challenges and research opportunities for genomic data sharing

Insertion in biblio/auragen.org at line 661 [2.197864]
[2.219100]
[2.219100]
```
:URL:  https://www.nature.com/articles/s41588-020-0651-0
```

Replacement in biblio/auragen.org at line 664 [2.197864]

B:BD[2.219154] → [2.219154:219311]

Non lu, ne semble pas apporter grand-chose
** KILL Genetic data are not always personal—disaggregating the identifiability and sensitivity of genetic data

[2.219154]

[2.219311]

*** KILL Genetic data are not always personal—disaggregating the identifiability and sensitivity of genetic data

Replacement in biblio/auragen.org at line 679 [2.197864]

B:BD[2.219704] → [2.219704:219777]

** KILL Identification of anonymous DNA using genealogical triangulation

[2.219704]

[2.219777]

*** KILL Identification of anonymous DNA using genealogical triangulation

Replacement in biblio/auragen.org at line 692 [2.197864]

B:BD[2.220160] → [2.220160:220230]

** KILL [#B] https://www.cell.com/ajhg/fulltext/S0002-9297(15)00200-1

[2.220160]

[2.220230]

*** KILL [#B] https://www.cell.com/ajhg/fulltext/S0002-9297(15)00200-1

Replacement in biblio/auragen.org at line 695 [2.197864]

B:BD[2.220298] → [2.220298:220379]

** KILL [#B] https://www.sciencedirect.com/science/article/pii/S1872497321000132

[2.220298]

[2.220379]

*** KILL [#B] https://www.sciencedirect.com/science/article/pii/S1872497321000132

Replacement in biblio/auragen.org at line 697 [2.197864]

B:BD[2.220411] → [2.220411:220504]

** DONE Identification of individuals by trait prediction using whole-genome sequencing data

[2.220411]

[2.220504]

*** DONE Identification of individuals by trait prediction using whole-genome sequencing data

Replacement in biblio/auragen.org at line 713 [2.197864]

B:BD[2.221158] → [2.221158:221228]

** KILL Identifying disease-causing mutations with privacy protection

[2.221158]

[2.221228]

*** KILL Identifying disease-causing mutations with privacy protection

Replacement in biblio/auragen.org at line 729 [2.197864]

B:BD[2.221751] → [2.221751:221892]

** DONE Identifying Participants in the Personal Genome Project by Name (A Re-identification Experiment) :identity_tracing:identity_tracing:

[2.221751]

[2.221892]

*** DONE Identifying Participants in the Personal Genome Project by Name (A Re-identification Experiment) :identity_tracing:identity_tracing:

Replacement in biblio/auragen.org at line 743 [2.197864]

B:BD[2.222270] → [2.222270:222347]

** DONE Identifying Personal Genomes by Surname Inference :identity_tracing:

[2.222270]

[2.222347]

*** DONE Identifying Personal Genomes by Surname Inference :identity_tracing:

Replacement in biblio/auragen.org at line 759 [2.197864]

B:BD[2.222800] → [2.222800:222897]

** DONE Identity inference of genomic data using long-range familial searches :identity_tracing:

[2.222800]

[2.222897]

*** DONE Identity inference of genomic data using long-range familial searches :identity_tracing:

Replacement in biblio/auragen.org at line 775 [2.197864]

B:BD[2.223344] → [2.223344:223439]

** DONE Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data

[2.223344]

[2.223439]

*** DONE Inference Attacks and Controls on Genotypes and Phenotypes for Individual Genomic Data

Replacement in biblio/auragen.org at line 791 [2.197864]

B:BD[2.223957] → [2.223957:224108]

** DONE Inferential Genotyping of Y Chromosomes in Latter-Day Saints Founders and Comparison to Utah Samples in the HapMap Project :surname_inference:

[2.223957]

[2.224108]

*** DONE Inferential Genotyping of Y Chromosomes in Latter-Day Saints Founders and Comparison to Utah Samples in the HapMap Project :surname_inference:

Replacement in biblio/auragen.org at line 810 [2.197864]

B:BD[2.224742] → [2.224742:224856]

** DONE Major flaws in “Identification of individuals by trait prediction using whole-genome sequencing data”

[2.224742]

[2.224856]

*** DONE Major flaws in “Identification of individuals by trait prediction using whole-genome sequencing data”

Replacement in biblio/auragen.org at line 824 [2.197864]

B:BD[2.225275] → [2.225275:225385]

** TODO On inferring presence of an individual in a mixture: a Bayesian approach
SCHEDULED: <2024-07-11 jeu.>

[2.225275]

[2.225385]

*** KILL On inferring presence of an individual in a mixture: a Bayesian approach
CLOSED: [2024-07-15 lun. 11:14] SCHEDULED: <2024-07-11 jeu.>

Replacement in biblio/auragen.org at line 840 [2.197864]

B:BD[2.225740] → [2.225740:225820]

** KILL Assessing and managing risk when sharing aggregate genetic variant data

[2.225740]

[2.225820]

*** KILL Assessing and managing risk when sharing aggregate genetic variant data

Replacement in biblio/auragen.org at line 856 [2.197864]

B:BD[2.226325] → [2.226325:226398]

** DONE On Jim Watson's APOE status: genetic information is hard to hide

[2.226325]

[2.226398]

*** DONE On Jim Watson's APOE status: genetic information is hard to hide

Replacement in biblio/auragen.org at line 871 [2.197864]

B:BD[2.226781] → [2.226781:226883]

** DONE Privacy in pharmacogenetics: An $\{$End-to-End$\}$ case study of personalized warfarin dosing

[2.226781]

[2.226883]

*** DONE Privacy in pharmacogenetics: An $\{$End-to-End$\}$ case study of personalized warfarin dosing

Replacement in biblio/auragen.org at line 884 [2.197864]
B:BD[2.227450] → [2.227450:227490]
```
** DONE [#B] Privacy in the Genomic Era
```
[2.227450]
[2.227490]
```
*** DONE [#B] Privacy in the Genomic Era
```

Replacement in biblio/auragen.org at line 903 [2.197864]

B:BD[2.228118] → [2.228118:228193]

** DONE Privacy risks from genomic data-sharing beacons :identity_tracing:

[2.228118]

[2.228193]

*** DONE Privacy risks from genomic data-sharing beacons :identity_tracing:

Replacement in biblio/auragen.org at line 918 [2.197864]

B:BD[2.228545] → [2.228545:228605]

** DONE Quantifying Interdependent Risks in Genomic Privacy

[2.228545]

[2.228605]

*** DONE Quantifying Interdependent Risks in Genomic Privacy

Replacement in biblio/auragen.org at line 934 [2.197864]

B:BD[2.229041] → [2.229041:229154]

** DONE Re-identification of individuals in genomic data-sharing beacons via allele inference :identity_tracing:

[2.229041]

[2.229154]

*** DONE Re-identification of individuals in genomic data-sharing beacons via allele inference :identity_tracing:

Replacement in biblio/auragen.org at line 948 [2.197864]

B:BD[2.229539] → [2.229539:229676]

** KILL Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

[2.229539]

[2.229676]

*** KILL Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

Replacement in biblio/auragen.org at line 964 [2.197864]

B:BD[2.230345] → [2.230345:230404]

** DONE Simple demographics often identify people uniquely

[2.230345]

[2.230404]

*** DONE Simple demographics often identify people uniquely

Replacement in biblio/auragen.org at line 978 [2.197864]

B:BD[2.230693] → [2.230693:230767]

** DONE [#A] Routes for breaching and protecting genetic privacy :review:

[2.230693]

[2.230767]

*** DONE [#A] Routes for breaching and protecting genetic privacy :review:

Replacement in biblio/auragen.org at line 995 [2.197864]

B:BD[2.231239] → [2.231239:231300]

** DONE SNPs for a universal individual identification panel

[2.231239]

[2.231300]

*** DONE SNPs for a universal individual identification panel

Insertion in biblio/auragen.org at line 1007 [2.197864]

[2.231703]

:END:
** Décipher
*** DONE Framework ethique : inutile https://www.deciphergenomics.org/files/pdfs/decipher_ethical_framework.pdf
CLOSED: [2024-07-15 lun. 16:13]
*** DONE DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources
CLOSED: [2024-07-15 lun. 16:03]
:PROPERTIES:
:TITLE:    DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources
:BTYPE:    article
:CUSTOM_ID: firth2009decipher
:AUTHOR:   Firth, Helen V and Richards, Shola M and Bevan, A Paul and Clayton, Stephen and Corpas, Manuel and Rajan, Diana and Van Vooren, Steven and Moreau, Yves and Pettett, Roger M and Carter, Nigel P
:JOURNAL:  The American Journal of Human Genetics
:VOLUME:   84
:NUMBER:   4
:PAGES:    524--533
:YEAR:     2009
:PUBLISHER: Elsevier
:END:
inutile sur l'aspec réglèmentaire
*** DONE The GDPR and genomic data
CLOSED: [2024-07-15 lun. 16:43]
:PROPERTIES:
:TITLE:    The GDPR and genomic data
:CUSTOM_ID: mitchell2018gpdr
:BTYPE:  article 
:AUTHOR:  Mitchell, Colin  and Ordish, Johan and Johnson, Emma and Brigden, Tanya  and Hall, Alison
:YEAR:     2009

Insertion in biblio/auragen.org at line 1035 [2.197864]

[2.231709]

** Maladies rares
*** TODO The risk of re-identification versus the need to identify individuals in rare disease research
SCHEDULED: <2024-07-23 Tue>
:PROPERTIES:
:TITLE:    The risk of re-identification versus the need to identify individuals in rare disease research
:BTYPE:    article
:CUSTOM_ID: hansson2016risk
:AUTHOR:   Hansson, Mats G and Lochm{\"u}ller, Hanns and Riess, Olaf and Schaefer, Franz and Orth, Michael and Rubinstein, Yaffa and Molster, Caron and Dawkins, Hugh and Taruscio, Domenica and Posada, Manuel and others
:JOURNAL:  European Journal of Human Genetics
:VOLUME:   24
:NUMBER:   11
:PAGES:    1553--1558
:YEAR:     2016
:PUBLISHER: Nature Publishing Group
:END:
*** Prévalence maladies rare
**** KILL https://www.nature.com/articles/nrg.2017.116
CLOSED: [2024-07-18 Thu 14:55]
Généralité sur processus génétique
**** Stats
****** DONE Prevalence and practice for rare diseases in primary care: a national cross-sectional study in the USA
CLOSED: [2024-07-18 Thu 17:27] SCHEDULED: <2024-07-18 Thu>
:PROPERTIES:
:TITLE:    Prevalence and practice for rare diseases in primary care: a national cross-sectional study in the USA
:BTYPE:    article
:CUSTOM_ID: Jo_2019
:VOLUME:   9
:ISSN:     2044-6055
:URL:      http://dx.doi.org/10.1136/bmjopen-2018-027248
:DOI:      10.1136/bmjopen-2018-027248
:NUMBER:   4
:JOURNAL:  BMJ Open
:PUBLISHER: BMJ
:AUTHOR:   Jo, Ara and Larson, Samantha and Carek, Peter and Peabody, Michael R and Peterson, Lars E and Mainous, Arch G
:YEAR:     2019
:MONTH:    apr
:PAGES:    e027248
:END:
****** DONE A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
CLOSED: [2024-07-19 Fri 17:27] SCHEDULED: <2024-07-19 Fri>
:PROPERTIES:
:TITLE:    A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes
:BTYPE:    article
:CUSTOM_ID: macarthur2012systematic
:AUTHOR:   Daniel G. MacArthur and Suganthi Balasubramanian and Adam Frankish and Ni Huang and James Morris and Klaudia Walter and Luke Jostins and Lukas Habegger and Joseph K. Pickrell and Stephen B. Montgomery and Cornelis A. Albers and Zhengdong D. Zhang and Donald F. Conrad and Gerton Lunter and Hancheng Zheng and Qasim Ayub and Mark A. DePristo and Eric Banks and Min Hu and Robert E. Handsaker and Jeffrey A. Rosenfeld and Menachem Fromer and Mike Jin and Xinmeng Jasmine Mu and Ekta Khurana and Kai Ye and Mike Kay and Gary Ian Saunders and Marie-Marthe Suner and Toby Hunt and If H. A. Barnes and Clara Amid and Denise R. Carvalho-Silva and Alexandra H. Bignell and Catherine Snow and Bryndis Yngvadottir and Suzannah Bumpstead and David N. Cooper and Yali Xue and Irene Gallego Romero and Jun Wang and Yingrui Li and Richard A. Gibbs and Steven A. McCarroll and Emmanouil T. Dermitzakis and Jonathan K. Pritchard and Jeffrey C. Barrett and Jennifer Harrow and Matthew E. Hurles and Mark B. Gerstein and Chris Tyler-Smith and 1000 Genomes Project Consortium
:JOURNAL:  Science
:YEAR:     2012
:VOLUME:   335
:NUMBER:   6070
:PAGES:    823-828
:DOI:      10.1126/science.1215040
:URL:      http://dx.doi.org/10.1126/science.1215040
:END:
****** DONE Estimating the number of diseases – the concept of rare, ultra-rare, and hyper-rare
CLOSED: [2024-07-19 Fri 17:28] SCHEDULED: <2024-07-18 Thu>
:PROPERTIES:
:TITLE:    Estimating the number of diseases – the concept of rare, ultra-rare, and hyper-rare
:BTYPE:    article
:CUSTOM_ID: smith2022estimating
:VOLUME:   25
:ISSN:     2589-0042
:URL:      http://dx.doi.org/10.1016/j.isci.2022.104698
:DOI:      10.1016/j.isci.2022.104698
:NUMBER:   8
:JOURNAL:  iScience
:PUBLISHER: Elsevier BV
:AUTHOR:   Smith, C. I. Edvard and Bergman, Peter and Hagey, Daniel W.
:YEAR:     2022
:MONTH:    aug
:PAGES:    104698
:END:
****** DONE How many rare diseases are there?
CLOSED: [2024-07-19 Fri 17:24] SCHEDULED: <2024-07-19 Fri>
:PROPERTIES:
:TITLE:    How many rare diseases are there?
:BTYPE:    article
:CUSTOM_ID: haendel2019how
:AUTHOR:   Melissa Haendel and Nicole Vasilevsky and Deepak Unni and Cristian Bologa and Nomi Harris and Heidi Rehm and Ada Hamosh and Gareth Baynam and Tudor Groza and Julie McMurry and Hugh Dawkins and Ana Rath and Courtney Thaxton and Giovanni Bocci and Marcin P. Joachimiak and Sebastian Köhler and Peter N. Robinson and Chris Mungall and Tudor I. Oprea
:JOURNAL:  Nature Reviews Drug Discovery
:YEAR:     2019
:VOLUME:   19
:NUMBER:   2
:PAGES:    77-78
:DOI:      10.1038/d41573-019-00180-y
:URL:      http://dx.doi.org/10.1038/d41573-019-00180-y
:END:
****** KILL Prévalence française revoir avec Julien
CLOSED: [2024-07-22 Mon 17:05] SCHEDULED: <2024-07-22 Mon>
****** DONE BNDMR
CLOSED: [2024-07-19 Fri 15:46]
BNDMR https://www.bndmr.fr/publications/nombre-de-cas-par-mr/
****** DONE Orphadata: épidémiologie  (XML)
CLOSED: [2024-07-19 Fri 09:38]
:PROPERTIES:
:TITLE:    Epidemiology of Rare Disease
:BTYPE:   misc
:CUSTOM_ID: orphadata2024epidemio
:URL: https://www.orphadata.com/epidemiology/
:AUTHOR:   Orphanet
:YEAR:     2024
:MONTH:    jul
:END:
****** DONE The HPO - ORDO ontological module
CLOSED: [2024-07-19 Fri 14:59]
:PROPERTIES:
:TITLE: The HPO - ORDO ontological module
:BTYPE:   misc
:CUSTOM_ID: hoomm2024ordo
:URL: https://www.orphadata.com/hoom/
:AUTHOR:   Orphanet
:YEAR:     2024
:MONTH:    jul
:END:
****** DONE Orphadata : fréquence phénotypes associé
CLOSED: [2024-07-19 Fri 12:19]
:PROPERTIES:
:TITLE: Phenotypes Associated with Rare Disorders
:BTYPE:   misc
:CUSTOM_ID: orphadata2024phenotype
:URL: https://www.orphadata.com/phenotypes/
:AUTHOR:   Orphanet
:YEAR:     2024
:MONTH:    jul
:END:
****** DONE Orphadata : zygosite, age de début
CLOSED: [2024-07-19 Fri 12:25]
:PROPERTIES:
:TITLE: Natural History of Rare Diseases
:BTYPE:   misc
:CUSTOM_ID: orphadata2024natural
:URL: https://www.orphadata.com/phenotypes/
:AUTHOR:   Orphanet
:YEAR:     2024
:MONTH:    jul
:END:
https://www.orphadata.com/natural-history/
****** DONE Orphanet: prevalence et incidence : biblio
CLOSED: [2024-07-19 Fri 09:42]
:PROPERTIES:
:TITLE: Prevalence and incidence of rare diseases: Bibliographic data
:BTYPE:   misc
:CUSTOM_ID: orphanet2023prevalence
:URL: https://www.orpha.net/pdfs/orphacom/cahiers/docs/GB/Prevalence_of_rare_diseases_by_alphabetical_list.pdf
:AUTHOR:   Orphanet
:YEAR:     2023
:MONTH:    nov
:END:
****** DONE The burden of rare diseases
CLOSED: [2024-07-18 Thu 17:34] SCHEDULED: <2024-07-18 Thu>
:PROPERTIES:
:TITLE:    The burden of rare diseases
:BTYPE:    article
:CUSTOM_ID: ferreira2019burden
:VOLUME:   179
:ISSN:     1552-4833
:URL:      http://dx.doi.org/10.1002/ajmg.a.61124
:DOI:      10.1002/ajmg.a.61124
:NUMBER:   6
:JOURNAL:  American Journal of Medical Genetics Part A
:PUBLISHER: Wiley
:AUTHOR:   Ferreira, Carlos R.
:YEAR:     2019
:MONTH:    mar
:PAGES:    885–892
:END:
****** KILL Frequency-based rare diagnoses as a novel and accessible approach for studying rare diseases in large datasets: a cross-sectional study
CLOSED: [2024-07-18 Thu 14:45]
:PROPERTIES:
:TITLE:    Frequency-based rare diagnoses as a novel and accessible approach for studying rare diseases in large datasets: a cross-sectional study
:BTYPE:    article
:CUSTOM_ID: troster2023frequence
:VOLUME:   23
:ISSN:     1471-2288
:URL:      http://dx.doi.org/10.1186/s12874-023-01972-y
:DOI:      10.1186/s12874-023-01972-y
:NUMBER:   1
:JOURNAL:  BMC Medical Research Methodology
:PUBLISHER: Springer Science and Business Media LLC
:AUTHOR:   Tröster, Thomas S. and von Wyl, Viktor and Beeler, Patrick E. and Dressel, Holger
:YEAR:     2023
:MONTH:    jun
:END:
****** DONE Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database
CLOSED: [2024-07-19 Fri 15:05] SCHEDULED: <2024-07-18 Thu>
:PROPERTIES:
:TITLE:    Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database
:BTYPE:    article
:CUSTOM_ID: nguengang2019estimating
:VOLUME:   28
:ISSN:     1476-5438
:URL:      http://dx.doi.org/10.1038/s41431-019-0508-0
:DOI:      10.1038/s41431-019-0508-0
:NUMBER:   2
:JOURNAL:  European Journal of Human Genetics
:PUBLISHER: Springer Science and Business Media LLC
:AUTHOR:   Nguengang Wakap, Stéphanie and Lambert, Deborah M. and Olry, Annie and Rodwell, Charlotte and Gueydan, Charlotte and Lanneau, Valérie and Murphy, Daniel and Le Cam, Yann and Rath, Ana
:YEAR:     2019
:MONTH:    sep
:PAGES:    165–173
:END:
**** Modèles
****** DONE Determining the incidence of rare diseases
CLOSED: [2024-07-18 Thu 17:09] SCHEDULED: <2024-07-18 Thu>
:PROPERTIES:
:TITLE:    Determining the incidence of rare diseases
:BTYPE:    article
:CUSTOM_ID: bainbridge2020determining
:VOLUME:   139
:ISSN:     1432-1203
:URL:      http://dx.doi.org/10.1007/s00439-020-02135-5
:DOI:      10.1007/s00439-020-02135-5
:NUMBER:   5
:JOURNAL:  Human Genetics
:PUBLISHER: Springer Science and Business Media LLC
:AUTHOR:   Bainbridge, Matthew N.
:YEAR:     2020
:MONTH:    feb
:PAGES:    569–574
:END:
****** DONE Prevalence estimation for monogenic autosomal recessive diseases using population-based genetic data
CLOSED: [2024-07-18 Thu 17:15] SCHEDULED: <2024-07-18 Thu>
:PROPERTIES:
:TITLE:    Prevalence estimation for monogenic autosomal recessive diseases using population-based genetic data
:BTYPE:    article
:CUSTOM_ID: schrodi2015prevalence
:VOLUME:   134
:ISSN:     1432-1203
:URL:      http://dx.doi.org/10.1007/s00439-015-1551-8
:DOI:      10.1007/s00439-015-1551-8
:NUMBER:   6
:JOURNAL:  Human Genetics
:PUBLISHER: Springer Science and Business Media LLC
:AUTHOR:   Schrodi, Steven J. and DeBarber, Andrea and He, Max and Ye, Zhan and Peissig, Peggy and Van Wormer, Jeffrey J. and Haws, Robert and Brilliant, Murray H. and Steiner, Robert D.
:YEAR:     2015
:MONTH:    apr
:PAGES:    659–669
:END:
****** TODO Statistical methods for assessing the effects of de novo variants on birth defects
:PROPERTIES:
:TITLE:    Statistical methods for assessing the effects of de novo variants on birth defects
:BTYPE:    article
:CUSTOM_ID: xie2024statistical
:VOLUME:   18
:ISSN:     1479-7364
:URL:      http://dx.doi.org/10.1186/s40246-024-00590-z
:DOI:      10.1186/s40246-024-00590-z
:NUMBER:   1
:JOURNAL:  Human Genomics
:PUBLISHER: Springer Science and Business Media LLC
:AUTHOR:   Xie, Yuhan and Wu, Ruoxuan and Li, Hongyu and Dong, Weilai and Zhou, Geyu and Zhao, Hongyu
:YEAR:     2024
:MONTH:    mar
:END:
****** TODO A framework for the interpretation of de novo mutation in human disease
:PROPERTIES:
:TITLE:    A framework for the interpretation of de novo mutation in human disease
:BTYPE:    article
:CUSTOM_ID: samocha2014framework
:AUTHOR:   Kaitlin E Samocha and Elise B Robinson and Stephan J Sanders and Christine Stevens and Aniko Sabo and Lauren M McGrath and Jack A Kosmicki and Karola Rehnström and Swapan Mallick and Andrew Kirby and Dennis P Wall and Daniel G MacArthur and Stacey B Gabriel and Mark DePristo and Shaun M Purcell and Aarno Palotie and Eric Boerwinkle and Joseph D Buxbaum and Edwin H Cook and Richard A Gibbs and Gerard D Schellenberg and James S Sutcliffe and Bernie Devlin and Kathryn Roeder and Benjamin M Neale and Mark J Daly
:JOURNAL:  Nature Genetics
:YEAR:     2014
:VOLUME:   46
:NUMBER:   9
:PAGES:    944-950
:DOI:      10.1038/ng.3050
:URL:      http://dx.doi.org/10.1038/ng.3050
:END:
****** DONE Patterns and rates of exonic de novo mutations in autism spectrum disorders
CLOSED: [2024-07-22 Mon 10:44]
:PROPERTIES:
:TITLE:    Patterns and rates of exonic de novo mutations in autism spectrum disorders
:BTYPE:    article
:CUSTOM_ID: neale2012patterns
:VOLUME:   485
:ISSN:     1476-4687
:URL:      http://dx.doi.org/10.1038/nature11011
:DOI:      10.1038/nature11011
:NUMBER:   7397
:JOURNAL:  Nature
:PUBLISHER: Springer Science and Business Media LLC
:AUTHOR:   Neale, Benjamin M. and Kou, Yan and Liu, Li and Ma’ayan, Avi and Samocha, Kaitlin E. and Sabo, Aniko and Lin, Chiao-Feng and Stevens, Christine and Wang, Li-San and Makarov, Vladimir and Polak, Paz and Yoon, Seungtai and Maguire, Jared and Crawford, Emily L. and Campbell, Nicholas G. and Geller, Evan T. and Valladares, Otto and Schafer, Chad and Liu, Han and Zhao, Tuo and Cai, Guiqing and Lihm, Jayon and Dannenfelser, Ruth and Jabado, Omar and Peralta, Zuleyma and Nagaswamy, Uma and Muzny, Donna and Reid, Jeffrey G. and Newsham, Irene and Wu, Yuanqing and Lewis, Lora and Han, Yi and Voight, Benjamin F. and Lim, Elaine and Rossin, Elizabeth and Kirby, Andrew and Flannick, Jason and Fromer, Menachem and Shakir, Khalid and Fennell, Tim and Garimella, Kiran and Banks, Eric and Poplin, Ryan and Gabriel, Stacey and DePristo, Mark and Wimbish, Jack R. and Boone, Braden E. and Levy, Shawn E. and Betancur, Catalina and Sunyaev, Shamil and Boerwinkle, Eric and Buxbaum, Joseph D. and Cook Jr, Edwin H. and Devlin, Bernie and Gibbs, Richard A. and Roeder, Kathryn and Schellenberg, Gerard D. and Sutcliffe, James S. and Daly, Mark J.
:YEAR:     2012
:MONTH:    apr
:PAGES:    242–245
:END:

File addition: auragen.org (----------)

[3.2]

* Variants interprétés
:PROPERTIES:
:CATEGORY: excel
:END:
*** TODO Écrire tutorial confluence
SCHEDULED: <2024-07-30 Tue>
  /Entered on/  [2024-05-21 mar. 11:18]
*** KILL Vérifier diag RNU42 rendus
CLOSED: [2024-07-04 jeu. 11:12] SCHEDULED: <2024-07-08 lun.>
  /Entered on/  [2024-05-28 mar. 10:40]
À voir avec Nicolas, Virginie envoie un mail
** DONE Rattraper retard
CLOSED: [2024-07-09 mar. 11:13] SCHEDULED: <2024-07-09 mar.>
:LOGBOOK:
CLOCK: [2024-07-09 mar. 11:00]--[2024-07-09 mar. 11:15]
:END:
** WAIT 15 variants
:PROPERTIES:
:LAST_REPEAT: [2024-07-18 Thu 11:16]
:END:
- State "DONE"       from "TODO"       [2024-07-18 Thu 11:16]
- State "DONE"       from "TODO"       [2024-07-17 mer. 11:15]
- State "DONE"       from "TODO"       [2024-07-16 mar. 11:15]
- State "DONE"       from "TODO"       [2024-07-09 mar. 11:00]
- State "DONE"       from "TODO"       [2024-07-08 lun. 16:12]
:LOGBOOK:
CLOCK: [2024-07-09 mar. 08:45]--[2024-07-09 mar. 11:00] =>  2:15
CLOCK: [2024-07-08 lun. 15:54]--[2024-07-08 lun. 16:12] =>  0:18
CLOCK: [2024-07-08 lun. 09:05]--[2024-07-08 lun. 09:41] =>  0:36
:END:
- State "DONE"       from "TODO"       [2024-07-01 lun. 15:02]
- State "DONE"       from "TODO"       [2024-06-27 jeu. 14:39]
- State "DONE"       from "TODO"       [2024-06-25 mar. 10:55]
- State "DONE"       from "TODO"       [2024-06-24 lun. 16:57]
  /Entered on/  [2024-06-24 lun. 16:20]
** DONE Prototype Couchdb
CLOSED: [2024-07-02 mar. 11:09] SCHEDULED: <2024-07-02 mar.>
  /Entered on/  [2024-07-02 mar. 11:09]
** DONE Discussion Julien (Facebook)
CLOSED: [2024-07-15 lun. 16:39] SCHEDULED: <2024-07-15 lun. 13:30>
  /Entered on/  [2024-07-02 mar. 15:49]
  Ne pas parler de couchdb, ni des internes de Lyon.
  faire point Facebook +/- pseudogene
  Interne lyon: 2 à 5 avec présentatino bioinfo virginie + moi le matin et solvathon l'après-midi
** DONE Script pour vérifier colonnes bien remplies
CLOSED: [2024-07-15 lun. 11:16] SCHEDULED: <2024-07-15 lun.>
  /Entered on/  [2024-07-15 lun. 09:22]
** DONE Rajouter héritabilité + gènes manquant (check-variant/check.py)
CLOSED: [2024-07-23 Tue 11:15] SCHEDULED: <2024-07-19 ven.>
  /Entered on/  [2024-07-15 lun. 09:22]
** TODO Voir avec virginie del(5)(q35.3q35.3)(?177249773_?177257478)dn manqué
SCHEDULED: <2024-08-05 Mon>
MR-2400262
Rendu par N. Chatron “à l’oeil” sur la tlinique
Suggestion de N. Chatron “sauver les CNVs de CNVnator inférieur au seuil mais qui sont dans des gènes ranké par PhenoGenius. Ou a minima ceux qui touchent de la séquence codante.”
  /Entered on/  [2024-07-19 Fri 12:13]
** TODO Virginie Pourquoi  variant KCNB1 chr20:g.49374327del non rendu v7 et v8  ?
MR-2304498-t
Mis sur "variants manqué" confluence
SCHEDULED: <2024-08-06 Tue>
  /Entered on/  [2024-07-19 Fri 12:15]
* Curagen2
:PROPERTIES:
:CATEGORY: curagenv2
:END:
*** DONE Regarder variants non vus "en aveugle" [15/15]
CLOSED: [2024-06-26 mer. 15:01] SCHEDULED: <2024-06-26 mer.>
:LOGBOOK:
CLOCK: [2024-06-11 mar. 11:27]--[2024-06-11 mar. 12:38] =>  1:11
CLOCK: [2024-06-10 lun. 14:37]--[2024-06-10 lun. 15:01] =>  0:24
CLOCK: [2024-05-27 lun. 16:43]--[2024-05-27 lun. 17:15] =>  0:32
CLOCK: [2024-05-27 lun. 13:51]--[2024-05-27 lun. 16:00] =>  2:47
CLOCK: [2024-05-27 lun. 10:47]--[2024-05-27 lun. 11:51] =>  1:04
:END:
**** DONE MR-2102170 -> pas d'accès seqone
. 1er variant intronique profond (mais clinique pouvait coller !)
**** DONE MR-2200237 : rien trouvé
Note: aurapport : le variant  chr12:g.111347618_111347619insAC n'est pas dans IGV ?
attente seqone
**** DONE MR-2201162 : rien trouvé
Aurapport
VOUS- SON
**** DONE MR-2201495 htz composite SPATA5L1 3+ ?
CLOSED: [2024-06-10 lun. 14:33]
**** DONE MR-2202491 GBA -> pas dans VCF
**** DONE MR-2202512 attente seqone -> pas dans VCF !
Gène SBDS
chaque parent htz -> htz composite chez patient
variant mosaïque VAF18%
**** DONE MR-2201470 LEF1 classe 3 -> plutôt 4 en fait
CLOSED: [2024-06-10 lun. 14:45]
publi 2020 https://pubmed.ncbi.nlm.nih.gov/32022899/
**** DONE MR-2203331 RERE ? 3 -> FOXI3 en fait
CLOSED: [2024-06-10 lun. 14:54]
**** DONE MR-2203418 rien trouvé
aurapport
****** ATRX : intronique profond avec spliceai DG 20, pas d'élément régulateur ucsc ?
****** XRCC4 = récessif sans 2e variant dans seqone.  clinique + clinvar patho mais hérité mère
seqone
****** HNRNPU: encéphalopathie épiletique : bof
**** DONE MR-2203508 SRNBP ? pas de score -> oui
CLOSED: [2024-06-10 lun. 16:44]
**** DONE MR-2203533 seqone échec
DEADLINE: <2024-07-02 mar.> SCHEDULED: <2024-06-25 mar.>
:LOGBOOK:
CLOCK: [2024-07-01 lun. 15:02]--[2024-07-01 lun. 15:03] =>  0:01
:END:
**** DONE MR-2301965 NSD2
DEADLINE: <2024-06-28 ven.>
NSD2 : frameshift pLI 1 clinique colle
framshift INLS3 ? bof
ok cryptorchidie mais gène plI = 0
**** DONE MR-2303770 idem
DEADLINE: <2024-07-02 mar.> SCHEDULED: <2024-06-26 mer.>
POU3F3 VOUS-
CACNA1E VOUS-
**** DONE MR-2400054 mauvaise qualité reads !
IKB
Mais un read avec deletion ok ne s'aligne pas si mal. Avec BLAT:
149     1   150   150   100.0%  chrX                 -   154643828 154643979    152
149     1   150   150   100.0%  chrX                 +   154560459 154560610    152
 28     3    47   150    83.4%  chrX                 -   130249297 130249341     45
 23   110   133   150   100.0%  chr9                 +   134170923 134170948     26
 22   106   135   150    69.6%  chr6_GL000251v2_alt  +     1408511   1408533     23   What is chrom_alt?
 21    39    61   150    95.7%  chr8                 +    66429131  66429153     23
 20    15    34   150   100.0%  chr10                +    72875848  72875867     20
 18    31    48   150   100.0%  chr16                +    47049679  47049696     18
**** DONE MR-2400402 RBPJ ? g.26415496T>G
EXT1 connu (hygen)
Seqone
- RBPJ faux sens avec clinique en faveur (retard psychomot et raccourissement doigts), score patho, mais hérité du père.
*** TODO Vérifier variants non vus avec mon intérprétations
SCHEDULED: <2024-07-25 Thu>
*** WAIT Comprendre nouveaux filtres
  /Entered on/  [2024-05-21 mar. 11:04]
*** PROJ Présenter les trous de Curagen aux bios
  /Entered on/  [2024-05-27 lun. 10:00]
** DONE Relire newsletter
CLOSED: [2024-06-12 mer. 14:17] SCHEDULED: <2024-06-12 mer.>
  /Entered on/  [2024-06-12 mer. 14:08]
* Projets
** Pseudo-gènes (ou régions répétées)
:PROPERTIES:
:CATEGORY: pseudogene
:END:
*** TODO Biblio
*** TODO Porter script en hg19
  /Entered on/  [2024-05-21 mar. 11:07]
** Facebook
:PROPERTIES:
:CATEGORY: facebook
:END:
** WAIT Contact BM Knopper
  /Entered on/  [2024-07-15 lun. 15:37]
** WAIT Contact Heidi Howard (ESHGH, chaire éthique)
  /Entered on/  [2024-07-15 lun. 15:38]
** DONE Chercher méthodologie decipher
CLOSED: [2024-07-16 mar. 09:52] SCHEDULED: <2024-07-16 mar.>
  /Entered on/  [2024-07-15 lun. 15:38]
** DONE Lire GDPDR
CLOSED: [2024-07-15 lun. 16:39] SCHEDULED: <2024-07-15 lun.>
  /Entered on/  [2024-07-15 lun. 15:38]
** DONE Présentation CAD biblio
CLOSED: [2024-07-16 mar. 09:52] SCHEDULED: <2024-07-15 lun. 17:00>
Entered on [2024-07-15 lun. 15:40]
** TODO Mise à jour draft1
SCHEDULED: <2024-07-23 Tue>
Fusionner notes
- [[denote:20240722T095640][Monday 22 July 2024 09:56]] surtout
- [[denote:20240716T172506][Tuesday 16 July 2024 17:25]]
- [[denote:20240718T153145][Thursday 18 July 2024 15:31]]
- [[denote:20240719T093836][Friday 19 July 2024 09:38]]
** TODO Trouver algo de simulation de probab d’un variant (2-3 nucléotides)
SCHEDULED: <2024-07-23 Tue>
  /Entered on/  [2024-07-22 Mon 17:17]
** Case report CHD7 :article:
:PROPERTIES:
:CATEGORY: chd7
:END:
** DONE Mail Marine pour suivi Nanopore
CLOSED: [2024-06-24 lun. 11:51] SCHEDULED: <2024-06-21 ven.>
  /Entered on/  [2024-06-21 ven. 16:48]
** DONE Mail Dr Frédérique Bilan CHU Poitiers pour détails MLPA
CLOSED: [2024-06-24 lun. 11:51] SCHEDULED: <2024-06-21 ven.>
  /Entered on/  [2024-06-21 ven. 16:48]
** DONE Mail Xavier Nanopore
CLOSED: [2024-06-24 lun. 14:49] SCHEDULED: <2024-06-24 lun.>
  /Entered on/  [2024-06-24 lun. 14:48]
** DONE Demande à Pauline si prélèvement possible
CLOSED: [2024-06-24 lun. 15:57] SCHEDULED: <2024-06-24 lun.>
  /Entered on/  [2024-06-24 lun. 14:48]
  Mail envoyé <2024-06-24 lun.>
** DONE Revoir avec Gaelle pour transfert ADN
CLOSED: [2024-06-25 mar. 12:00] SCHEDULED: <2024-06-25 mar.>
  /Entered on/  [2024-06-25 mar. 10:56]
** DONE Répondre MLPA
CLOSED: [2024-06-25 mar. 12:00] SCHEDULED: <2024-06-25 mar.>
  /Entered on/  [2024-06-25 mar. 10:56]
** WAIT Bon de demande + prescription + consentement (voir avec Pauline)
  /Entered on/  [2024-06-25 mar. 13:56]
** DONE Vérifier absence dup liste CNV non filtré
CLOSED: [2024-06-25 mar. 16:05] SCHEDULED: <2024-06-25 mar.>
  /Entered on/  [2024-06-25 mar. 13:57]
  Rien vu sur IGV probant
  Attente quentin
** DONE Récupérer ADN parents
CLOSED: [2024-07-02 mar. 12:08]
  /Entered on/  [2024-06-25 mar. 13:57]
** TODO Envoi ADN biomnis (parent + cas index)
SCHEDULED: <2024-08-02 ven.>
  /Entered on/  [2024-06-25 mar. 13:58]
** Génomes péruvien
:PROPERTIES:
:CATEGORY: peru
:END:
** TODO Biblio julien
SCHEDULED: <2024-07-23 Tue>
** WAIT Biblio M1
* Divers
** KILL Compte admin sur DELL
CLOSED: [2024-07-11 jeu. 10:07]
/Créé le/ [2024-05-16 jeu. 11:11]
Échec: besoin d'un adaptateur
    auradmin
    axetrois
** DONE Présentation ACRAA CHD7
CLOSED: [2024-06-19 mer. 11:01] DEADLINE: <2024-06-20 jeu. 14:00>
  /Entered on/  [2024-06-18 mar. 14:52]
Compléter diapo avec
*** Clinique : CHARGE
*** Clinique : phénotype étendu
   https://www.ncbi.nlm.nih.gov/books/NBK1117/
-   Colobome oculaire (petit colobome rétinien -> anophtalmie) : 80%
-   Atrésie/ Sténose choanale : 45%
-   Dysfonctionnement / Anomalie des nerfs crâniens :
    -   I : hyposmie ou anosmie : 90%
    -   VII : paralysie faciale : 40%
    -   VIII : surdité neurosensorielle: >95%
    -   IX/X : succion et déglutition, motilité gastro-intestinale anormale : 60%-80%
-   Malformations de l'oreille : *caractéristique!*
    -   Auricule : 90%
    -   Malformations ossiculaires : 80%
    -   hypoplasie cochléaire : 90%
    -   *canaux semi-circulaire absent/hypoplasiques* : 94%
-   *Fente labiale* et/ou palatine : 25%-50%
-   Endocrinien :
    -   Hypogonadisme hypogonadotrope : 50%-70%
    -   Déficit de croissance : 70%
    -   Hypothyroïdie : 15%-20%
-   Retard de développement / Déficience intellectuelle : \>90% / 60%
-   *Malformation cardiovasculaire* : 74%
-   Anomalies trachéo-oesophagiennes : 20% (*difficultés respiratoires*, trachéo *laryngomalacie*)
-   Cerveau :
    -   Hypoplasie du clivus : 95%
    -   Autres anomalies : 50%
-   Crises épileptiques : 30%
-   Anomalies rénales : 30%
*** CHD7 et phénotype cardiaque
   - phéno cardiaque à repréciser
     mettre figure
     https://onlinelibrary.wiley.com/doi/full/10.1002/ajmg.c.31761
*** CHD7 et phénotype cardiaque
     Source https://onlinelibrary.wiley.com/doi/full/10.1002/ajmg.c.31761
- Implication des cellules de la crêtes neurale dans le CHARGE. en effet
  - fréq augmenté des défaut conovventricailaire et "arch vessels"
  - cellules cretes neptarale rôle : septation of the outflow tract and conal septum and the pharyngeal arches
- Problème : AVSD surreprésenté (c. crêtes neurole non essentilé dans la formation du "cushion endocardial") -> probablement
  - Mesoderm lineage-specific ablation (Mesp1) of CHD7 leads to disruption of endocardial cushion formation, which may explain the overrepresentation of AVSD defects in CHARGE syndrome (Payne et al., 2015).
  - Probablement multiple pathway
    - overlap avec
      - 22q11.2) : TBX1 (phéno cardiaque) = synergique CHD7 et TBX1, médiation partielle p53
    - syndrome kabuki (KTMD2D, KDM6A (mécanisme de remodelage chromatique similaire à CHD7)
    - rôle chromatine et méthylation
*** CHD7 et bulbles olfactifs
Source https://onlinelibrary.wiley.com/doi/full/10.1002/ajmg.c.31585
    - Olfactory testing and/or MRI imaging in individuals with CHARGE with gonadal defects revealed defective olfaction/olfactory bulb development in a significant number of patients (Chalouhi et al., 2005; Pinto et al., 2005). ""
    - fetus: "studies in a human fetus with CHARGE syndrome has confirmed that the CHARGE fetus showed arhinencephaly (olfactory bulb agenesis) with absence of GnRH neurons in the forebrain (Teixeira et al., 2010). The migrating olfactory and GnRH neurons accumulated in the fronto-nasal region with the formation of bilateral spherical structures consistent with neuromas near the cribriform plate, implicating a significant migratory defect (Teixeira et al., 2010)"
    - souris "Chd7 deficient mice display smaller olfactory bulbs, reduced number of olfactory sensory neurons, defective senses of smell with loss of odor-evoked electro-olfactogram responses, reduced hypothalamic GnRH neuronal numbers, hypoplastic genitalia, hypogonadotropism, and impaired pubertal timing (Bergman et al., 2010; Layman et al., 2011, 2009).
    - The GnRH deficiency in CHARGE syndrome, thus results from the olfactogenital pathological sequence, implicating the disruption of olfactory axon migration to the forebrain as the primary cause of the defective migration of GnRH synthesizing cells, which normally migrate along these nerve fibers.
*** Rôle moléculaire CHD7
Genereviews :
- protéine impliquée remodelage de la chromatine dépendante ATP
- INteraction avec dizaines de gènes et > 10k site mammifère
- Mécanisme non connu (perte biogénèse ribosomale ?)
- Régulateur épigénétique
https://onlinelibrary.wiley.com/doi/10.1002/ajmg.c.31592
*** Rôle moléculaire CHD7
Mécanisme = Perte ou diminution de fonction (Genereviews)
- 78% allèle null
- 9% faux-sens
- 13 anomalie de splice : allèle nul (frameshift) ou hypomorhpe (saut d'exons)
Limites
- Modèle animal: faux-sens/allèle hypomorphes non testé pour le phénotype
- quid formes atypiques/légères ?
*** Variants pathologiques
Extrait de chd7.org 18 juin 2014
| Type                | Nombre | Pourcentage |
|---------------------+--------+-------------|
| deletion            |      8 |        1.38 |
| deletion whole gene |     10 |        1.72 |
| duplication         |      1 |        0.17 |
| frameshift          |    267 |       45.96 |
| missense            |     47 |        8.09 |
| nonsense            |    174 |       29.95 |
| splice site         |     71 |       12.22 |
| translocation       |      3 |        0.52 |
*** Ressources
https://chd7.org/
** DONE Présentation CHD7 journée biologiste avec correction charles
CLOSED: [2024-07-08 lun. 08:42] SCHEDULED: <2024-06-28 ven.> DEADLINE: <2024-07-04 jeu. 13:15>
  /Entered on/  [2024-06-21 ven. 17:05]
  Attente retour Charles + véronique
** DONE Question Jean-François sur stockage
CLOSED: [2024-06-25 mar. 12:00]
  /Entered on/  [2024-06-24 lun. 09:49]
** DONE Pourquoi 2101694 ré-archivé seqone ?
CLOSED: [2024-07-01 lun. 11:52] SCHEDULED: <2024-06-28 ven.>
  /Entered on/  [2024-06-28 ven. 15:18]
** DONE Aider Paul : 2e variant MR-2203140  DISP1 ?
CLOSED: [2024-07-03 mer. 14:41] SCHEDULED: <2024-07-02 mar.>
  /Entered on/  [2024-07-02 mar. 11:15]
** WAIT Vérifier CR corrigé MR-2304760 Hygen
  /Entered on/  [2024-07-08 lun. 08:40]
  Mail envoyé <2024-07-10 mer.>
** DONE Vérifier interêt STR multiples non rendus
CLOSED: [2024-07-08 lun. 10:09] SCHEDULED: <2024-07-08 lun.>
:LOGBOOK:
CLOCK: [2024-07-08 lun. 09:53]--[2024-07-08 lun. 10:09] =>  0:16
:END:
  /Entered on/  [2024-07-08 lun. 09:03]
** DONE Question: MR-2400594 variants décochés mais restent de la liste "à envoyer"
CLOSED: [2024-07-19 Fri 11:21] SCHEDULED: <2024-07-19 Fri>
  /Entered on/  [2024-07-19 Fri 11:06]
  Bug ID HGNC, ne devrait pas réarriver
* Formation
:PROPERTIES:
:CATEGORY: formation
:END:
** WAIT Améliorations slides bioinfo :bioinfo:
*** Général
- EBV: bien précisé qu'il est gardé dans le génome et non masqué (faire une liste sur la diapo)
- [X] contrôle qualité progressif : 20x -> 10x (1.1 et 4.1) représentation trompeuse car on a plus de résultat en 10x qu'en 20x -> corrigé par virginie
- différence aurapport-curagen-seqone n'est pas du tout claire, notamment rôle de curagenène. Il faudrait rajouter cette figure dans la présentation générale (voir
[[https://auragen.atlassian.net/wiki/spaces/~7120201ca2598be5ef4936a1110033f28f4fed/overview][Vue d'ensemble du pipeline]]
*** TODO Refaire le point avec Virginie sur commentaires
SCHEDULED: <2024-09-01 dim.>
** WAIT Figure curagen
/Créé le/ [2024-05-16 jeu. 16:22]
Attendre la v2
** TODO Vidéos pas-à-pas [[https://app.videas.fr/v/6dbbf878-740f-4e31-9587-76202736c9ae/][IGV]] :faq:
SCHEDULED: <2024-07-31 mer.>
  /Entered on/  [2024-05-27 lun. 10:00]
** TODO [[https://anpgm.fr/media/documents/BP-NGSDiag_001_Interpretation_Variants_v2.pdf][Recos NGS-diag SNV]]
  /Entered on/  [2024-05-27 lun. 14:18]
** TODO Compléter FAQ bio : un même variant peut sur plusieurs gènes :faq:
  /Entered on/  [2024-05-28 mar. 12:02]
On peut avoir plusieures lignes pour un variant : présenter un cas (découvert sur mais MR-2305018 pas assez propre (VAF=28=))
Attention: pour clinvar, on utilise la position donc on peut flagger sur le mauvais gènes...
Mettre à jour https://auragen.atlassian.net/wiki/spaces/~7120201ca2598be5ef4936a1110033f28f4fed/pages/1524695047/Questions
** TODO Prévoir réunion julien avec [[id:d87c8b18-ea67-4a81-ab7e-20c8fbca0123][Questions pour Julien]]
  /Entered on/  [2024-06-06 jeu. 16:07]
* Kalilab
:PROPERTIES:
:CATEGORY: kalilab
:END:
** DONE SH-REF-02 REV 07 Exigences pou
CLOSED: [2024-07-03 mer. 14:47] SCHEDULED: <2024-07-03 mer.>
** DONE NF EN ISO 15189 LBM Exigences
CLOSED: [2024-07-23 Tue 14:31] SCHEDULED: <2024-07-22 Mon>
** DONE SH-FORM-43 VDM WGS génétique c
CLOSED: [2024-06-26 mer. 10:58] SCHEDULED: <2024-06-26 mer.>
* Auragen
:PROPERTIES:
:CATEGORY: auragen
:END:
** Downgrader nom de gène pour OMIM :pipeline:omim:
**** Notes
Problème: certains variants ne sont pas flaggés OMIM.
Cause: vieille version de GENCODE (utilisé pour l'annotation par VEP)
Idéalement il faudrait  obtenir le nom de gène depuis ID hgnc avant annot OMIM.
Cela sera "corrigé" avec la mise à jour GENCODE.
On utilise GENCODE32 qui est en septembre 2019 ([[https://www.gencodegenes.org/human/releases.html][source]])
Algorithme : pour les gène ayant été modifié >= septembre 2019, on remplace le nom du gène par les anciennes versions (donc dpublication des lignes)
Tests
- KIFBP -> downgrader KIF1BP
- GBA -> ?
**** WAIT Mettre à jour https://auragen.atlassian.net/wiki/spaces/~7120201ca2598be5ef4936a1110033f28f4fed/pages/1524924423/Suggestions+d+am+liorations
SCHEDULED: <2024-08-22 Thu>
Test
KIFBP -> KIF1BP
**** DONE Récupérer données OMIM + fichier HGNC avec identifiant
SCHEDULED: <2024-05-28 mar.>
**** DONE Script python pour downgrade noms de gènes
CLOSED: [2024-06-11 mar. 10:34] SCHEDULED: <2024-06-17 lun.> DEADLINE: <2024-08-01 jeu.>
:LOGBOOK:
CLOCK: [2024-05-31 ven. 09:37]--[2024-05-31 ven. 10:00] =>  0:23
:END:
envoyé quentin
  /Entered on/  [2024-05-27 lun. 13:38]
**** DONE Envoyer code virginie pour review
CLOSED: [2024-06-11 mar. 10:57] SCHEDULED: <2024-06-11 mar.>
**** DONE Utiliser la date de GENCOD32
**** DONE Vérifier sur KIF1BP et GBA
GBA1 -> GBA antérieur
** DONE Nettoyer tâches finies dans "améliorations" et "questions" :doc:
CLOSED: [2024-06-11 mar. 10:44] SCHEDULED: <2024-06-11 mar.>
:LOGBOOK:
CLOCK: [2024-06-11 mar. 10:42]--[2024-06-11 mar. 10:44] =>  0:02
:END:
  /Entered on/  [2024-06-11 mar. 10:26]
** DONE Mastermind ? :aurapport:
CLOSED: [2024-06-19 mer. 11:00] SCHEDULED: <2024-06-19 mer.>
  /Entered on/  [2024-06-11 mar. 10:31]
  Démo non convaincate à véronique: n'arrivait pas à voir les articles par variant
  Retesté : ok
  Limite: impossible de trier par pertinence les articles donc moins intéressant...
** TODO Pubmatcher sur variants sans clinvar ni HPO
SCHEDULED: <2024-07-25 Thu>
  /Entered on/  [2024-06-11 mar. 10:30]
* Réunions
:PROPERTIES:
:CATEGORY: réunion
:END:
** Projet Facebook :facebook:
** RVI Montpellier :montpellier:rvi:
*** TODO RVI
SCHEDULED: <2024-07-25 Thu 09:30 +7d>
:PROPERTIES:
:END:
*** TODO Clinico-biologique
SCHEDULED: <2024-07-26 Fri 00:00>
:PROPERTIES:
:LAST_REPEAT: [2024-07-22 Mon 09:31]
:END:
- State "DONE"       from "TODO"       [2024-07-19 Fri 09:31]
- State "DONE"       from "TODO"       [2024-07-15 lun. 11:14]
- State "DONE"       from "TODO"       [2024-06-28 ven. 16:15]
- State "DONE"       from "TODO"       [2024-06-24 lun. 11:51]
- State "DONE"       from "TODO"       [2024-06-21 ven. 11:43]
Entered on [2024-06-18 mar. 09:53]
** RVI Grenoble :grenoble:rvi:
** TODO Laboratoire
SCHEDULED: <2024-08-22 Thu 13:30 +1w>
:PROPERTIES:
:LAST_REPEAT: [2024-07-11 jeu. 14:41]
:END:
- State "DONE"       from "TODO"       [2024-07-11 jeu. 14:41]
- State "KILLED"     from "WAIT"       [2024-07-04 jeu. 11:05]
- State "KILL"       from "TODO"       [2024-06-27 jeu. 14:40]
- State "DONE"       from "TODO"       [2024-06-20 jeu. 12:03]
- State "KILL"       from "TODO"       [2024-06-13 jeu. 16:43]
- State "KILL"       from "TODO"       [2024-06-06 jeu. 15:16]
- State "DONE"       from "TODO"       [2024-05-30 jeu. 17:48]
Entered on [2024-05-30 jeu. 13:30]
** TODO Axe 3
SCHEDULED: <2024-07-25 jeu. 09:00 +2w>
:PROPERTIES:
:LAST_REPEAT: [2024-07-11 jeu. 10:05]
:END:
- State "DONE"       from "TODO"       [2024-07-11 jeu. 10:05]
** Réunion biologistes Auragen :bio:auragen:
** DONE Julien
CLOSED: [2024-07-23 Tue 09:53] SCHEDULED: <2024-07-22 lun. 13:30>
Entered on [2024-07-16 mar. 09:53]
** TODO Philippe Jean (heure approx)
SCHEDULED: <2024-07-29 lun. 17:00>
Entered on [2024-07-16 mar. 09:53]
* Interprétation génomes
:PROPERTIES:
:CATEGORY: génomes
:END:
** Montpellier :montpellier:
** TODO RVI MR-2302861 MYH10 vous+, attente seqone
BAZB1: compris dans la microdel du sd williams mais rien de plus. Touche épissage ??
FH = donnée incidente ? (cancer) "Hereditary leiomyomatosis and renal cell cancer is an autosomal dominant tumor predisposition syndrome"
MYH10: site accepteur, non connu, non présent gnomAD. Article récent avce clinique overlap
cnv dup chr1 800kb, pas de gène codant
seqone : NOTCH2 chr1:g.120069404C>T : avis Jérémy ?
DDR2 bof
** DONE MR-2400087
CLOSED: [2024-06-28 ven. 12:11]
- DYM pas de 2e allele
- ANO5: tronquant mais pli 0, clinique différente (récessif = dystrophie musculaire, dominant = sd osseux mais pas de pied bot
#+begin_quote
"fibro-osseous lesions of jawbones and sclerosis of tubular bones (Andreeva et al., 2016). In this skeletal syndrome, a phenotype of bone fragility as well as lesions in the mandible can be observed, which can result in facial deformities and susceptibility to purulent osteomyelitis (" https://onlinelibrary.wiley.com/doi/10.1002/mgg3.2004
#+end_quote
hérité de la mère asympto
- RAI1 mauvaise qualité
- /NOTCH3/ clinique ne colle pas vraiment (méningocèle) mais 1 patient avec dysplasie valve, sino score bioinfo rouges, gènes nb faux-sens patho
- del 36kb prenant dernier exon *GPC3*: colle mais récessif, qq del plus petites DGV
** DONE MR-2303166
CLOSED: [2024-06-28 ven. 16:20]
** DONE MR-2304637 Remplir CR hygen
CLOSED: [2024-07-11 jeu. 10:05] SCHEDULED: <2024-07-11 jeu.>
:LOGBOOK:
CLOCK: [2024-07-08 lun. 10:19]--[2024-07-08 lun. 11:04] =>  0:45
:END:
Le séquençage du génome du patient en duo n'a pas permis d'identifier de variant clairement pathogène pouvant expliquer le phénotype de la patiente.
Cependant, une variation hétérozygote faux-sens de signification incertaine dans l'exon 13 du gène CACNA1C a été identifiée.NM_000719.7:c.1736G>A p.(Gly579Asp). Cette variation est héritée de la mère dans un génome en duo. Cette variation est absente de la base de données populationnelles gnomAD v4.0. Les différents scores de prédiction bio-informatique appliqués soutiennent un impact fonctionnel.Elle n'est pas dans un domaine fonctionnel mais l'acide aminé est très conservé.
Le gain de fonction du gène CACNA1C est lié à un allongement du QT chez quasiment tous-les patients avant l'âge de 4 ans, ainsi que de manière fréquente à un trouble du spectre autistique et parfois des malformations cardiaques et un retard de devéloppement (Napolitano et al, 2006 Genereviews). Cependant, un phénotype extra-cardiaque prédominant a été également décrit avec des trouble du neurodéveloppement (OMIM #620029). Celui-ci comprend une hypotonie, retard de language et déficience intellectuelle avec trouble du comportement. Les atteintes cardiaques sont rares (PMID: 34163037).
L'étude de la ségrégation de cette variation dans la famille avec l'analyse du père et la confrontation aux phénotypes permettraient d'affiner l'interprétation de cette variation. La
confirmation de ce résultat sur un second prélèvement indépendant est recommandée.
*Une consultation de génétique est nécessaire pour expliquer ce résultat.*
** DONE MR-2302630
CLOSED: [2024-06-28 ven. 16:20]
** WAIT MR-2304058
  /Entered on/  [2024-06-24 lun. 11:39]
  SRCAP: fréquent cohorte, qq score bioinfo, fin de gène, 71x gnomad, clinvar conflicting
  PKD2 bof sur score,
  NUP85 score bioinfo
  recql4 récessif
  trnbc6 non bionfo
  GTF2IRD1 = VOUS- neurodev (sd wiliams), peu connu (1 faux sens patho decihpre))
  ZBTB10 tronquant pli=1 mais non connu rien dans la biblio, vu en exome
  FREM1 VOUS- : pas de score binfo in faveur
  Exome avait déjà retrouvée ADCY10 rendu probablement patho : bilan phoshpocalciurie non fait
  RYR1 vous
  ZBTB10 VOUS
  SV: MAGI2 ?? perte de fonction patho mais décrit récessiif
  RICB:
  - MAGI2 transloc 3,7 mais 1 seul à allèle a priori alors que récessif (syndrome néphrotique). 2017 hmz ou htzc avec 2 codon stop prématuré  https://pubmed.ncbi.nlm.nih.gov/27932480/
  - ZBTB10 à genematcher si non fait mais déjà connu et VOUS. Tronquant, de novo non présent gnomad, non OMIM, rien pubmed
  - ADCY10: clinvar patho2x, hypercalciurie, tronquant, gène assez peu connu, qq tronqunt mais pLI 0, héritèr père
  - NAV3 del mais pas très clair (bruit ?)
*** DONE Auramatcher zbtb10
CLOSED: [2024-07-19 Fri 16:14]
1 tronquant de novo
- MR-2303393: trouble neuroved, TSA. Pas au  mme endroit. Pas dans le seul domaine fonctionnel
*** WAIT Genematcher ZBT10 attente Jérémie sur dossier toulouse  ːMR-2304058ː
SCHEDULED: <2024-07-25 Thu>
fait.
Doute sur TND poru notre patient.
TND et TSɑ sur dossier Toulouse MR-2303393  -> Jérémie va le lire
Demande avis ʍarjolaine pour la suite si ɡenematcher
** DONE MR-2400693 attente hygen + faire CR
CLOSED: [2024-07-04 jeu. 11:04] SCHEDULED: <2024-07-04 jeu.>
  /Entered on/  [2024-06-24 lun. 11:50]
  - NF1 = diag (suspi clinique, clinivarpatho)
  n'explique pas le reste de la clinique. Surdité possible ? pas dans genereviews mais https://pubmed.ncbi.nlm.nih.gov/36583617/. Pectus excatavum peut être retrouvé dans le phénotype nf1-noonan (genereviews)
  - GJB2 clinvar bénin, sans 2e allèle
  - AILP1= dystrophie rétinienne, clinique ne colle pas, hérité mère mais bien rouge, gène plutôt lof
    forme plutôt récessive ?
i
    OK CR à préparer avec mention IRM selon modèle Jérémie
chr17(GRCh38):g.31221401A>G Gène NF1
NM_001042492.3:c.1642-449A>G
p.?, hétérozygote, De novo, Pathogène
MR-2102480
Mise en évidence d’une variation pathogène hétérozygote dans le gène NF1, survenue de novo (absente chez les parents).
Cette variation hétérozygote intronique profond est prédite comme ayant un effet sur l’épissage (spliceAI AG=0.88, SPiP=69.33%) avec possiblement la création d'un pseudo-exon. Cette variation est absente de la base de données populationnelles gnomAD v4.0.
Elle a été décrite 4 fois comme pathogène dans Clinvar (ID:216394), dont une fois pour la neurofibromatose de type 1.
Les variations pathogènes dans le gène NF1 sont associées à la neurofibromatose de type 1 (NF1) de transmissione autosomique dominante (OMIM *182390). À noter que le phénotype du syndrome NF1-Noonan, retrouvé dans 12% des patients atteints de NF1, comporte des anomalies du pectus (Genereviews). La présence de neurofibromes plexiformes à la base du crâne peut entraîner une déficience auditive (PMID: 36583617)
Cette variation est considérée comme pathogène (classe 4, critères ACMG: PM2, PS2, PS4).
La présence de cette variation pathogène hétérozygote peut expliquer le phénotype observé chez la patiente. IL serait souhaitable de réaliser une IRM pour évaluer la presence de neurofibromes plexiformes pouvant expliquer la surdité. Ce résultat doit être confronté au contexte clinique et aux données familiales. La confirmation de ce résultat sur un second prélèvement indépendant est recommandée.
Une consultation de génétique est nécessaire pour expliquer ce résultat.
** WAIT MR-2301158
** DONE Auramatcher MYH10 MR-2302861
CLOSED: [2024-07-10 mer. 14:09] SCHEDULED: <2024-07-08 lun.>
  /Entered on/  [2024-07-02 mar. 15:47]
  1 faux-sens de novo poussé Hygen . Reste = non lu ou hérité. Jamais rendu apparement
** DONE Écrire formule remaniement MR-2402030
CLOSED: [2024-07-08 lun. 15:54] SCHEDULED: <2024-07-08 lun.>
:LOGBOOK:
CLOCK: [2024-07-08 lun. 13:56]--[2024-07-08 lun. 15:54] =>  1:58
CLOCK: [2024-07-08 lun. 13:39]--[2024-07-08 lun. 13:47] =>  0:08
CLOCK: [2024-07-08 lun. 11:07]--[2024-07-08 lun. 12:07] =>  1:00
:END:
seq[GRCh38]inv(8)(q12.2)inv(8)(q12.2)del(8)(q12.2)dn
NC_000008.11:g.60859596_60862961inv
NC_000008.11:g.60862561_60863010inv
NC_000008.11:g.60862564_60866381del
Présence d'un remaniement complexe en 8q12.2 d'environ 6.7kbp, de novo. Il contient les 3 derniers exons de CHD7. 5 points de cassures ont été identifiés, dont une probable délétion comprenant les deux derniers exons. Il n'est pas possible d'exclure le caractère en mosaïque de cette délétion.
L'haploinsuffisance de CHD7 est associée au syndrome CHARGE (OMIM #214800). Ce remaniement est donc pathogène (classe 5) et explique le phénotype.
Un conseil génétique est souhaitable.
La caractérisation précise de ce variant structurel nécessiterait une technique complémentaire (long-read).
** WAIT MR-2400512
  /Entered on/  [2024-07-04 jeu. 11:03]
  COL6A3: gène plutôt tronquant, 2 fois cohorte, 21 gnomAD génome, domaine fonctionnel, score bioinfo mitigés, présent chez père non en mosaïque, VOUS-clinvar. AD ou AR sans 2e allèl  e -> vérif clinique père
** DONE MR-2401415: négatif poussé hygen
CLOSED: [2024-07-15 lun. 12:15] SCHEDULED: <2024-07-15 lun.>
  /Entered on/  [2024-07-08 lun. 16:52]
  VOUS+ STAG2 site canonique d'épissage seqone
  WNT5A score bionfo non en faveur mais 2x gnomAD, clinique partiellement mais forme dominant plus mild  https://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.61884peu. hérité de la mère
  Deletion qui prend quaisiment tout APOL1 sur gène de néphropathie (pas d'hydropnéphrose associé), non présent DGV
** WAIT MR-2400560
NPRL3 3x gnomad mais score vert... faux-sens décrit dans la pathologie, colle clinique, clinvar VOUS... -> revoir le père ?
** WAIT MR-2400334 attente Jérémie
  /Entered on/  [2024-07-08 lun. 16:53]
*
** WAIT MR-2102277
  /Entered on/  [2024-07-16 mar. 10:10]
  Vérif seqone les récessif
  - TALDO1
  - USH1C
  - USH2A
  - NRL/PCK2 (selon source annot)
    -> rien
 del smpd4 ?
 seqone
 VOUS intronique ASH1L chr1:g.155410322_155410323del : gène DI + cryptorchidie
** WAIT MR-2102278 attente Jérémie
  /Entered on/  [2024-07-16 mar. 10:10]
  Del RAPGEF2 : artefact ? les soft-clips s’alignent
  VOUS- SOS1 seqone (noonan)
 VOUS- MYH2 seqone (myopathie)
** TODO MR-2200072: attente seqone
SCHEDULED: <2024-07-24 Wed>
  /Entered on/  [2024-07-16 mar. 10:10]
VOUS biallélique INST11 pour DI : notre tronquant est rapporté en 2023 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10183469/

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