apraga/org - Change 32QB2VUPHXYATA4CKX65QOK5QWKULJK36RJCEYRYS2LGA3C3WLHAC

Auragen note transfert (continued)

Created by Alexis Praga on July 25, 2024

32QB2VUPHXYATA4CKX65QOK5QWKULJK36RJCEYRYS2LGA3C3WLHAC

Dependencies

In channels

main

Change contents

File deletion: 20240724T104200--validation__pipeline.org

BF:BFD[4.188] → [3.2087:2152]

BF:BFD[3.2152] → [3.1796:1796]

B:BD[3.1796] → [3.1797:2086]

#+title:      Validation
#+date:       [2024-07-24 Wed 10:42]
#+filetags:   :pipeline:auragen:
#+identifier: 20240724T104200
- SNV hap.py sur données gIAB
- CNV: truvaria sur  Chaisson. et al., (2019): Multi-platform discovery of haplotype-resolved structural variation in human genomes

File deletion: problemes_connus.org

BF:BFD[4.188] → [5.13602:13646]

BF:BFD[5.13646] → [5.13290:13290]

B:BD[5.13290] → [5.13291:13601]

:PROPERTIES:
:ID:       cef32d57-e0a3-4b76-afd2-326830576462
:END:
#+title: Problèmes connus
#+filetags:  auragen
[[id:2228958a-bcde-4256-819d-00237877e5e5][Limite appels de variants]]
[[id:7310f8fa-7518-48f7-bc11-ec14d8e0cbf1][Limites annotation]]
[[id:f4582bec-9f09-4068-8cd0-65b4fb22413d][Limite rendus]]

File deletion: outils_pour_la_détection_de_variants.org

BF:BFD[4.188] → [5.14732:14797]

BF:BFD[5.14797] → [5.14346:14346]

B:BD[5.14346] → [5.14347:14731]

:PROPERTIES:
:ID:       30db1b6c-6f95-40db-a363-202b20412d4f
:END:
#+title: Outils pour la détection de variants
- région d'homozygotie [[id:92f64d28-a582-484b-8181-ea04c13d850d][ROH]]
- détection des points de cassure (avec Manta)
- Estimation ploïdie : profondeur sur chromosome/profondeur génome
- non signalées si couveture insuffisante/librairie atypiques (avertissement)

File deletion: exemples_de_variants_structurels.org

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BF:BFD[5.95492] → [5.95156:95156]

B:BD[5.95156] → [5.95157:95431]

:PROPERTIES:
:ID:       0f58767c-07ff-401b-977d-15d454a3ab0f
:END:
#+title: Exemples de variants structurels
invdup MR-2203330 rendu chr8:g.( ?_8,231,549)_10,888,653delins11,100,482_(12,035,836_?)inv
inversion paracentrique 18q MR-2402177 30Mb chr18:36,491,658-67,312,508

File addition: 20240725T095524--runs-of-homozygosity-roh__pipeline_auragen.org (----------)

[4.188]

#+title:      Runs of Homozygosity (ROH)
#+date:       [2024-07-25 Thu 09:55]
#+filetags:   :pipeline:auragen:
#+identifier: 20240725T095524
 - attention, on renvoie des RoH et LoH (loss of heterozygotie)
 - Utile pour voir si consanguinité, disomie uniparentale
 - limite basse 2Mb
 - résultat sous forme de tableau. Les courbes brutes semblent utiles mais non rendus car on ne sait pas les interpréter ?

File move: roh.org → 20240725T095245--regions-of-homozygosity__auragen_pipeline.org
BF:BFD[4.188] → [5.8918:8949]
BF:BF[5.8949] → [5.8527:8527]
[4.188]
[5.8527]

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:PROPERTIES:
:ID:       92f64d28-a582-484b-8181-ea04c13d850d
:END:
#+title: ROH
#+filetags auragen

[5.8527]

[5.8627]

#+title:      Regions of Homozygosity
#+date:       [2024-07-25 Thu 09:52]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T095245

Deletion in notes/20240725T095245--regions-of-homozygosity__auragen_pipeline.org at line 6 [5.8527]
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```
Runs of homozygosity
```

File addition: 20240725T095212--outils-pour-la-détection-des-variants__auragen_pipeline.org (----------)

[4.188]

#+title:      Outils pour la détection des variants
#+date:       [2024-07-25 Thu 09:52]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T095212
- région d'homozygotie [[denote:20240725T095524][Runs of Homozygosity (ROH)]]
- détection des points de cassure (avec Manta)
- Estimation ploïdie : profondeur sur chromosome/profondeur génome
- non signalées si couveture insuffisante/librairie atypiques (avertissement)

File move: annotations.org → 20240725T094853--annotations__auragen_pipeline.org
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[4.188]
[5.180193]

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:PROPERTIES:
:ID:       0b163c10-63c2-44e0-b694-f3749139a3d5
:END:
#+title: Annotations

[5.180193]

[5.180282]

#+title:      Annotations
#+date:       [2024-07-25 Thu 09:48]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T094853

Deletion in notes/20240725T094853--annotations__auragen_pipeline.org at line 12 [5.180193]
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```
$x^2$
```
File move: expansionhunter.org → 20240725T093303--expansionhunter__auragen_pipeline.org
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:PROPERTIES:
:ID:       e4568e0f-e9e1-4432-9b56-c2cece9d9d11
:END:
#+title: Expansionhunter
#+filetags: auragen appelvariants

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#+title:      ExpansionHunter
#+date:       [2024-07-25 Thu 09:33]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T093303

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[5.94422]

File addition: 20240725T093105--exemples-de-variants-structurels__auragen_interprétation.org (----------)

[4.188]

#+title:      Exemples de variants structurels
#+date:       [2024-07-25 Thu 09:31]
#+filetags:   :auragen:interprétation:
#+identifier: 20240725T093105
invdup MR-2203330 rendu chr8:g.( ?_8,231,549)_10,888,653delins11,100,482_(12,035,836_?)inv
inversion paracentrique 18q MR-2402177 30Mb chr18:36,491,658-67,312,508

File addition: 20240725T092957--rétrotranscription-de-transcrits-grips__auragen_pipeline.org (----------)

[4.188]

#+title:      Rétrotranscription de transcrits (GRIPS)
#+date:       [2024-07-25 Thu 09:29]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T092957
GRIPS = Retrocopy insertion polymorphism
définition: insertion d'ADN médiée par ARN messager
Le gène rétrotranscrit est fonctionnellement actif (contraiment au pseudogène)
On le voit avec des reads qui sont sur l'exon d'un autre chromosome avec l'autre extrémité du paired-end sur des zones communes (en blue ci-dessous)
Image:
https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-3-r22
Source : https://genomebiology.biomedcentral.com/articles/10.1186/gb-2013-14-3-r22
* Y penser si
Pendant l'interprétation, on soupçone ça si il y a une poly-Tail (plein d'adénosine) avec des BLAT sur des intervalles énormes
[[http://172.25.219.90:8080/help/mroc/faq/slides/PasAPas_grips.pdf][Exemple]] : ARN messager de KYAT3 (chr1) inséré sur le chormosome 6
 - augmentation de la profondeur sur les exons d'un gènes
 - soft-clip aux jonction introns/exons
 - le dernier exon s'aligne à la foir sur le chrome 1 (+ queue poly-A) et sur le chromosome 6

File move: variants_structurels.org → 20240725T092901--variants-structurels__auragen_pipeline.org
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[4.188]
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:PROPERTIES:
:ID:       325fe1c2-98c7-4636-8d9f-72135a566bc7
:END:
#+title: Variants structurels
#+filetags: appelvariants auragen

[5.1733]

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#+title:      Variants structurels
#+date:       [2024-07-25 Thu 09:29]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T092901

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```
* [[id:0f58767c-07ff-401b-977d-15d454a3ab0f][Exemples de variants structurels]]
```
[5.3744]
[5.3824]
```
* [[denote:20240725T093105][Exemples de variants structurels]]
```

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    [[id:8bdb9dba-1270-4c4c-8192-1012e50c2464][Rétrotranscription de transcription de gène / GRIPS]]

[5.3843]

   [[denote:20240725T092957][Rétrotranscription de transcrits (GRIPS)]]

File move: gains_et_pertes_>_21kb.org → 20240725T092541--gains-et-pertes->-21kb__auragen_pipeline.org
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:PROPERTIES:
:ID:       6ee24af9-f9fd-4046-8c3a-3b0d077123b3
:END:
#+title: Gains et pertes > 21kb
#+filetags: appelvariants cnv

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#+title:      Gains et pertes > 21kb
#+date:       [2024-07-25 Thu 09:25]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T092541

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- approche "read depth" = rupture de profondeur (par opposition à Manta [[id:7c2aae7d-c1a3-4ff5-91f4-14888c6fd590][Délétion et duplications 50bp - 21kb]])

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- approche "read depth" = rupture de profondeur (par opposition à Manta [[denote:20240725T092255][Délétion et duplications 50pb-21kb]])

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```
[[id:587dc7c4-1dd5-4068-8d24-6e3825f01e66][Validation]] :
```
[5.82343]
[5.82401]
```
[[denote:20240724T104200][Validation]]
```

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- Découverts sur 1 cas + rétrospectif [[id:116b858b-5dd5-4b77-bd67-55fc3b7b76ea][Cas intéressants]]

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- Découverts sur 1 cas + rétrospectif:[[denote:20240716T104823][Cas intéressants]]

File move: 20240719T113251--délétion-et-duplications-50bp-21kb__auragen_pipeline.org → 20240725T092255--délétion-et-duplications-50pb-21kb__pipeline_auragen.org
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[4.188]
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#+title:      Délétion et duplications 50bp - 21kb
#+date:       [2024-07-19 Fri 11:32]
#+filetags:   :pipeline:manta:cnv
#+identifier: 20240719T113251

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#+title:      Délétion et duplications 50pb-21kb
#+date:       [2024-07-25 Thu 09:22]
#+filetags:   :pipeline:auragen:
#+identifier: 20240725T092255

File addition: 20240725T092233--appel-de-variants__auragen_pipeline.org (----------)

[4.188]

#+title:      Appel de variants
#+date:       [2024-07-25 Thu 09:22]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T092233
- SNV et petits indel <= 50bp : haplotypecaller
  - taille des indel : haplotypecaller semble monter jusque 108bp ?
  - +genotypevcf = appel par groupe après hapolytpecaller
- [[denote:20240725T092255][Délétion et duplications 50pb-21kb]]
- [[denote:20240725T092541][Gains et pertes > 21kb]]
- [[denote:20240725T092901][Variants structurels]]
- STR : [[denote:20240725T093303][ExpansionHunter]]
[[denote:20240725T092157][Limites appel de variant]]

File addition: 20240725T092157--limites-appel-de-variant__auragen_pipeline.org (----------)

[4.188]

#+title:      Limites appel de variant
#+date:       [2024-07-25 Thu 09:21]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T092157
* CNV
Ploïdies : voir
* STR
STR avec expansionhunter
- seulement en ciblé
- estimation du nombre de répétition (peu précis)

File addition: 20240725T092103--problèmes-connus__auragen_pipeline.org (----------)

[4.188]

#+title:      Problèmes connus
#+date:       [2024-07-25 Thu 09:21]
#+filetags:   :auragen:pipeline:
#+identifier: 20240725T092103
[[denote:20240725T092157][Limites appel de variant]]
[[id:7310f8fa-7518-48f7-bc11-ec14d8e0cbf1][Limites annotation]]
[[id:f4582bec-9f09-4068-8cd0-65b4fb22413d][Limite rendus]]

File addition: 20240725T091334--absplice__pipeline_prédiction_épissage.org (----------)

[4.188]

#+title:      Absplice
#+date:       [2024-07-25 Thu 09:13]
#+filetags:   :prédiction:épissage:pipeline:
#+identifier: 20240725T091334
Prédiction des anomales d’épissage (“aberrant”) grâce à l’amélioration récente des outils de prédiction (utilisations de tissus humain)
Apport
- Considère les anomalies "extrêmes" d’épissage (outlier) depuis au moins 2 tissus d'1 individus
- Combine 3 outils : MMSplice, SpliceAI + 1 outil “tissue-specific” SpiceMap
- Données ADN +/- données RNAsq si disponibles pour améliorer les prédiction
- Base de données de test : annotation de tissus basé sur GTEx (49) avec sites accepteur et donneur crée avec [[https://github.com/gagneurlab/FRASER][FRASER]] (le pipeline correspondant est [[https://github.com/gagneurlab/drop][DROP]])

File move: validation.org → 20240724T104200--validation__pipeline_auragen.org
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[4.188]
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:PROPERTIES:
:ID:       587dc7c4-1dd5-4068-8d24-6e3825f01e66
:END:
#+title: Validation
#+filetags: auragen pipeline

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#+title:      Validation
#+date:       [2024-07-24 Wed 10:42]
#+filetags:   :pipeline:auragen:
#+identifier: 20240724T104200

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  - CNV: 75 en acpa + patients test (quelques CNV et T21)

[5.5766]

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  - CNV: 75 en acpa + patients test (quelques CNV et T21). Truvaria sur  Chaisson. et al., (2019): Multi-platform discovery of haplotype-resolved structural variation in human genomes

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- [[id:cc54e449-12a7-41d6-832b-33937255be92][Contrôle qualité]] et [[id:117f7970-2579-48e1-b7b0-026b4c9fd0a6][Avertissement]]
- [[id:ee261ae7-3511-46e0-8c9a-ad4318850104][Appel de variant]]

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- [[denote:20240719T113354][Controle qualité]] et [[denote:20240719T113108][Avertissement]]
- [[denote:20240725T092233][Appel de variants]]

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- [[id:0b163c10-63c2-44e0-b694-f3749139a3d5][Annotations]]

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- [[denote:20240725T095212][Outils pour la détection des variants]]
- [[denote:20240725T094853][Annotations]]
  TODO

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[5.197019]
[5.197020]
```
:PROPERTIES:
:CUSTOM_ID: h:09677e72-c8bf-4eae-8e7e-d3e0f79407e0
:END:
```

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

[6.424]

* Prédiction bioinformatique
** Épissage
*** Aberrant splicing prediction across human tissues
:PROPERTIES:
:TITLE:    Aberrant splicing prediction across human tissues
:BTYPE:    article
:CUSTOM_ID: wagner2023aberrant
:AUTHOR:   Wagner, Nils and {\c{C}}elik, Muhammed H and H{\"o}lzlwimmer, Florian R and Mertes, Christian and Prokisch, Holger and Y{\'e}pez, Vicente A and Gagneur, Julien
:JOURNAL:  Nature genetics
:VOLUME:   55
:NUMBER:   5
:PAGES:    861--870
:YEAR:     2023
:PUBLISHER: Nature Publishing Group US New York
:URL:      https://www.nature.com/articles/s41588-023-01373-3
:END:

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∅:D[3.2512] → [7.51183:51211]

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*** STRT The risk of re-identification versus the need to identify individuals in rare disease research
SCHEDULED: <2024-07-23 Tue>

[7.51079]

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*** DONE The risk of re-identification versus the need to identify individuals in rare disease research
CLOSED: [2024-07-24 Wed 18:16] SCHEDULED: <2024-07-23 Tue>

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```
SCHEDULED: <2024-07-25 Thu>
```
[7.69992]
[7.70020]
```
SCHEDULED: <2024-07-30 Tue>
```

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*** TODO Exemple de données identifiantes sur forum maladie rare
SCHEDULED: <2024-07-24 Wed>

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*** DONE Exemple de données identifiantes sur forum maladie rare
CLOSED: [2024-07-24 Wed 17:47] SCHEDULED: <2024-07-24 Wed>

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*** TODO Genematcher ARID4A
SCHEDULED: <2024-07-24 Wed>

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*** DONE Genematcher ARID4A
CLOSED: [2024-07-24 Wed 17:47] SCHEDULED: <2024-07-24 Wed>

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B:BD[3.20778] → [3.20778:20853]

*** WAIT Mail GeneDx: attente relecture julien
SCHEDULED: <2024-07-25 Thu>

[3.20778]

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*** DONE Mail GeneDx: attente relecture julien
CLOSED: [2024-07-25 Thu 08:57] SCHEDULED: <2024-07-25 Thu>

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```
SCHEDULED: <2024-07-25 Thu>
```
[7.83982]
[7.84010]
```
SCHEDULED: <2024-08-01 Thu>
```
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```
SCHEDULED: <2024-07-25 Thu 09:30 +7d>
```
[7.84182]
[7.84220]
```
SCHEDULED: <2024-07-25 Thu 10:00 +7d>
```

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*** TODO Présentation axe3 absplice
SCHEDULED: <2024-07-24 Wed> DEADLINE: <2024-07-25 Thu 09:00>

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*** DONE Présentation axe3 absplice
CLOSED: [2024-07-25 Thu 08:57] SCHEDULED: <2024-07-24 Wed> DEADLINE: <2024-07-25 Thu 09:00>

Auragen note transfert (continued)

Dependencies

In channels

Change contents

File deletion: 20240724T104200--validation__pipeline.org

File deletion: problemes_connus.org

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