Smit AFA, Hubley R, Green P (2013–2015) RepeatMasker Open-4.0. from http://www.repeatmasker.org. Accessed 31 Jan 2014

Ashley EA (2016) Towards precision medicine. Nat Rev Genet 17(9):507–522. https://doi.org/10.1038/nrg.2016.86

Article  CAS  PubMed  Google Scholar 

Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, Klee EW, Kalari KR, Kocher JP (2012) TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics 28(2):277–278. https://doi.org/10.1093/bioinformatics/btr612

Article  CAS  PubMed  Google Scholar 

Baker SW, Murrell JR, Nesbitt AI, Pechter KB, Balciuniene J, Zhao X, Yu Z, Denenberg EH, DeChene ET, Wilkens AB, Bhoj EJ, Guan Q, Dulik MC, Conlin LK, Abou Tayoun AN, Luo M, Wu C, Cao K, Sarmady M, Bedoukian EC, Tarpinian J, Medne L, Skraban CM, Deardorff MA, Krantz ID, Krock BL, Santani AB (2019) Automated clinical exome reanalysis reveals novel diagnoses. J Mol Diagn 21(1):38–48. https://doi.org/10.1016/j.jmoldx.2018.07.008

Article  CAS  PubMed  Google Scholar 

Caporali L, Magri S, Legati A, Del Dotto V, Tagliavini F, Balistreri F, Nasca A, La Morgia C, Carbonelli M, Valentino ML, Lamantea E, Baratta S, Schols L, Schule R, Barboni P, Cascavilla ML, Maresca A, Capristo M, Ardissone A, Pareyson D, Cammarata G, Melzi L, Zeviani M, Peverelli L, Lamperti C, Marzoli SB, Fang M, Synofzik M, Ghezzi D, Carelli V, Taroni F (2020) ATPase domain AFG3L2 mutations alter OPA1 processing and cause optic neuropathy. Ann Neurol 88(1):18–32. https://doi.org/10.1002/ana.25723

Article  CAS  PubMed  PubMed Central  Google Scholar 

Epilepsy Genetics Initiative (2019) The epilepsy genetics initiative: systematic reanalysis of diagnostic exomes increases yield. Epilepsia 60(5):797–806. https://doi.org/10.1111/epi.14698

Article  CAS  Google Scholar 

Ewans LJ, Schofield D, Shrestha R, Zhu Y, Gayevskiy V, Ying K, Walsh C, Lee E, Kirk EP, Colley A, Ellaway C, Turner A, Mowat D, Worgan L, Freckmann ML, Lipke M, Sachdev R, Miller D, Field M, Dinger ME, Buckley MF, Cowley MJ, Roscioli T (2018) Whole-exome sequencing reanalysis at 12 months boosts diagnosis and is cost-effective when applied early in Mendelian disorders. Genet Med 20(12):1564–1574. https://doi.org/10.1038/gim.2018.39

Article  PubMed  Google Scholar 

Farwell KD, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Tippin Davis B, Baxter RM, Zeng W, Mroske C, Parra MC, Gandomi SK, Lu I, Li X, Lu H, Lu HM, Salvador D, Ruble D, Lao M, Fischbach S, Wen J, Lee S, Elliott A, Dunlop CL, Tang S (2015) Enhanced utility of family-centered diagnostic exome sequencing with inheritance model-based analysis: results from 500 unselected families with undiagnosed genetic conditions. Genet Med 17(7):578–586. https://doi.org/10.1038/gim.2014.154

Article  CAS  PubMed  Google Scholar 

Ji J, Leung ML, Baker S, Deignan JL, Santani A (2021) Clinical exome reanalysis: current practice and beyond. Mol Diagn Ther 25(5):529–536. https://doi.org/10.1007/s40291-021-00541-7

Article  PubMed  PubMed Central  Google Scholar 

Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alfoldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP, Gauthier LD, Brand H, Solomonson M, Watts NA, Rhodes D, Singer-Berk M, England EM, Seaby EG, Kosmicki JA, Walters RK, Tashman K, Farjoun Y, Banks E, Poterba T, Wang A, Seed C, Whiffin N, Chong JX, Samocha KE, Pierce-Hoffman E, Zappala Z, O’Donnell-Luria AH, Minikel EV, Weisburd B, Lek M, Ware JS, Vittal C, Armean IM, Bergelson L, Cibulskis K, Connolly KM, Covarrubias M, Donnelly S, Ferriera S, Gabriel S, Gentry J, Gupta N, Jeandet T, Kaplan D, Llanwarne C, Munshi R, Novod S, Petrillo N, Roazen D, Ruano-Rubio V, Saltzman A, Schleicher M, Soto J, Tibbetts K, Tolonen C, Wade G, Talkowski ME, C. Genome Aggregation Database, B. M. Neale, M. J. Daly and D. G. MacArthur, (2020) The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581(7809):434–443. https://doi.org/10.1038/s41586-020-2308-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Klee EW, Cousin MA, Pinto EVF, Morales-Rosado JA, Macke EL, Jenkinson WG, Ferrer A, Schultz-Rogers LE, Olson RJ, Oliver GR, Sigafoos AN, Schwab TL, Zimmermann MT, Urrutia RA, Kaiwar C, Gupta A, Blackburn PR, Boczek NJ, Prochnow CA, Lowy RJ, Mulvihill LA, McAllister TM, Aoudia SL, Kruisselbrink TM, Gunderson LB, Kemppainen JL, Fisher LJ, Tarnowski JM, Hager MM, Kroc SA, Bertsch NL, Agre KE, Jackson JL, Macklin-Mantia SK, Murphree MI, Rust LM, Summer Bolster JM, Beck SA, Atwal PS, Ellingson MS, Barnett SS, Rasmussen KJ, Lahner CA, Niu Z, Hasadsri L, Ferber MJ, Marcou CA, Clark KJ, Pichurin PN, Deyle DR, Morava-Kozicz E, Gavrilova RH, Dhamija R, Wierenga KJ, Lanpher BC, Babovic-Vuksanovic D, Farrugia G, Schimmenti LA, Stewart AK, Lazaridis KN (2021) Impact of integrated translational research on clinical exome sequencing. Genet Med 23(3):498–507. https://doi.org/10.1038/s41436-020-01005-9

Article  PubMed  Google Scholar 

Kocher JP, Quest DJ, Duffy P, Meiners MA, Moore RM, Rider D, Hossain A, Hart SN, Dinu V (2014) The biological reference repository (BioR): a rapid and flexible system for genomics annotation. Bioinformatics 30(13):1920–1922. https://doi.org/10.1093/bioinformatics/btu137

Article  CAS  PubMed  PubMed Central  Google Scholar 

Landrum MJ, Lee JM, Benson M, Brown GR, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Jang W, Karapetyan K, Katz K, Liu C, Maddipatla Z, Malheiro A, McDaniel K, Ovetsky M, Riley G, Zhou G, Holmes JB, Kattman BL, Maglott DR (2018) ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res 46(D1):D1062–D1067. https://doi.org/10.1093/nar/gkx1153

Article  CAS  PubMed  Google Scholar 

Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CG, Dipple KM, Grody WW, Vilain E, Nelson SF (2014) Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 312(18):1880–1887. https://doi.org/10.1001/jama.2014.14604

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu P, Meng L, Normand EA, Xia F, Song X, Ghazi A, Rosenfeld J, Magoulas PL, Braxton A, Ward P, Dai H, Yuan B, Bi W, Xiao R, Wang X, Chiang T, Vetrini F, He W, Cheng H, Dong J, Gijavanekar C, Benke PJ, Bernstein JA, Eble T, Eroglu Y, Erwin D, Escobar L, Gibson JB, Gripp K, Kleppe S, Koenig MK, Lewis AM, Natowicz M, Mancias P, Minor L, Scaglia F, Schaaf CP, Streff H, Vernon H, Uhles CL, Zackai EH, Wu N, Sutton VR, Beaudet AL, Muzny D, Gibbs RA, Posey JE, Lalani S, Shaw C, Eng CM, Lupski JR, Yang Y (2019) Reanalysis of clinical exome sequencing data. N Engl J Med 380(25):2478–2480. https://doi.org/10.1056/NEJMc1812033

Article  PubMed  PubMed Central  Google Scholar 

Masuda T, Wang X, Maeda M, Canver MC, Sher F, Funnell AP, Fisher C, Suciu M, Martyn GE, Norton LJ, Zhu C, Kurita R, Nakamura Y, Xu J, Higgs DR, Crossley M, Bauer DE, Orkin SH, Kharchenko PV, Maeda T (2016) Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin. Science 351(6270):285–289. https://doi.org/10.1126/science.aad3312

Article  CAS  PubMed  PubMed Central  Google Scholar 

Munz M, Ruark E, Renwick A, Ramsay E, Clarke M, Mahamdallie S, Cloke V, Seal S, Strydom A, Lunter G, Rahman N (2015) CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting. Genome Med 7:76. https://doi.org/10.1186/s13073-015-0195-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nambot S, Thevenon J, Kuentz P, Duffourd Y, Tisserant E, Bruel AL, Mosca-Boidron AL, Masurel-Paulet A, Lehalle D, Jean-Marcais N, Lefebvre M, Vabres P, El Chehadeh-Djebbar S, Philippe C, Tran Mau-Them F, St-Onge J, Jouan T, Chevarin M, Poe C, Carmignac V, Vitobello A, Callier P, Riviere JB, Faivre L, Thauvin-Robinet C, Orphanomix Physicians G (2018) 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 20(6):645–654. https://doi.org/10.1038/gim.2017.162

Article  CAS  PubMed  Google Scholar 

O’Daniel JM, McLaughlin HM, Amendola LM, Bale SJ, Berg JS, Bick D, Bowling KM, Chao EC, Chung WK, Conlin LK, Cooper GM, Das S, Deignan JL, Dorschner MO, Evans JP, Ghazani AA, Goddard KA, Gornick M, Farwell Hagman KD, Hambuch T, Hegde M, Hindorff LA, Holm IA, Jarvik GP, Knight Johnson A, Mighion L, Morra M, Plon SE, Punj S, Richards CS, Santani A, Shirts BH, Spinner NB, Tang S, Weck KE, Wolf SM, Yang Y, Rehm HL (2017) A survey of current practices for genomic sequencing test interpretation and reporting processes in US laboratories. Genet Med 19(5):575–582. https://doi.org/10.1038/gim.2016.152

Article  PubMed  Google Scholar 

Ohishi A, Masunaga Y, Iijima S, Yamoto K, Kato F, Fukami M, Saitsu H, Ogata T (2020) De novo ZBTB7A variant in a patient with macrocephaly, intellectual disability, and sleep apnea: implications for the phenotypic development in 19p13.3 microdeletions. J Hum Genet 65(2):181–186. https://doi.org/10.1038/s10038-019-0690-5

Article  CAS  PubMed  Google Scholar 

Posey JE, Harel T, Liu P, Rosenfeld JA, James RA, Coban Akdemir ZH, Walkiewicz M, Bi W, Xiao R, Ding Y, Xia F, Beaudet AL, Muzny DM, Gibbs RA, Boerwinkle E, Eng CM, Sutton VR, Shaw CA, Plon SE, Yang Y, Lupski JR (2017) Resolution of disease phenotypes resulting from multilocus genomic variation. N Engl J Med 376(1):21–31. https://doi.org/10.1056/NEJMoa1516767

Article  CAS  PubMed  Google Scholar 

Ramoni RB, Mulvihill JJ, Adams DR, Allard P, Ashley EA, Bernstein JA, Gahl WA, Hamid R, Loscalzo J, McCray AT, Shashi V, Tifft CJ, Undiagnosed Diseases N, Wise AL (2017) The undiagnosed diseases network: accelerating discovery about health and disease. Am J Hum Genet 100(2):185–192. https://doi.org/10.1016/j.ajhg.2017.01.006

Article  CAS  PubMed  PubMed Central  Google Scholar 

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL, Committee ALQA (2015) Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American college of medical genetics and genomics and the association for molecular pathology. Genet Med 17(5):405–424. https://doi.org/10.1038/gim.2015.30

Article  PubMed  PubMed Central  Google Scholar 

Salfati EL, Spencer EG, Topol SE, Muse ED, Rueda M, Lucas JR, Wagner GN, Campman S, Topol EJ, Torkamani A (2019) Re-analysis of whole-exome sequencing data uncovers novel diagnostic variants and improves molecular diagnostic yields for sudden death and idiopathic diseases. Genome Med 11(1):83. https://doi.org/10.1186/s13073-019-0702-2

Article  CAS  PubMed  PubMed Central  Google Scholar 

Seo GH, Lee H, Lee J, Han H, Cho YK, Kim M, Choi Y, Choi J, Choi IH, Rhie S, Chae KY, Kim YM, Cheon CK, Kim SJ, Lee J, Kang E, Byeon JH, Yu HJ, Shin YL, Oh A, Kim WJ, Yum MS, Lee BH, Eun BL (2022) Diagnostic performance of automated, streamlined, daily updated exome analysis in patients with neurodevelopmental delay. Mol Med 28(1):38. https://doi.org/10.1186/s10020-022-00464-x

Article  CAS  PubMed  PubMed Central  Google Scholar 

Stenson PD, Ball EV, Mort M, Phillips AD, Shiel JA, Thomas NS, Abeysinghe S, Krawczak M, Cooper DN (2003) Human gene mutation database (HGMD): 2003 update. Hum Mutat 21(6):577–581. https://doi.org/10.1002/humu.10212

Article