VF7UKNIF73KICCJULRNI4TBTFIRQDFXIP2SEFXPK7NX5H3B4XMCQC
S32SLJEJHNKPYCVO3Z7PEDTGKLIJLQVGTB6ZIF4AJ6YDKEYXOSKQC
Y2SHXHEPVYTZSL3ZW222W7E76VCBHEVZLFLPAMW6Y5CKAHPK6RPAC
EXXDISQ3I67ZY3JZP7BFBDXLHLL5YIPQMXYMN4IPTNYJFOFPLOPAC
AUFMQO2LZBUBVDU2XKUSJWAPFLEW4UI2K4RHVORJYDZUS6OD5UTQC
RUPKCDDFWKIVFSSAXYEIW3WKSEQD422O4RXEJZWWE6FGB2IB7GSAC
2QF7HCG5CLNOBSZUKSHRI2MR4FHHXWY22ZP7JMWD52ZSO2LO2DLAC
D7C6HJBOMSGMIVHXWDTYRK5GJ2LWWPKQKI3GFQLHN3XHGH4KEKXQC
NYVNCQBOFVVGMADGLIF2AHIZBZDWB45EJVGBBJBTFV4UTNOC2PUQC
Faux espoir pour le côté technique mais utile pour introduire.
À lire
* Besoin
- Pour le diagonstic, il faut une base de données de connaissances, qui nécessite un volume de données clinique et d’échantillons important
- Cela permet étude génotype-phénotype pour un lien physiopathologique
- Not. pour maladie rare (1 seul changement génétique -> 1 phénotype)
- La rareté des maladies conduit à une quantité limité de données
(Le reste est sur l’importance d’indentifier les individus, ce qui ne nous concerne pas)
* Risque
- article de 2011 (El Emam et al) mais sur données de santé : 26-34%
* Balance bénéfice risque
- les patients atteints de maladies sont conscient du risque et nombreux considèrent que l’identification est un risque mineur (errance diagnostic, manqué d’inforamtion sur le pronostic, espérance de vie, absence de traitement)
- donnent leur information librement sur internet
- si patient information sur bénéfice du partage + création de bases de donnée ainsi que le cout de re-faire la recherche, ils peuvent consentir
#+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
@article{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},
title={Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome},
journal={Genome Biology},
year={2017},
volume={18},
number={1},
pages={36},
doi={10.1186/s13059-017-1158-6}
}
}
@article{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},
title={Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution},
journal={Genome research},
year={2007},
volume={17},
number={6},
pages={839--851}
}
@article{solovyev2006automatic,
author={Solovyev, Victor and Kosarev, Peter and Seledsov, Igor and Vorobyev, Denis},
title={Automatic annotation of eukaryotic genes, pseudogenes and promoters},
journal={Genome biology},
year={2006},
volume={7},
pages={1--12}
}
@article{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},
title={The GENCODE pseudogene resource},
journal={Genome biology},
year={2012},
volume={13},
pages={1--26}
}
@article{boer2023processen,
author={Esmee Ten Berk de Boer and Kristine Bilgrav Saether and Jesper Eisfeldt},
title={Discovery of non-reference processed pseudogenes in the Swedish population},
journal={Frontiers in Genetics},
year={2023},
volume={14},
doi={10.3389/fgene.2023.1176626}
}
@article{yang24loss,
author={Yi Yang and Pengzhi Wang and Samir El Qaidi and Philip R. Hardwidge and Jinlin Huang and Guoqiang Zhu},
title={Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance},
journal={Applied Microbiology and Biotechnology},
year={2024},
volume={108},
number={1},
pages={328},
doi={10.1007/s00253-023-12971-w}
}
@article{chen2020rerecognition,
author={Xu Chen and Lin Wan and Wei Wang and Wen-Jin Xi and An-Gang Yang and Tao Wang},
title={Re-recognition of pseudogenes: From molecular to clinical applications},
journal={Theranostics},
year={2020},
volume={10},
number={4},
pages={1479-1499},
doi={10.7150/thno.40659}
}
@article{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},
title={Evolutionary and expression signatures of pseudogenes in Arabidopsis and rice},
journal={Plant physiology},
year={2009},
volume={151},
number={1},
pages={3--15}
}
@article{Kirilenko_2023,
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},
title={Integrating gene annotation with orthology inference at scale},
journal={Science},
year={2023},
volume={380},
number={6643},
month={apr},
doi={10.1126/science.abn3107}
@article{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},
title={Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation},
journal={Nature Communications},
year={2023},
volume={14},
number={1},
pages={6845},
doi={10.1038/s41467-023-42531-9}
}
}
@article{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},
title={DECIPHER: database of chromosomal imbalance and phenotype in humans using ensembl resources},
journal={The American Journal of Human Genetics},
year={2009},
volume={84},
number={4},
pages={524--533}
}
@article{mitchell2018gpdr,
author={Mitchell, Colin and Ordish, Johan and Johnson, Emma and Brigden, Tanya and Hall, Alison},
title={The GDPR and genomic data},
year={2009}
}
@article{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},
title={The risk of re-identification versus the need to identify individuals in rare disease research},
journal={European Journal of Human Genetics},
year={2016},
volume={24},
number={11},
pages={1553--1558}
}
@article{Jo_2019,
author={Jo, Ara and Larson, Samantha and Carek, Peter and Peabody, Michael R and Peterson, Lars E and Mainous, Arch G},
title={Prevalence and practice for rare diseases in primary care: a national cross-sectional study in the USA},
journal={BMJ Open},
year={2019},
volume={9},
number={4},
pages={e027248},
month={apr},
doi={10.1136/bmjopen-2018-027248}
}
@article{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},
title={A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes},
journal={Science},
year={2012},
volume={335},
number={6070},
pages={823-828},
doi={10.1126/science.1215040}
}
@article{smith2022estimating,
author={Smith, C. I. Edvard and Bergman, Peter and Hagey, Daniel W.},
title={Estimating the number of diseases – the concept of rare, ultra-rare, and hyper-rare},
journal={iScience},
year={2022},
volume={25},
number={8},
pages={104698},
month={aug},
doi={10.1016/j.isci.2022.104698}
}
@article{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},
title={How many rare diseases are there?},
journal={Nature Reviews Drug Discovery},
year={2019},
volume={19},
number={2},
pages={77-78},
doi={10.1038/d41573-019-00180-y}
}
@misc{orphadata2024epidemio,
author={Orphanet},
title={Epidemiology of Rare Disease},
month={jul},
year={2024},
url={https://www.orphadata.com/epidemiology/}
}
@misc{hoomm2024ordo,
author={Orphanet},
title={The HPO - ORDO ontological module},
month={jul},
year={2024},
url={https://www.orphadata.com/hoom/}
}
@misc{orphadata2024phenotype,
author={Orphanet},
title={Phenotypes Associated with Rare Disorders},
month={jul},
year={2024},
url={https://www.orphadata.com/phenotypes/}
}
@misc{orphadata2024natural,
author={Orphanet},
title={Natural History of Rare Diseases},
month={jul},
year={2024},
url={https://www.orphadata.com/phenotypes/}
}
@misc{orphanet2023prevalence,
author={Orphanet},
title={Prevalence and incidence of rare diseases: Bibliographic data},
month={nov},
year={2023},
url={https://www.orpha.net/pdfs/orphacom/cahiers/docs/GB/Prevalence_of_rare_diseases_by_alphabetical_list.pdf}
}
@article{ferreira2019burden,
author={Ferreira, Carlos R.},
title={The burden of rare diseases},
journal={American Journal of Medical Genetics Part A},
year={2019},
volume={179},
number={6},
pages={885–892},
month={mar},
doi={10.1002/ajmg.a.61124}
}
@article{troster2023frequence,
author={Tröster, Thomas S. and von Wyl, Viktor and Beeler, Patrick E. and Dressel, Holger},
title={Frequency-based rare diagnoses as a novel and accessible approach for studying rare diseases in large datasets: a cross-sectional study},
journal={BMC Medical Research Methodology},
year={2023},
volume={23},
number={1},
month={jun},
doi={10.1186/s12874-023-01972-y}
}
@article{nguengang2019estimating,
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},
title={Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database},
journal={European Journal of Human Genetics},
year={2019},
volume={28},
number={2},
pages={165–173},
month={sep},
doi={10.1038/s41431-019-0508-0}
@article{bainbridge2020determining,
author={Bainbridge, Matthew N.},
title={Determining the incidence of rare diseases},
journal={Human Genetics},
year={2020},
volume={139},
number={5},
pages={569–574},
month={feb},
doi={10.1007/s00439-020-02135-5}
}
@article{schrodi2015prevalence,
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.},
title={Prevalence estimation for monogenic autosomal recessive diseases using population-based genetic data},
journal={Human Genetics},
year={2015},
volume={134},
number={6},
pages={659–669},
month={apr},
doi={10.1007/s00439-015-1551-8}
}
@article{xie2024statistical,
author={Xie, Yuhan and Wu, Ruoxuan and Li, Hongyu and Dong, Weilai and Zhou, Geyu and Zhao, Hongyu},
title={Statistical methods for assessing the effects of de novo variants on birth defects},
journal={Human Genomics},
year={2024},
volume={18},
number={1},
month={mar},
doi={10.1186/s40246-024-00590-z}
}
@article{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},
title={A framework for the interpretation of de novo mutation in human disease},
journal={Nature Genetics},
year={2014},
volume={46},
number={9},
pages={944-950},
doi={10.1038/ng.3050}
}
@article{neale2012patterns,
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.},
title={Patterns and rates of exonic de novo mutations in autism spectrum disorders},
journal={Nature},
year={2012},
volume={485},
number={7397},
pages={242–245},
month={apr},
doi={10.1038/nature11011}
}
** ARID4A
:PROPERTIES:
:CATEGORY: ARID4A
:END:
*** TODO Genematcher ARID4A
SCHEDULED: <2024-07-24 Wed>
Julien intéressé pour que cela reste à Grenoble car une de ses équipes travaille sur l’épigénétique.
4 patients candidats sur auramatcher :
2 faux sens en 620 et 621
2 tronquants
1 autre de novo moins évident à priori
sur la fonction du domaine tuudor-knot où sont les résidus 620 et 621 et sur l’importance de cette région pour la reconnaissance de marques épigénétiques
https://europepmc.org/article/MED/22247551
/Entered on/ [2024-07-24 Wed 10:37]
*** WAIT Mail GeneDx: attente relecture julien
SCHEDULED: <2024-07-25 Thu>
*** DONE Mail Marjolaine pour accord genematcher
CLOSED: [2024-07-24 Wed 14:10] SCHEDULED: <2024-07-24 Wed>
** 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]
** 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:
** 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...
* 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
* Kalilab
:PROPERTIES:
:CATEGORY: kalilab
:END:
VOUS biallélique INST11 pour DI : notre tronquant est rapporté en 2023 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10183469/
- VOUS biallélique INST11 pour DI : notre tronquant est rapporté en 2023 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10183469/
- tronquant CNOT3 connu LOF pour trouble neurodev mais hérité
# -*- mode: org -*-
Archived entries from file /home/alexis/org/auragen.org
* DONE SH-REF-02 REV 07 Exigences pou
CLOSED: [2024-07-03 mer. 14:47] SCHEDULED: <2024-07-03 mer.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:01
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Kalilab
:ARCHIVE_CATEGORY: kalilab
:ARCHIVE_TODO: DONE
:END:
* DONE NF EN ISO 15189 LBM Exigences
CLOSED: [2024-07-23 Tue 14:31] SCHEDULED: <2024-07-22 Mon>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:01
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Kalilab
:ARCHIVE_CATEGORY: kalilab
:ARCHIVE_TODO: DONE
:END:
* DONE SH-FORM-43 VDM WGS génétique c
CLOSED: [2024-06-26 mer. 10:58] SCHEDULED: <2024-06-26 mer.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:01
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Kalilab
:ARCHIVE_CATEGORY: kalilab
:ARCHIVE_TODO: DONE
:END:
* DONE Présentation ACRAA CHD7
CLOSED: [2024-06-19 mer. 11:01] DEADLINE: <2024-06-20 jeu. 14:00>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/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>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/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]
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/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.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/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.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2024-07-02 mar. 11:15]
* DONE Vérifier interêt STR multiples non rendus
CLOSED: [2024-07-08 lun. 10:09] SCHEDULED: <2024-07-08 lun.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
: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>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/Entered on/ [2024-07-19 Fri 11:06]
Bug ID HGNC, ne devrait pas réarriver
* DONE Nettoyer tâches finies dans "améliorations" et "questions" :doc:
CLOSED: [2024-06-11 mar. 10:44] SCHEDULED: <2024-06-11 mar.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
: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.>
:PROPERTIES:
:ARCHIVE_TIME: 2024-07-24 Wed 14:02
:ARCHIVE_FILE: ~/org/auragen.org
:ARCHIVE_OLPATH: Divers
:ARCHIVE_CATEGORY: auragen
:ARCHIVE_TODO: DONE
:END:
/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...