. .. Généralités,

. .. I-le-génome-humain,

, 23 I.1.2-Variations génomiques (SNV, indel, CNV et variations de structures)

I. , 3-Mécanismes de rétrotransposition des rétrotransposons non-LTR

I. .. ,

. .. Ii-séquençage-de-première-génération-;-sanger, 3-Particularités de l'étude moléculaire de l'ADNmt

. .. De-génome, 1.1-Les technologies de séquençage à haut débit d'exome, III-Séquençage de deuxième génération : l'avènement du séquençage à haut débit d'exome

, Les limites du séquençage à haut débit d'exome

, 2-L'essor du séquençage à haut débit de l'exome dans les

. Objectifs and . .. De-thèse,

. Première-partie, Intérêt de la réanalyse recherche des données de séquençage d'exome dans les anomalies du développement et déficience intellectuelle, vol.87

. .. I-introduction,

. .. Ii-matériel,

T. Des and . Ii, 4-Validation de la variation du gène OTUD7A par méthode Sanger, Traitement et alignement des données brutes de séquençage d'exome dans un but de réanalyse

, 5.5-Détection des protéines ubiquitinées via la lysine 48

, 1-Identification d'une variation homozygote faux-sens au sein du gène OTUD7A

. .. Gène-dlgap2, 110 III.2.1-Présentation clinique de la patiente

, IV-Discussion générale : la réanalyse recherche, une stratégie pour identifier de nouveaux gènes impliqués dans les AD

. Deuxième-partie, Analyse de l'ADN mitochondrial à partir de données de séquençage d'exome

. .. Ii-matériel, 5-Validations par Sanger et par PCR-RFLP de variations mitochondriales, Mise en évidence de variations mitochondriales pathogènes causales et secondaires

. Troisième-partie, Identification des éléments mobiles à partir de données de séquençage d'exome

. .. Ii-matériel, -Outils bioinformatiques testés au cours du projet

M. .. -pipeline,

V. Endris, K. Hackmann, and T. M. Neuhann, Homozygous loss of CHRNA7 on chromosome 15q13.3 causes severe encephalopathy with seizures and hypotonia, Am J Med Genet A, vol.152, issue.11, pp.2908-2911, 2010.

A. J. Sharp, H. C. Mefford, and K. Li, A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures, Nat Genet, vol.40, issue.3, pp.322-328, 2008.

A. Masurel-paulet, J. Andrieux, and P. Callier, Delineation of 15q13.3 microdeletions, Clin Genet, vol.78, issue.2, pp.149-161, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00466147

A. Masurel-paulet, I. Drumare, and M. Holder, Further delineation of eye manifestations in homozygous 15q13.3 microdeletions including TRPM1: a differential diagnosis of ceroid lipofuscinosis, Am J Med Genet A, vol.164, issue.6, pp.1537-1544, 2014.

C. Lowther, G. Costain, and D. J. Stavropoulos, Delineating the 15q13.3 microdeletion phenotype: a case series and comprehensive review of the literature, Genet Med, vol.17, issue.2, pp.149-157, 2015.

J. Simon, K. Stoll, R. Fick, J. Mott, and A. Lawson-yuen, Homozygous 15q13.3 microdeletion in a child with hypotonia and impaired vision: a new report and review of the literature, Clin Case Rep, vol.7, issue.12, pp.2311-2315, 2019.

M. Spielmann, G. Reichelt, and C. Hertzberg, Homozygous deletion of chromosome 15q13.3 including CHRNA7 causes severe mental retardation, seizures, muscular hypotonia, and the loss of KLF13 and TRPM1 potentially cause macrocytosis and congenital retinal dysfunction in siblings, Eur J Med Genet, vol.54, issue.4, pp.441-445, 2011.

M. Uddin, B. K. Unda, and V. Kwan,

, Am J Hum Genet, vol.102, issue.2, pp.278-295, 2018.

, syndrome shows prefrontal neurophysiological dysfunctions and attentional impairment, Psychopharmacology (Berl), vol.233, pp.2151-2163, 2016.

A. Forsingdal, K. Fejgin, V. Nielsen, T. Werge, J. Nielsen et al., 3 homozygous knockout mouse model display epilepsy-, autism-and schizophrenia-related phenotypes, Transl Psychiatry, vol.6, issue.7, p.860, 2016.

C. Soler-alfonso, C. M. Carvalho, and J. Ge, CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a three-generation pedigree, Eur J Hum Genet, vol.22, issue.9, pp.1071-1076, 2014.

M. E. Hasselmo, The role of acetylcholine in learning and memory, Curr Opin Neurobiol, vol.16, pp.710-715, 2006.

E. D. Levin, ?7-Nicotinic receptors and cognition, Curr Drug Targets, vol.13, issue.5, pp.602-606, 2012.

N. Hoppman-chaney, W. K. Seger, P. Superneau, D. Hodge, and J. , Identification of single gene deletions at 15q13.3: further evidence that CHRNA7 causes the 15q13.3 microdeletion syndrome phenotype: identification of CHRNA7 deletions at 15q13.3, Clin Genet, vol.83, issue.4, pp.345-351, 2013.

P. Prasun, M. Hankerd, M. Kristofice, L. Scussel, L. Sivaswamy et al., Compound heterozygous microdeletion of chromosome 15q13.3 region in a child with hypotonia, impaired vision, and global developmental delay, Am J Med Genet A, vol.164, issue.7, pp.1815-1820, 2014.

J. Yin, W. Chen, H. Yang, M. Xue, and C. P. Schaaf, Chrna7 deficient mice manifest no consistent neuropsychiatric and behavioral phenotypes, Sci Rep, vol.7, p.39941, 2017.

J. Yin, W. Chen, and E. S. Chao, Otud7a knockout mice recapitulate many neurological features of 15q13.3 microdeletion syndrome

, Am J Hum Genet, vol.102, issue.2, pp.296-308, 2018.

G. R. Abecasis, A. Auton, L. D. Brooks, M. A. Depristo, R. M. Durbin et al., An integrated map of genetic variation from 1,092 human genomes, Genomes Project Consortium, 2012.

, Nature, vol.491, issue.7422, pp.56-65

R. M. Andrews, I. Kubacka, P. F. Chinnery, R. N. Lightowlers, D. M. Turnbull et al., Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nature Genetics, vol.23, issue.2, p.147, 1999.

R. K. Bai and L. J. Wong, Simultaneous detection and quantification of mitochondrial DNA deletion(s), depletion, and over-replication in patients with mitochondrial disease, The Journal of Molecular Diagnostics, vol.7, issue.5, pp.60595-60603, 2005.

S. Bannwarth, V. Procaccio, A. S. Lebre, C. Jardel, A. Chaussenot et al., Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders, Journal of Medical Genetics, vol.50, pp.704-714, 2013.

, Broad Institute. (n.d). Picard Tools. Retrieved, 2016.

C. Calabrese, D. Simone, M. A. Diroma, M. Santorsola, C. Guttà et al., MToolBox: A highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing, Bioinformatics, vol.30, issue.21, pp.3115-3117, 2014.

F. M. Calabrese, R. Clima, P. Pignataro, V. A. Lasorsa, M. D. Hogarty et al., A comprehensive characterization of rare mitochondrial DNA variants in neuroblastoma, Oncotarget, vol.7, issue.31, pp.49246-49258, 2016.

F. M. Calabrese, D. Simone, and M. Attimonelli, Primates and mouse NumtS in the UCSC Genome Browser, BMC Bioinformatics, vol.13, 2012.

R. A. Casano, D. F. Johnson, Y. Bykhovskaya, F. Torricelli, M. Bigozzi et al., Inherited susceptibility to aminoglycoside GARRET ET AL. | 2441 ototoxicity: Genetic heterogeneity and clinical implications, American Journal of Otolaryngology, vol.20, issue.3, pp.90062-90067, 1999.

P. F. Chinnery, Inheritance of mitochondrial disorders, Mitochondrion, vol.2, issue.1-2, pp.46-52, 2002.

M. B. Coulter-mackie, D. A. Applegarth, J. R. Toone, and L. Gagnier, A protocol for detection of mitochondrial DNA deletions: Characterization of a novel deletion, Clinical Biochemistry, issue.8, pp.627-632, 1998.

D. L. Dinwiddie, L. D. Smith, N. A. Miller, A. M. Atherton, E. G. Farrow et al., Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome, Genomics, vol.102, pp.148-156, 2013.

M. A. Diroma, C. Calabrese, D. Simone, M. Santorsola, F. M. Calabrese et al., Extraction and annotation of human mitochondrial genomes from 1000 genomes whole exome sequencing data, S2, vol.15, 2014.

M. J. Falk, E. A. Pierce, M. Consugar, M. H. Xie, M. Guadalupe et al., Mitochondrial disease genetic diagnostics: Optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome, Discovery Medicine, vol.14, issue.79, pp.389-399, 2012.

N. Fischel-ghodsian, T. R. Prezant, X. Bu, and S. Öztas, , 1993.

G. S. -l-gorman, P. F. Chinnery, S. Dimauro, M. Hirano, Y. Koga et al., Mitochondrial ribosomal RNA gene mutation in a patient with sporadic aminoglycoside ototoxicity, American Journal of Otolaryngology, vol.14, issue.6, p.16080, 2016.

H. R. Griffin, A. Pyle, E. L. Blakely, C. L. Alston, J. Duff et al., Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations, Genetics In Medicine, vol.16, issue.12, pp.962-971, 2014.

M. Guan, Molecular pathogenetic mechanism of maternally inherited deafness, Annals of the New York Academy of Sciences, vol.1011, issue.1, pp.259-271, 2004.

Y. Guo, J. Li, C. Li, Y. Shyr, and D. C. Samuels, MitoSeek: Extracting mitochondria information and performing high-throughput mitochondria sequencing analysis, Bioinformatics, vol.29, issue.9, pp.1210-1211, 2013.

L. He, P. F. Chinnery, S. E. Durham, E. L. Blakely, T. M. Wardell et al., Detection and quantification of mitochondrial DNA deletions in individual cells by real-time PCR, Nucleic Acids Research, vol.30, issue.14, p.68, 2002.

Y. He, J. Wu, D. C. Dressman, C. Iacobuzio-donahue, S. D. Markowitz et al., Heteroplasmic mitochondrial DNA mutations in normal and tumour cells, Nature, vol.464, issue.7288, pp.610-614, 2010.

I. J. Holt, A. E. Harding, R. K. Petty, and J. A. Morgan-hughes, A new mitochondrial disease associated with mitochondrial DNA heteroplasmy, American Journal of Human Genetics, vol.46, pp.428-433, 1990.

M. J. Landrum, J. M. Lee, M. Benson, G. R. Brown, C. Chao et al., ClinVar: Improving access to variant interpretations and supporting evidence, Nucleic Acids Research, vol.46, pp.1062-1067, 2018.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-1760, 2009.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The sequence alignment/map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2079, 2009.

M. T. Lott, J. N. Leipzig, O. Derbeneva, H. M. Xie, D. Chalkia et al., mtDNAVariation and analysis using mitomap and mitomaster, Current Protocols in Bioinformatics, vol.44, issue.1, 2013.

T. Matsunaga, H. Kumanomido, M. Shiroma, A. Ohtsuka, K. Asamura et al., Deafness due to A1555G mitochondrial mutation without use of aminoglycoside, The Laryngoscope, vol.114, issue.6, pp.1085-1091, 2004.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The genome analysis toolkit: A map reduce framework for analyzing next-generation DNA sequencing data, Genome Research, vol.20, issue.9, pp.1297-1303, 2010.

A. Patowary, R. Nesbitt, M. Archer, R. Bernier, and Z. Brkanac, Next generation sequencing mitochondrial DNA analysis in autism spectrum disorder, Online Mendelian Inheritance in Man (OMIM), vol.10, pp.1338-1343, 1996.

G. Pfeffer, E. L. Blakely, C. L. Alston, A. Hassani, M. Boggild et al., Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations, Neurosurgery & Psychiatry, vol.83, issue.9, pp.883-886, 2012.

A. R. Quinlan and I. M. Hall, BEDTools: A flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-842, 2010.

D. C. Samuels, L. Han, J. Li, S. Quanghu, T. A. Clark et al., Finding the lost treasures in exome sequencing data, Trends in Genetics, vol.29, issue.10, pp.593-599, 2013.

M. Santorsola, C. Calabrese, G. Girolimetti, M. A. Diroma, G. Gasparre et al., A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest, Human Genetics, vol.135, pp.1-136, 2016.

S. T. Sherry, M. Ward, M. Kholodov, J. Baker, L. Phan et al., dbSNP: The NCBI database of genetic variation, Nucleic Acids Research, vol.29, issue.1, pp.308-311, 2001.

S. Sonney, J. Leipzig, M. T. Lott, S. Zhang, V. Procaccio et al., Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP, PLOS Computational Biology, vol.13, issue.12, p.1005867, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-02149524

J. Thevenon, Y. Duffourd, A. Masurel-paulet, M. Lefebvre, F. Feillet et al., Diagnostic odyssey in severe neurodevelopmental disorders: Toward clinical whole-exome sequencing as a first-line diagnostic test, Clinical Genetics, vol.89, issue.6, pp.700-707, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01405124

P. Vabres, A. Sorlin, S. S. Kholmanskikh, B. Demeer, J. St-onge et al., Postzygotic inactivating mutations of RHOA cause a mosaic neuroectodermal syndrome, Nature Genetics. Van der Auwera, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02622254

, Current Protocols in Bioinformatics, vol.11, 1110.

M. Van-oven, PhyloTree Build 17: Growing the human mitochondrial DNA tree, Forensic Science International, vol.5, pp.392-394, 2015.

V. Vasta, S. B. Ng, E. H. Turner, J. Shendure, and S. H. Hahn, Next generation sequence analysis for mitochondrial disorders, Genome Medicine, vol.1, issue.10, p.100, 2009.

S. K. Vellarikkal, H. Dhiman, K. Joshi, Y. Hasija, S. Sivasubbu et al., mit-o-matic: A comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets, Human Mutation, vol.36, issue.4, pp.419-424, 2015.

D. Wallace, G. Singh, M. Lott, J. Hodge, T. Schurr et al., Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy, Science, vol.242, issue.4884, pp.1427-1430, 1988.

D. C. Wallace, W. Fan, and V. Procaccio, Mitochondrial energetics and therapeutics, Annual Review of Pathology, vol.5, pp.297-348, 2010.

D. C. Wallace, M. T. Lott, H. P-a-c-h-e-r, D. ;. F-o-r-e-r, L. S-p-e-c-h-t et al., HaploGrep 2: Mitochondrial haplogroup classification in the era of high-throughput sequencing, Pharmacology of Mitochondria, vol.240, pp.58-63, 2016.

F. Ye, D. C. Samuels, T. Clark, and Y. Guo, High-throughput sequencing in mitochondrial DNA research. Mitochondrion, vol.17, pp.157-163, 2014.

P. Zhang, D. C. Samuels, B. Lehmann, T. Stricker, J. Pietenpol et al., Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data, Briefings in Bioinformatics, vol.17, issue.2, pp.224-232, 2016.

F. Zhao, M. Guan, X. Zhou, M. Yuan, M. Liang et al., Leber's hereditary optic neuropathy is associated with mitochondrial ND6 T14502C mutation, Biochemical and Biophysical Research Communications, vol.389, issue.3, pp.466-472, 2009.

H. Zhao, R. Li, Q. Wang, Q. Yan, J. Deng et al., Maternally inherited aminoglycoside-induced and nonsyndromic deafness is associated with the novel C1494T mutation in the mitochondrial 12S rRNA gene in a large chinese family. The American DEUXIÈME PARTIE : Analyse de l'ADN mitochondrial à partir de données de séquençage d'exome DISCUSSION, CONCLUSION ET PERSPECTIVES Plusieurs perspectives peuvent être considérées dans l'optique de réduire les situations d'impasse diagnostique, que cela soit dans l'amélioration des connaissances clinicobiologiques, des techniques ou des pipelines bioinformatiques. Différentes pistes peuvent être évoquées pour optimiser l'analyse des données. Citons la réanalyse des données d'exome, qui grâce à l'augmentation des connaissances, 2004.

. Exomiser-(robinson, qui pourrait permettre un gain de temps lors de l'interprétation en seconde intention, 2014.

. Goudenège, Sur le plan bioinformatique, d'autres perspectives peuvent être citées

&. Tankard, , 2018.

. Gilissen, Il existe donc des variations dans les régions non codantes qui peuvent avoir un impact sur l'expression des gènes, la stabilité de l'ARNm ou la fonction des protéines ; et qui ne sont détectables qu'en génome. D'autres pistes commencent donc à être explorées en combinant bioinformatique, séquençage du génome et analyses multi-omiques. Ainsi, il a été montré que le séquençage à haut débit de génome permet d'augmenter le taux diagnostique, 2014.

, A global reference for human genetic variation, Genomes Project, vol.526, p.68, 2015.

, A map of human genome variation from population scale sequencing, Genomes Project Consortium, vol.467, pp.1061-1073, 2010.

G. R. Abecasis, A. Auton, L. D. Brooks, M. A. Depristo, R. M. Durbin et al., An integrated map of genetic variation from 1,092 human genomes, Genomes Project Consortium, vol.491, pp.56-65, 2012.

S. S. Adav and S. K. Sze, Insight of brain degenerative protein modifications in the pathology of neurodegeneration and dementia by proteomic profiling, Mol Brain, vol.9, 2016.

J. Aicardi, The etiology of developmental delay, Seminars in Pediatric Neurology, vol.5, pp.15-20, 1998.

B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts et al., Molecular Biology of the Cell, 2002.

M. Al-nabhani, S. Al-rashdi, F. Al-murshedi, A. Al-kindi, K. Al-thihli et al., Reanalysis of exome sequencing data of intellectual disability samples: Yields and benefits, Clinical Genetics, vol.94, pp.495-501, 2018.

S. Andrews, FastQC: a quality control tool for high throughput sequence data, 2010.

R. M. Andrews, I. Kubacka, P. F. Chinnery, R. N. Lightowlers, D. M. Turnbull et al.,

, Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA, Nature Genetics, vol.23, p.147

J. L. Badano and N. Katsanis, Beyond Mendel: an evolving view of human genetic disease transmission, Nat Rev Genet, vol.3, pp.779-789, 2002.

R. Bai and L. C. Wong, Detection and Quantification of Heteroplasmic Mutant Mitochondrial DNA by Real-Time Amplification Refractory Mutation System Quantitative PCR Analysis: A Single-Step Approach, Clinical Chemistry, vol.50, pp.996-1001, 2004.

R. Bai and L. C. Wong, Simultaneous Detection and Quantification of Mitochondrial DNA Deletion(s), Depletion, and Over-Replication in Patients with Mitochondrial Disease, The Journal of Molecular Diagnostics, vol.7, pp.613-622, 2005.

J. A. Bailey, L. Carrel, A. Chakravarti, and E. E. Eichler, Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis, Proc Natl Acad Sci U S A, vol.97, pp.6634-6639, 2000.

R. Balestrieri, E. Matteucci, C. Cipriani, C. Grelli, S. Ricceri et al., Endogenous Retroviruses Activity as a Molecular Signature of Neurodevelopmental Disorders, Int J Mol Sci, vol.20, 2019.

K. Balogh, A. Patócs, J. Majnik, K. Rácz, and L. Hunyady, Genetic screening methods for the detection of mutations responsible for multiple endocrine neoplasia type 1, Molecular Genetics and Metabolism, vol.83, pp.74-81, 2004.

S. Bannwarth, V. Procaccio, and V. Paquis-flucklinger, Surveyor Nuclease: a new strategy for a rapid identification of heteroplasmic mitochondrial DNA mutations in patients with respiratory chain defects, Hum. Mutat, vol.25, pp.575-582, 2005.

S. Bannwarth, V. Procaccio, A. S. Lebre, C. Jardel, A. Chaussenot et al., Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders, Journal of Medical Genetics, pp.2013-101604, 2013.

W. Bao, K. K. Kojima, and O. Kohany, Repbase Update, a database of repetitive elements in eukaryotic genomes, Mob DNA, vol.6, 2015.

C. R. Beck, J. L. Garcia-perez, R. M. Badge, and J. V. Moran, LINE-1 Elements in Structural Variation and Disease, Annu Rev Genomics Hum Genet, vol.12, pp.187-215, 2011.

D. R. Bentley, S. Balasubramanian, H. P. Swerdlow, G. P. Smith, J. Milton et al., Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry, Nature, vol.456, pp.53-59, 2008.

G. Bergant, A. Maver, L. Lovrecic, G. ?uturilo, A. Hodzic et al., , 2018.

, Comprehensive use of extended exome analysis improves diagnostic yield in rare disease: a retrospective survey in 1,059 cases, Genet Med, vol.20, pp.303-312

V. Boeva, T. Popova, K. Bleakley, P. Chiche, J. Cappo et al., Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data, Bioinformatics, vol.28, pp.423-425, 2012.

A. M. Bolger, M. Lohse, and B. Usadel, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, pp.2114-2120, 2014.

D. Bonneau, E. Colin, F. Oca, M. Ferré, A. Chevrollier et al., Early-onset Behr syndrome due to compound heterozygous mutations in OPA1, Brain, vol.137, pp.301-301, 2014.

L. Boucret, C. Bris, V. Seegers, D. Goudenège, V. Desquiret-dumas et al., Deep sequencing shows that oocytes are not prone to accumulate mtDNA heteroplasmic mutations during ovarian ageing, Hum Reprod, vol.32, pp.2101-2109, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-01815346

A. Vitobello, A. , T. Mau-them, F. Nambot, S. Sorlin et al., Next-Generation Sequencing, Picard Tools, 2020.

A. Bruel, S. Nambot, V. Quéré, A. Vitobello, J. Thevenon et al., Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing, Eur J Hum Genet, pp.1-13, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02626363

A. Bruel, A. Vitobello, F. T. Mau-them, S. Nambot, Y. Duffourd et al., 2.5 years' experience of GeneMatcher datasharing: a powerful tool for identifying new genes responsible for rare diseases, Genet Med, vol.21, pp.1657-1661, 2019.
URL : https://hal.archives-ouvertes.fr/hal-00399293

H. P. Buermans and J. T. Den-dunnen, Next generation sequencing technology: Advances and applications, Biochimica et Biophysica Acta (BBA) -Molecular Basis of Disease 1842, pp.1932-1941, 2014.

R. Bumgarner, DNA microarrays: Types, Applications and their future, Curr Protoc Mol Biol, vol.0, issue.22, 2013.

F. M. Calabrese, D. Simone, A. , and M. , Primates and mouse NumtS in the UCSC Genome Browser, BMC Bioinformatics, vol.13, p.15, 2012.

F. M. Calabrese, R. Clima, P. Pignataro, V. A. Lasorsa, M. D. Hogarty et al., A comprehensive characterization of rare mitochondrial DNA variants in neuroblastoma, Oncotarget, vol.7, pp.49246-49258, 2016.

J. Chen, D. N. Cooper, N. Chuzhanova, C. Férec, and G. P. Patrinos, Gene conversion: mechanisms, evolution and human disease, Nat Rev Genet, vol.8, pp.762-775, 2007.

L. Chen, J. N. Decerbo, and G. G. Carmichael, Alu element-mediated gene silencing, EMBO J, vol.27, pp.1694-1705, 2008.

B. Chenais, Transposable Elements in Cancer and Other Human Diseases, Current Cancer Drug Targets, vol.15, pp.227-242, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01905441

W. Chien, S. Gau, Y. Wu, Y. Huang, J. Fang et al., Identification and molecular characterization of two novel chromosomal deletions associated with autism, Clinical Genetics, vol.78, pp.449-456, 2010.

W. Chien, S. S. Gau, .. Liao, H. Chiu, Y. Wu et al., , 2013.

M. Choi, U. I. Scholl, W. Ji, T. Liu, I. R. Tikhonova et al., Genetic diagnosis by whole exome capture and massively parallel DNA sequencing, Proc Natl Acad Sci U S A, vol.106, pp.19096-19101, 2009.

P. Cingolani, A. Platts, L. L. Wang, M. Coon, T. Nguyen et al., A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff. Fly (Austin), vol.6, pp.80-92, 2012.

R. Clark, M. J. Chen, R. Lam, H. Y. Karczewski, K. J. Chen et al., Performance comparison of exome DNA sequencing technologies, Nat Biotechnol, vol.29, pp.908-914, 2011.

F. S. Collins, M. Morgan, P. , and A. , The Human Genome Project: Lessons from Large-Scale Biology, Science, vol.300, pp.286-290, 2003.

D. N. Cooper, M. Krawczak, C. Polychronakos, C. Tyler-smith, and H. Kehrer-sawatzki, Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease, Human Genetics, vol.132, p.1077, 2013.

R. Cordaux and M. A. Batzer, The impact of retrotransposons on human genome evolution, Nat Rev Genet, vol.10, pp.691-703, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00419189

H. Cui, F. Li, D. Chen, G. Wang, C. K. Truong et al., Comprehensive next-generation sequence analyses of the entire mitochondrial genome reveal new insights into the molecular diagnosis of mitochondrial DNA disorders, Genet. Med, vol.15, pp.388-394, 2013.

A. Damert, J. Raiz, A. V. Horn, J. Löwer, H. Wang et al., 5?-Transducing SVA retrotransposon groups spread efficiently throughout the human genome, Genome Res, vol.19, 1992.

P. L. Deininger and M. A. Batzer, Alu Repeats and Human Disease, Molecular Genetics and Metabolism, vol.67, pp.183-193, 1999.

D. L. Dinwiddie, L. D. Smith, N. A. Miller, A. M. Atherton, E. G. Farrow et al., Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome, Genomics, vol.102, pp.148-156, 2013.

M. A. Diroma, C. Calabrese, D. Simone, M. Santorsola, F. M. Calabrese et al., Extraction and annotation of human mitochondrial genomes from 1000, 2014.

, Genomes Whole Exome Sequencing data, BMC Genomics, vol.15

A. Dobin, C. A. Davis, F. Schlesinger, J. Drenkow, C. Zaleski et al., STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

E. Dolzhenko, V. Deshpande, F. Schlesinger, P. Krusche, R. Petrovski et al., ExpansionHunter: a sequencegraph-based tool to analyze variation in short tandem repeat regions, Bioinformatics, vol.35, pp.4754-4756, 2019.

A. Dracopoulos, E. Widjaja, C. Raybaud, C. A. Westall, and O. C. Snead, Vigabatrinassociated reversible MRI signal changes in patients with infantile spasms, Epilepsia, vol.51, pp.1297-1304, 2010.

M. K. Eldomery, Z. Coban-akdemir, T. Harel, J. A. Rosenfeld, T. Gambin et al., Lessons learned from additional research analyses of unsolved clinical exome cases, Genome Med, vol.9, 2017.

V. Références-endris, K. Hackmann, T. M. Neuhann, U. Grasshoff, M. Bonin et al., Homozygous loss of CHRNA7 on chromosome 15q13.3 causes severe encephalopathy with seizures and hypotonia, American Journal of Medical Genetics Part A, vol.152, pp.2908-2911, 2010.

C. Esnault, J. Maestre, and T. Heidmann, Human LINE retrotransposons generate processed pseudogenes, Nat Genet, vol.24, pp.363-367, 2000.

H. Fan and J. Chu, A Brief Review of Short Tandem Repeat Mutation, Genomics Proteomics Bioinformatics, vol.5, pp.7-14, 2007.

K. D. Farwell, L. Shahmirzadi, D. El-khechen, Z. Powis, E. C. Chao et al., Enhanced utility of familycentered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions, Genetics in Medicine, vol.17, pp.578-586, 2015.

G. J. Faulkner, Y. Kimura, C. O. Daub, S. Wani, C. Plessy et al., The regulated retrotransposon transcriptome of mammalian cells, Nat Genet, vol.41, pp.563-571, 2009.

L. Feuk, A. R. Carson, and S. W. Scherer, Structural variation in the human genome, Nature Reviews Genetics, vol.7, pp.85-97, 2006.

D. J. Finnegan, Retrotransposons. Current Biology, vol.22, pp.432-437, 2012.

, Fondation Maladies Rares La définition des maladies rares | Fondation maladies rares

J. M. Friedman, Á. Baross, A. D. Delaney, A. Ally, L. Arbour et al., Oligonucleotide Microarray Analysis of Genomic Imbalance in Children with Mental Retardation, Am J Hum Genet, vol.79, pp.500-513, 2006.

M. Fromer and S. M. Purcell, Using XHMM software to detect copy number variation in whole-exome sequencing data, Curr Protoc Hum Genet, vol.81, 2014.

E. J. Gardner, V. K. Lam, D. N. Harris, N. T. Chuang, E. C. Scott et al., The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology, Genome Res, vol.27, pp.1916-1929, 2017.

E. J. Gardner, E. Prigmore, G. Gallone, P. Danecek, K. E. Samocha et al., Contribution of retrotransposition to developmental disorders, Nat Commun, vol.10, pp.1-10, 2019.

S. L. Gasior, T. P. Wakeman, B. Xu, and P. L. Deininger, The Human LINE-1, 2006.

, Retrotransposon Creates DNA Double-strand Breaks, J Mol Biol, vol.357, pp.1383-1393

V. Geoffroy, Y. Herenger, A. Kress, C. Stoetzel, A. Piton et al., , 2018.

, AnnotSV: an integrated tool for structural variations annotation, Bioinformatics, vol.34, pp.3572-3574

A. K. Ghosh, M. Majumder, R. Steele, R. A. White, and R. B. Ray, A Novel 16-Kilodalton Cellular Protein Physically Interacts with and Antagonizes the Functional Activity of c-myc Promoter-Binding Protein 1, Mol Cell Biol, vol.21, pp.655-662, 2001.

R. Gifford, R. Tristem, and M. , The Evolution, Distribution and Diversity of Endogenous Retroviruses, vol.26, 2003.

R. E. Giles, H. Blanc, H. M. Cann, and D. C. Wallace, Maternal inheritance of human mitochondrial DNA, Proc Natl Acad Sci U S A, vol.77, pp.6715-6719, 1980.

C. Gilissen, J. Y. Hehir-kwa, D. T. Thung, M. Van-de-vorst, B. W. Van-bon et al., Genome sequencing identifies major causes of severe intellectual disability, Nature, vol.511, pp.344-347, 2014.

P. Goerner-potvin and G. Bourque, Computational tools to unmask transposable elements, Nature Reviews Genetics, vol.19, pp.688-704, 2018.

D. Golan and P. Medvedev, Using state machines to model the Ion Torrent sequencing process and to improve read error rates, Bioinformatics, vol.29, pp.344-351, 2013.

S. Goodwin, J. D. Mcpherson, and W. R. Mccombie, Coming of age: ten years of nextgeneration sequencing technologies, Nat Rev Genet, vol.17, pp.333-351, 2016.

V. Gotea and W. Makalowski, Do transposable elements really contribute to proteomes?, Trends in Genetics, vol.22, pp.260-267, 2006.

D. Goudenège, C. Bris, V. Hoffmann, V. Desquiret-dumas, C. Jardel et al., eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data, Genet Med, vol.21, pp.1407-1416, 2019.

J. M. Greally, Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome, Proc Natl Acad Sci U S A, vol.99, pp.327-332, 2002.

T. R. Gregory, Synergy between sequence and size in Large-scale genomics, Nat Rev Genet, vol.6, pp.699-708, 2005.

H. R. Griffin, A. Pyle, E. L. Blakely, C. L. Alston, J. Duff et al., Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations, Genet Med, vol.16, pp.962-971, 2014.

A. Guilmatre, G. Huguet, R. Delorme, and T. Bourgeron, The emerging role of SHANK genes in neuropsychiatric disorders: SHANK Genes in Neuropsychiatric Disorders, Developmental Neurobiology, vol.74, pp.113-122, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01579806

J. S. Han, S. T. Szak, and J. D. Boeke, Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes, Nature, vol.429, pp.268-274, 2004.

D. C. Hancks and H. Kazazian, SVA retrotransposons: Evolution and genetic instability, Semin Cancer Biol, vol.20, pp.234-245, 2010.

D. C. Hancks and H. H. Kazazian, Roles for retrotransposon insertions in human disease, Mob DNA, vol.7, 2016.

R. Hayakawa, T. Satta, Y. Gagneux, P. Varki, A. Takahata et al., Alu-mediated inactivation of the human CMP-N-acetylneuraminic acid hydroxylase gene, PNAS, vol.98, pp.11399-11404, 2001.

I. J. Holt, A. E. Harding, R. K. Petty, and J. A. Morgan-hughes, A new mitochondrial disease associated with mitochondrial DNA heteroplasmy, Am J Hum Genet, vol.46, pp.428-433, 1990.

C. C. Homan, R. Kumar, L. S. Nguyen, E. Haan, F. L. Raymond et al., Mutations in USP9X are associated with Xlinked intellectual disability and disrupt neuronal cell migration and growth, Am. J. Hum. Genet, vol.94, pp.470-478, 2014.

H. Hu, S. A. Haas, J. Chelly, H. Van-esch, M. Raynaud et al., , 2016.

M. Hu, A. R. Jex, B. E. Campbell, and R. B. Gasser, Long PCR amplification of the entire mitochondrial genome from individual helminths for direct sequencing, Nature Protocols, vol.2, pp.2339-2344, 2007.

, Initial sequencing and analysis of the human genome, International Human Genome Sequencing Consortium, vol.409, pp.860-921, 2001.

I. Iossifov, B. J. O'roak, S. J. Sanders, M. Ronemus, N. Krumm et al., The contribution of de novo coding mutations to autism spectrum disorder, Nature, vol.515, pp.216-221, 2014.

L. Jiang-xie, H. Liao, C. Chen, Y. Chen, S. Ho et al., , 2014.

K. Katoh and D. M. Standley, MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability, Mol Biol Evol, vol.30, pp.772-780, 2013.

H. H. Kazazian, C. Wong, H. Youssoufian, A. F. Scott, D. G. Phillips et al.,

E. Kim, S. Naisbitt, Y. Hsueh, A. Rao, A. Rothschild et al., , 1997.

, Novel Synaptic Protein That Interacts with the Guanylate Kinase-like Domain of the PSD-95/SAP90 Family of Channel Clustering Molecules, The Journal of Cell Biology, vol.136, pp.669-678

J. M. Kim, S. Vanguri, J. D. Boeke, A. Gabriel, and D. F. Voytas, Transposable Elements and Genome Organization: A Comprehensive Survey of Retrotransposons Revealed by the Complete Saccharomyces cerevisiae Genome Sequence, Genome Res, vol.8, pp.464-478, 1998.

K. Kochinke, C. Zweier, B. Nijhof, M. Fenckova, P. Cizek et al., , 0200.

, Références Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules, The American Journal of Human Genetics, vol.98, pp.149-164

D. Komander, M. J. Clague, and S. Urbé, Breaking the chains: structure and function of the deubiquitinases, Nature Reviews Molecular Cell Biology, vol.10, pp.550-563, 2009.

E. Kondo-iida, K. Kobayashi, M. Watanabe, J. Sasaki, T. Kumagai et al., Novel Mutations and Genotype-Phenotype Relationships in 107 Families With Fukuyama-Type Congenital Muscular Dystrophy (FCMD), 1999.

, Hum Mol Genet, vol.8, pp.2303-2309

C. Kopanos, V. Tsiolkas, A. Kouris, C. E. Chapple, M. Aguilera et al., VarSome: the human genomic variant search engine, Bioinformatics, vol.35, pp.1978-1980, 2019.

J. R. Kowalski, J. , and P. , The Role of Deubiquitinating Enzymes in Synaptic Function and Nervous System Diseases, Neural Plast, 2012.

M. J. Landrum, J. M. Lee, M. Benson, G. R. Brown, C. Chao et al., ClinVar: improving access to variant interpretations and supporting evidence, Nucleic Acids Res, vol.46, pp.1062-1067, 2018.

T. W. Laver, E. D. Franco, M. B. Johnson, K. Patel, S. Ellard et al., SavvyCNV: genome-wide CNV calling from off-target reads, BioRxiv 617605, 2019.

R. M. Layer, C. Chiang, A. R. Quinlan, and I. M. Hall, LUMPY: a probabilistic framework for structural variant discovery, Genome Biology, vol.15, p.84, 2014.

H. Lee, J. L. Deignan, N. Dorrani, S. P. Strom, S. Kantarci et al., Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders, JAMA, vol.312, pp.1880-1887, 2014.

W. Lee, M. P. Stromberg, A. Ward, C. Stewart, E. P. Garrison et al., , 2014.

, MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping, PLoS One, vol.9

M. Lek, K. J. Karczewski, E. V. Minikel, K. E. Samocha, E. Banks et al., Analysis of protein-coding genetic variation in 60,706 humans, Nature, vol.536, pp.285-291, 2016.

S. H. Lelieveld, J. A. Veltman, and C. Gilissen, Novel bioinformatic developments for exome sequencing, Hum Genet, vol.135, pp.603-614, 2016.

I. Leong, J. Skinner, and D. Love, Application of Massively Parallel Sequencing in the Clinical Diagnostic Testing of Inherited Cardiac Conditions, Medical Sciences, vol.2, pp.98-126, 2014.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

R. Li, H. Handsaker, B. Wysoker, A. Fennell, T. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

J. Li, C. Lu, M. Cheng, S. Luu, S. Hsu et al., , 2014.

J. De-ligt, M. H. Willemsen, B. W. Van-bon, T. Kleefstra, H. G. Yntema et al., Diagnostic Exome Sequencing in Persons with Severe Intellectual Disability, N Engl J Med, vol.367, pp.1921-1929, 2012.

L. Liu, Y. Li, S. Li, N. Hu, Y. He et al., Comparison of Next-Generation Sequencing Systems, 2012.

Z. Liu, L. Zhu, R. Roberts, and W. Tong, Toward Clinical Implementation of Next-Generation Sequencing-Based Genetic Testing in Rare Diseases: Where Are We?, Trends in Genetics, vol.35, pp.852-867, 2019.

N. J. Loman, C. Constantinidou, J. Z. Chan, M. Halachev, M. Sergeant et al., High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity, Nat Rev Microbiol, vol.10, pp.599-606, 2012.

M. T. Lott, J. N. Leipzig, O. Derbeneva, H. M. Xie, D. Chalkia et al., mtDNA Variation and Analysis Using MITOMAP and MITOMASTER, Curr Protoc Bioinformatics, vol.1, p.1, 2013.

S. Loublier, M. Schiff, P. Bénit, R. , and P. , Les maladies mitochondriales : une médecine à part ?, Immuno-Analyse & Biologie Spécialisée, vol.24, pp.240-253, 2009.

C. Lowther, G. Costain, D. J. Stavropoulos, R. Melvin, C. K. Silversides et al., Delineating the 15q13.3 microdeletion phenotype: a case series and comprehensive review of the literature, Genet Med, vol.17, pp.149-157, 2015.

S. Luo, C. A. Valencia, J. Zhang, N. Lee, J. Slone et al., Biparental Inheritance of Mitochondrial DNA in Humans, Proc Natl Acad Sci U S A, vol.115, pp.13039-13044, 2018.

Z. Ma, R. W. Lee, B. Li, P. Kenney, Y. Wang et al., , 2013.

, Isothermal amplification method for next-generation sequencing, Proceedings of the National Academy of Sciences, vol.110, pp.14320-14323

R. N. Mackinnon, C. Selan, A. Zordan, M. Wall, H. Nandurkar et al., , 2012.

, CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens, Mol Cytogenet, vol.5, p.10

A. Maitra, Y. Cohen, S. E. Gillespie, E. Mambo, N. Fukushima et al., The Human MitoChip: A High-Throughput Sequencing Microarray for Mitochondrial Mutation Detection, Genome Res, vol.14, pp.812-819, 2004.

J. Références-majewski, J. Schwartzentruber, E. Lalonde, A. Montpetit, J. et al., What can exome sequencing do for you?, Journal of Medical Genetics, vol.48, pp.580-589, 2011.

W. Maneechay, T. Boonpipattanapong, S. Kanngurn, P. Puttawibul, S. L. Geater et al., Single Nucleotide Polymorphisms in the Gc Gene for Vitamin D Binding Protein in Common Cancers in Thailand, Asian Pacific Journal of Cancer Prevention, vol.16, pp.3339-3344, 2015.

K. B. Manheimer, F. Richter, L. J. Edelmann, S. L. Souza, L. Shi et al., Robust identification of mosaic variants in congenital heart disease, Hum Genet, vol.137, pp.183-193, 2018.

E. R. Mardis, The impact of next-generation sequencing technology on genetics, Trends in Genetics, vol.24, pp.133-141, 2008.

M. Margulies, M. Egholm, W. E. Altman, S. Attiya, J. S. Bader et al., , 2005.

, Genome Sequencing in Open Microfabricated High Density Picoliter Reactors, Nature, vol.437, pp.376-380

C. R. Marshall, A. Noor, J. B. Vincent, A. C. Lionel, L. Feuk et al., Structural Variation of Chromosomes in Autism Spectrum Disorder, Am J Hum Genet, vol.82, pp.477-488, 2008.

A. Masurel-paulet, J. Andrieux, P. Callier, J. Cuisset, C. Le-caignec et al., Delineation of 15q13.3 microdeletions, Clinical Genetics, vol.78, pp.149-161, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00466147

A. Masurel-paulet, I. Drumare, M. Holder, J. Cuisset, L. Vallée et al., Further delineation of eye manifestations in homozygous 15q13.3 microdeletions including TRPM1: A differential diagnosis of ceroid lipofuscinosis, American Journal of Medical Genetics Part A, vol.164, pp.1537-1544, 2014.

A. Matsumoto, M. Mizuno, N. Hamada, Y. Nozaki, E. F. Jimbo et al., LIN7A Depletion Disrupts Cerebral Cortex Development, Contributing to Intellectual Disability in 12q21-Deletion Syndrome, PLoS One, vol.9, 2014.

F. Mazzarotto, I. Olivotto, W. , and R. , Advantages and Perils of Clinical Whole-Exome and Whole-Genome Sequencing in Cardiomyopathy, Cardiovasc Drugs Ther, 2020.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

C. Meischl, M. De-boer, A. Åhlin, R. , and D. , , 2000.

T. E. Mevissen, M. K. Hospenthal, P. P. Geurink, P. R. Elliott, M. Akutsu et al., OTU Deubiquitinases Reveal, p.203, 2013.

, Références Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis, Cell, vol.154, pp.169-184

T. E. Mevissen, Y. Kulathu, M. P. Mulder, P. P. Geurink, S. L. Maslen et al., Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne, Nature, vol.538, pp.402-405, 2016.

R. E. Mills, C. T. Luttig, C. E. Larkins, A. Beauchamp, C. Tsui et al.,

, An initial map of insertion and deletion (INDEL) variation in the human genome

, Genome Res, vol.16, pp.1182-1190

T. A. Morrish, N. Gilbert, J. S. Myers, B. J. Vincent, T. D. Stamato et al., DNA repair mediated by endonuclease-independent LINE-1 retrotransposition, Nat Genet, vol.31, pp.159-165, 2002.

J. M. Mullaney, R. E. Mills, W. S. Pittard, and S. E. Devine, Small insertions and deletions (INDELs) in human genomes, Hum Mol Genet, vol.19, pp.131-136, 2010.

S. Naisbitt, J. Valtschanoff, D. W. Allison, C. Sala, E. Kim et al., Interaction of the Postsynaptic Density-95/Guanylate Kinase Domain-Associated Protein Complex with a Light Chain of Myosin-V and Dynein, J. Neurosci, vol.20, pp.4524-4534, 2000.

H. Najmabadi, H. Hu, M. Garshasbi, T. Zemojtel, S. S. Abedini et al., Deep sequencing reveals 50 novel genes for recessive cognitive disorders, Nature, vol.478, pp.57-63, 2011.

S. Nambot, J. Thevenon, P. Kuentz, Y. Duffourd, E. Tisserant et al., Clinical whole-exome sequencing for the diagnosis of rare disorders with congenital anomalies and/or intellectual disability: substantial interest of prospective annual reanalysis, Genet Med, vol.20, pp.645-654, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01635326

A. C. Need, V. Shashi, Y. Hitomi, K. Schoch, K. V. Shianna et al., Clinical application of exome sequencing in undiagnosed genetic conditions, J Med Genet, vol.49, pp.353-361, 2012.

S. B. Ng, E. H. Turner, P. D. Robertson, S. D. Flygare, A. W. Bigham et al., Targeted Capture and Massively Parallel Sequencing of Twelve Human Exomes, Nature, vol.461, pp.272-276, 2009.

S. B. Ng, K. J. Buckingham, C. Lee, A. W. Bigham, H. K. Tabor et al., Exome sequencing identifies the cause of a Mendelian disorder, Nat Genet, vol.42, pp.30-35, 2010.

U. S. Nih, National Library of Medecine

K. Nozu, K. Iijima, Y. Ohtsuka, X. J. Fu, H. Kaito et al.,

, Alport syndrome caused by a COL4A5 deletion and exonization of an adjacent AluY

, Mol Genet Genomic Med, vol.2, pp.451-453

P. Références-nyren, B. Pettersson, and M. Uhlen, Solid Phase DNA Minisequencing by an Enzymatic Luminometric Inorganic Pyrophosphate Detection Assay, Analytical Biochemistry, vol.208, pp.171-175, 1993.

K. Okamoto and J. M. Shaw, Mitochondrial Morphology and Dynamics in Yeast and Multicellular Eukaryotes, Annual Review of Genetics, vol.39, pp.503-536, 2005.

. Omim--online, McKusick-Nathans Institute of Genetic Medicine, 1996.

E. M. Ostertag and H. H. Kazazian, Biology of Mammalian L1 Retrotransposons, Annual Review of Genetics, vol.35, pp.501-538, 2001.

H. M. Ozgen, E. V. Daalen, P. F. Bolton, V. K. Maloney, S. Huang et al., Copy number changes of the microcephalin 1 gene (MCPH1) in patients with autism spectrum disorders, Clinical Genetics, vol.76, pp.348-356, 2009.

A. Patowary, R. Nesbitt, M. Archer, R. Bernier, and Z. Brkanac, Next Generation Sequencing Mitochondrial DNA Analysis in Autism Spectrum Disorder, Autism Res, vol.10, pp.1338-1343, 2017.

G. Pfeffer, E. L. Blakely, C. L. Alston, A. Hassani, M. Boggild et al., Adult-onset spinocerebellar ataxia syndromes due to MTATP6 mutations, J Neurol Neurosurg Psychiatry, vol.83, pp.883-886, 2012.

E. Picardi and G. Pesole, Mitochondrial genomes gleaned from human whole-exome sequencing, Nature Methods, vol.9, pp.523-524, 2012.

A. M. Pickering, A. L. Koop, C. Y. Teoh, G. Ermak, T. Grune et al., The Immunoproteasome, The 20S Proteasome, And The PA28?? Proteasome Regulator Are Oxidative-Stress-Adaptive Proteolytic Complexes, Biochem J, vol.432, pp.585-594, 2010.

D. Pinto, A. T. Pagnamenta, L. Klei, R. Anney, D. Merico et al., Functional Impact of Global Rare Copy Number Variation in Autism Spectrum Disorder, Nature, vol.466, pp.368-372, 2010.

A. Pinto-fernández, S. Davis, A. B. Schofield, H. C. Scott, P. Zhang et al., Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics, p.592, 2019.

P. Polak and E. Domany, Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes, BMC Genomics, vol.7, p.133, 2006.

H. Poquet, L. Faivre, S. E. Chehadeh, J. Morton, D. Mcmullan et al., Further Evidence for Dlgap2 as Strong Autism Spectrum Disorders/Intellectual Disability Candidate Gene, 2017.

C. Qi, S. Liu, R. Qin, Y. Zhang, G. Wang et al., , 2014.

, Coordinated Regulation of Dendrite Arborization by Epigenetic Factors CDYL and EZH2, J Neurosci, vol.34, pp.4494-4508

J. Références-raiz, A. Damert, S. Chira, U. Held, S. Klawitter et al., The non-autonomous retrotransposon SVA is transmobilized by the human LINE-1 protein machinery, Nucleic Acids Res, vol.40, pp.1666-1683, 2012.

A. H. Rasmussen, H. B. Rasmussen, and A. Silahtaroglu, The DLGAP family: neuronal expression, function and role in brain disorders, Molecular Brain, vol.10, 2017.

A. Rauch, D. Wieczorek, E. Graf, T. Wieland, S. Endele et al., Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study, The Lancet, vol.380, pp.1674-1682, 2012.

S. Reeg and T. Grune, Protein Oxidation in Aging: Does It Play a Role in Aging Progression?, Antioxid Redox Signal, vol.23, pp.239-255, 2015.

R. Rius, M. J. Cowley, L. Riley, C. Puttick, D. R. Thorburn et al., , 2019.

, Biparental inheritance of mitochondrial DNA in humans is not a common phenomenon, Genet Med, vol.21, pp.2823-2826

P. N. Robinson, S. Köhler, A. Oellrich, K. Wang, C. J. Mungall et al., Improved exome prioritization of disease genes through cross-species phenotype comparison, Genome Res, vol.24, pp.340-348, 2014.

M. Ronaghi, M. Uhlén, and P. Nyrén, A Sequencing Method Based on Real-Time Pyrophosphate, Science, vol.281, pp.363-365, 1998.

J. M. Rothberg, W. Hinz, T. M. Rearick, J. Schultz, W. Mileski et al., An integrated semiconductor device enabling non-optical genome sequencing, Nature, vol.475, pp.348-352, 2011.

A. Rousseau and A. Bertolotti, Regulation of proteasome assembly and activity in health and disease, Nat Rev Mol Cell Biol, vol.19, pp.697-712, 2018.

D. C. Samuels, L. Han, J. Li, S. Quanghu, T. A. Clark et al., Finding the lost treasures in exome sequencing data, Trends Genet, vol.29, pp.593-599, 2013.

F. Sanger and A. R. Coulson, A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase, J. Mol. Biol, vol.94, pp.441-448, 1975.

T. Santiago-sim, L. C. Burrage, F. Ebstein, M. J. Tokita, M. Miller et al., Biallelic Variants in OTUD6B Cause an Intellectual Disability Syndrome Associated with Seizures and Dysmorphic Features, Am. J. Hum. Genet, vol.100, pp.676-688, 2017.

M. Santorsola, C. Calabrese, G. Girolimetti, M. A. Diroma, G. Gasparre et al.,

, A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest, Hum Genet, vol.135, pp.121-136

M. Sato and K. Sato, Maternal inheritance of mitochondrial DNA by diverse mechanisms to eliminate paternal mitochondrial DNA, Biochimica et Biophysica Acta (BBA) -Molecular Cell Research, vol.1833, pp.1979-1984, 2013.

R. Schob, C. Morellini, F. Ohana, O. Bakota, L. Hrynchak et al., Cognitive impairment and autisticlike behaviour in SAPAP4-deficient mice, Transl Psychiatry, vol.9, 2019.

S. K. Sen, C. T. Huang, K. Han, and M. A. Batzer, Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome, Nucleic Acids Res, vol.35, pp.3741-3751, 2007.

R. Shankar, D. Grover, S. K. Brahmachari, and M. Mukerji, Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements, BMC Evol Biol, vol.4, p.37, 2004.

A. J. Sharp, H. C. Mefford, K. Li, C. Baker, C. Skinner et al., A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures, Nat Genet, vol.40, pp.322-328, 2008.

J. Shendure, J. , and H. , Next-generation DNA sequencing, Nat Biotechnol, vol.26, pp.1135-1145, 2008.

S. T. Sherry, M. Ward, M. Kholodov, J. Baker, L. Phan et al., dbSNP: the NCBI database of genetic variation, Nucleic Acids Res, vol.29, pp.308-311, 2001.

J. Simon, K. Stoll, R. Fick, J. Mott, and A. Lawson-yuen, Homozygous 15q13.3 microdeletion in a child with hypotonia and impaired vision: A new report and review of the literature, 2019.

W. Slotkin and K. Nishikura, Adenosine-to-inosine RNA editing and human disease, 2013.

, Genome Medicine, vol.5, p.105

A. Smit, R. Hubley, and P. Green, , 2008.

N. Sobreira, F. Schiettecatte, D. Valle, and A. Hamosh, GeneMatcher: A Matching Tool for Connecting Investigators with an Interest in the Same Gene, Hum Mutat, vol.36, pp.928-930, 2015.

C. Soler-alfonso, C. M. Carvalho, J. Ge, E. K. Roney, P. I. Bader et al., CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a three-generation pedigree, Eur J Hum Genet, vol.22, pp.1071-1076, 2014.

S. Sonney, J. Leipzig, M. T. Lott, S. Zhang, V. Procaccio et al., Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP, PLoS Comput Biol, vol.13, 2017.
URL : https://hal.archives-ouvertes.fr/inserm-02149524

R. Sorek, G. Ast, and D. Graur, Alu-Containing Exons are Alternatively Spliced, 2002.

, Genome Res, vol.12, pp.1060-1067

E. M. Southern, Detection of specific sequences among DNA fragments separated by gel electrophoresis, Journal of Molecular Biology, vol.98, pp.503-517, 1975.

M. Speek, Antisense Promoter of Human L1 Retrotransposon Drives Transcription of Adjacent Cellular Genes, Mol Cell Biol, vol.21, pp.1973-1985, 2001.

M. Références-spielmann, G. Reichelt, C. Hertzberg, M. Trimborn, S. Mundlos et al., Homozygous deletion of chromosome 15q13.3 including CHRNA7 causes severe mental retardation, seizures, muscular hypotonia, and the loss of KLF13 and TRPM1 potentially cause macrocytosis and congenital retinal dysfunction in siblings, European Journal of Medical Genetics, vol.54, pp.441-445, 2011.

D. Srikanta, S. K. Sen, C. T. Huang, E. Conlin, R. Rhodes et al., An alternative pathway for Alu retrotransposition suggests a role in DNA double-strand break repair, Genomics, vol.93, pp.205-212, 2009.

J. B. Stewart and P. F. Chinnery, The dynamics of mitochondrial DNA heteroplasmy: implications for human health and disease, Nat Rev Genet, vol.16, pp.530-542, 2015.

C. Stewart, D. Kural, M. P. Strömberg, J. A. Walker, M. K. Konkel et al., A Comprehensive Map of Mobile Element Insertion Polymorphisms in Humans, PLoS Genet, vol.7, 2011.

B. Suresh, J. Lee, H. Kim, and S. Ramakrishna, Regulation of pluripotency and differentiation by deubiquitinating enzymes, Cell Death Differ, vol.23, pp.1257-1264, 2016.

S. T. Szak, O. K. Pickeral, D. Landsman, and J. D. Boeke, Identifying related L1 retrotransposons by analyzing 3' transduced sequences, Genome Biol, vol.4, p.30, 2003.

H. Tang, E. F. Kirkness, C. Lippert, W. H. Biggs, M. Fabani et al., Profiling of Short-Tandem-Repeat Disease Alleles in 12,632 Human Whole Genomes, The American Journal of Human Genetics, vol.101, pp.700-715, 2017.

R. M. Tankard, M. F. Bennett, P. Degorski, M. B. Delatycki, P. J. Lockhart et al.,

, Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data, The American Journal of Human Genetics, vol.103, pp.858-873

R. W. Taylor and D. M. Turnbull, Mitochondrial DNA Mutations in Human Disease, Nat Rev Genet, vol.6, pp.389-402, 2005.

S. Ripke, A. R. Sanders, K. S. Kendler, D. F. Levinson, P. Sklar et al., The Schizophrenia Psychiatric Genome-Wide Association Study (GWAS) Consortium, 2011.

, Genome-wide association study identifies five new schizophrenia loci, Nature Genetics, vol.43, pp.969-976

J. Thevenon, M. Milh, F. Feillet, J. St-onge, Y. Duffourd et al., Mutations in SLC13A5 Cause Autosomal-Recessive Epileptic Encephalopathy with Seizure Onset in the First Days of Life, Am J Hum Genet, vol.95, pp.113-120, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01668025

J. Thevenon, Y. Duffourd, A. Masurel-paulet, M. Lefebvre, F. Feillet et al., Diagnostic odyssey in severe neurodevelopmental disorders: toward clinical whole-exome sequencing as a first-line diagnostic test, Clinical Genetics, vol.89, pp.700-707, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01405124

R. Thung, D. T. De-ligt, J. Vissers, L. E. Steehouwer, M. Kroon et al., Mobster: accurate detection of mobile element insertions in next generation sequencing data, Genome Biol, vol.15, 2014.

R. I. Torene, K. Galens, S. Liu, K. Arvai, C. Borroto et al., Mobile element insertion detection in 89,874 clinical exomes, Genet Med, pp.1-5, 2020.

R. M. Toydemir, A. Rutherford, F. G. Whitby, L. B. Jorde, J. C. Carey et al., Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome, Nat Genet, vol.38, pp.561-565, 2006.

J. M. Tubio, Y. Li, Y. S. Ju, I. Martincorena, S. L. Cooke et al., Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes, Science, vol.345, p.1251343, 2014.

G. Turner, M. Barbulescu, M. Su, M. I. Jensen-seaman, K. K. Kidd et al., Insertional polymorphisms of full-length endogenous retroviruses in humans, Current Biology, vol.11, pp.1531-1535, 2001.

M. Uddin, B. K. Unda, V. Kwan, N. T. Holzapfel, S. H. White et al., OTUD7A Regulates Neurodevelopmental Phenotypes in the 15q13.3 Microdeletion Syndrome, vol.102, pp.278-295, 2018.

A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B. C. Faircloth et al., Primer3-new capabilities and interfaces, vol.40, p.115, 2012.

P. Vabres, A. Sorlin, S. S. Kholmanskikh, B. Demeer, J. St-onge et al., Postzygotic inactivating mutations of RHOA cause a mosaic neuroectodermal syndrome, Nat Genet, vol.51, pp.1438-1441, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02622254

G. A. Van-der-auwera, M. O. Carneiro, C. Hartl, R. Poplin, G. Del-angel et al., From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline, Curr Protoc Bioinformatics, vol.11, 2013.

M. Van-oven, PhyloTree Build 17: Growing the human mitochondrial DNA tree, Forensic Science International: Genetics Supplement Series, vol.5, pp.392-394, 2015.

M. Van-oven and M. Kayser, Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation, Hum. Mutat, vol.30, pp.386-394, 2009.

V. Vasta, S. B. Ng, E. H. Turner, J. Shendure, and S. H. Hahn, Next generation sequence analysis for mitochondrial disorders, Genome Med, vol.1, p.100, 2009.

R. Vaz-drago, N. Custódio, and M. Carmo-fonseca, Deep intronic mutations and human disease, Hum Genet, vol.136, pp.1093-1111, 2017.

N. Vinckenbosch, I. Dupanloup, and H. Kaessmann, Evolutionary fate of retroposed gene copies in the human genome, Proc Natl Acad Sci U S A, vol.103, pp.3220-3225, 2006.

R. Vissers and L. E. , A de novo paradigm for mental retardation, Nature Genetics, vol.6, 2010.

L. E. Vissers, C. Gilissen, and J. A. Veltman, Genetic studies in intellectual disability and related disorders, Nat Rev Genet, vol.17, pp.9-18, 2016.

M. Wagner, R. Berutti, B. Lorenz-depiereux, E. Graf, G. Eckstein et al., Mitochondrial DNA mutation analysis from exome sequencing-A more holistic approach in diagnostics of suspected mitochondrial disease, Journal of Inherited Metabolic Disease, vol.42, pp.909-917, 2019.

D. C. Wallace, G. Singh, M. T. Lott, J. A. Hodge, T. G. Schurr et al., Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy, Science, vol.242, pp.1427-1430, 1988.

H. Wang, J. Xing, D. Grover, D. J. Hedges, K. Han et al., , 2005.

, SVA Elements: A Hominid-specific Retroposon Family, Journal of Molecular Biology, vol.354, pp.994-1007

H. Weissensteiner, D. Pacher, A. Kloss-brandstätter, L. Forer, G. Specht et al., HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing, Nucleic Acids Res, vol.44, pp.58-63, 2016.

P. G. Wells, S. Bhatia, D. M. Drake, and L. Miller-pinsler, Fetal oxidative stress mechanisms of neurodevelopmental deficits and exacerbation by ethanol and methamphetamine, Birth Defects Research Part C: Embryo Today: Reviews, vol.108, pp.108-130, 2016.

A. M. Wenger, H. Guturu, J. A. Bernstein, and G. Bejerano, Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers, Genet Med, vol.19, pp.209-214, 2017.

S. J. Wheelan, Y. Aizawa, J. S. Han, and J. D. Boeke, Gene-breaking: A new paradigm for human retrotransposon-mediated gene evolution, Genome Res, vol.15, pp.1073-1078, 2005.

T. Wicker, F. Sabot, A. Hua-van, J. L. Bennetzen, P. Capy et al., A unified classification system for eukaryotic transposable elements, Nature Reviews Genetics, vol.8, pp.973-982, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00169819

C. F. Wright, T. W. Fitzgerald, W. D. Jones, S. Clayton, J. F. Mcrae et al., Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data, The Lancet, vol.385, pp.1305-1314, 2015.

C. F. Wright, J. F. Mcrae, S. Clayton, G. Gallone, S. Aitken et al., Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1133 families with developmental disorders, Genet Med, vol.20, pp.1216-1223, 2018.

J. Wu, W. Lee, A. Ward, J. A. Walker, M. K. Konkel et al., , 2014.

J. Références-xing, H. Wang, V. P. Belancio, R. Cordaux, P. L. Deininger et al., Emergence of primate genes by retrotransposon-mediated sequence transduction, Proc Natl Acad Sci U S A, vol.15, pp.17608-17613, 2006.

J. Xing, H. Kimura, C. Wang, K. Ishizuka, I. Kushima et al., Resequencing and Association Analysis of Six PSD-95-Related Genes as Possible Susceptibility Genes for Schizophrenia and Autism Spectrum Disorders, 2016.

Y. Yang, D. M. Muzny, J. G. Reid, M. N. Bainbridge, A. Willis et al., Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders, N Engl J Med, vol.369, pp.1502-1511, 2013.

Y. Yang, D. M. Muzny, F. Xia, Z. Niu, R. Person et al., Molecular Findings Among Patients Referred for Clinical Whole-Exome Sequencing, JAMA, vol.312, pp.1870-1879, 2014.

B. Yates, B. Braschi, K. A. Gray, R. L. Seal, S. Tweedie et al., , 2017.

, Genenames.org: the HGNC and VGNC resources in 2017, vol.45, pp.619-625

F. Ye, D. C. Samuels, T. Clark, and Y. Guo, Mitochondrial DNA Research. Mitochondrion, vol.0, pp.157-163, 2014.

J. Yin, W. Chen, H. Yang, M. Xue, and C. P. Schaaf, Chrna7 deficient mice manifest no consistent neuropsychiatric and behavioral phenotypes, 2017.

J. Yin, W. Chen, E. S. Chao, S. Soriano, L. Wang et al., Otud7a Knockout Mice Recapitulate Many Neurological Features of 15q13.3 Microdeletion Syndrome, The American Journal of Human Genetics, vol.102, pp.296-308, 2018.

F. Zhang, W. Gu, M. E. Hurles, and J. R. Lupski, Copy Number Variation in Human Health, Disease, and Evolution, Annu Rev Genomics Hum Genet, vol.10, pp.451-481, 2009.

L. Zhang, W. Bai, N. Yuan, and Z. Du, Comprehensively benchmarking applications for detecting copy number variation, PLOS Computational Biology, vol.15, 2019.

W. Zhang, H. Cui, and L. C. Wong, Comprehensive One-Step Molecular Analyses of Mitochondrial Genome by Massively Parallel Sequencing, Clinical Chemistry, vol.58, pp.1322-1331, 2012.

F. Zhao, M. Guan, X. Zhou, M. Yuan, M. Liang et al., Leber's hereditary optic neuropathy is associated with mitochondrial ND6 T14502C mutation, Biochemical and Biophysical Research Communications, vol.389, pp.466-472, 2009.

C. Zwieb, R. W. Van-nues, M. A. Rosenbald, J. D. Brown, and T. Samuelsson, A nomenclature for all signal recognition particle RNAs, RNA, vol.11, pp.7-13, 2005.

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P. Garret, F. Ebstein, G. Delplancq, B. Dozieres-puyravel, A. Boughalem et al., Report of the first patient with a homozygous OTUD7A variant responsible for epileptic encephalopathy and related proteasome dysfunction, Clin Genet, 2020.

F. Lecoquierre, Y. Duffourd, A. Vitobello, A. Bruel, B. Urteaga et al., Laurence Faivre & Christel Thauvin-Robinet. Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants, Orphanomix Physician's Group, 2019.

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G. Philippine, P. Vincent, A. Bonneau-patrizia, C. Bris, V. Pierre et al., Thauvin-Robinet Christel, Duffourd Yannis. Décrypter les données de SHD d'exomes : les variations mitochondriales en lumière, 2019.

G. Philippine, P. Vincent, A. Bonneau-patrizia, C. Bris, V. Pierre et al., Thauvin-Robinet Christel, Duffourd Yannis. Intérêt de la recherche de variations mitochondriales à partir de données de ES chez des patients atteints d'anomalies du développement et/ou de déficience intellectuelle, 2019.

G. Philippine, P. Vincent, A. Bonneau-patrizia, C. Bris, V. Pierre et al., Intérêt de la recherche de variations mitochondriales à partir de données de ES chez des patients atteints d'anomalies du développement et/ou de déficience intellectuelle, vol.24

P. Posters, V. Garret, P. Procaccio, P. Bonneau, N. Vabres et al., Identification de variations pathogènes de l'ADN mitochondrial (ADNmt) à partir de données de séquençage à haut débit d'exome (SHD-E), vol.16, 2018.

P. Garret, V. Procaccio, P. Bonneau, P. Vabres, N. Houcinat et al., Identification of mitochondrial disease variants on whole exome sequencing data, vol.20, 2018.

P. Garret, C. Bris, V. Procaccio, P. Bonneau, P. Vabres et al., Deciphering exome sequencing data: bringing mitochondrial DNA variants to light, 2019.

G. Philippine, D. Geoffroy, E. Frédéric, D. Blandine, B. Aïcha et al., Report of the first patient with a homozygous OTUD7A variant responsible for epileptic encephalopathy, 2019.

G. Philippine, D. Geoffroy, E. Frédéric, D. Blandine, B. Aïcha et al., Description du premier patient atteint d'encéphalopathie épileptique porteur d'une variation homozygote dans le gène OTUD7A, vol.24

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