Veltman JA, Brunner HG. De novo mutations in human genetic disease. Nat Rev Genet. 2012;13:565–75.
Article
CAS
PubMed
Google Scholar
de Lange IM, Helbig KL, Weckhuysen S, Møller RS, Velinov M, Dolzhanskaya N, Marsh E, Helbig I, Devinsky O, Tang S, Mefford HC, Myers CT, van Paesschen W, Striano P, van Gassen K, van Kempen M, de Kovel CGF, Piard J, Minassian BA, Nezarati MM, Pessoa A, Jacquette A, Maher B, Balestrini S, Sisodiya S, Warde MTA, De St Martin A, Chelly J, Van‘t Slot R, Van Maldergem L, et al. De novo mutations of KIAA2022 in females cause intellectual disability and intractable epilepsy. J Med Genet. 2016. jmedgenet-2016-103909.
O’Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O’Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J, Kryukov GV, Shpunt A, Stamatoyannopoulos JA, Sunyaev SR, et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science. 2012;338:1619–22.
Article
PubMed
PubMed Central
Google Scholar
Petrovski S, Küry S, Myers CT, Anyane-Yeboa K, Cogné B, Bialer M, Xia F, Hemati P, Riviello J, Mehaffey M, Besnard T, Becraft E, Wadley A, Politi AR, Colombo S, Zhu X, Ren Z, Andrews I, Dudding-Byth T, Schneider AL, Wallace G, Rosen ABI, Schelley S, Enns GM, Corre P, Dalton J, Mercier S, Latypova X, Schmitt S, Guzman E, et al. Germline De Novo Mutations in GNB1 Cause Severe Neurodevelopmental Disability, Hypotonia, and Seizures. Am J Hum Genet. 2016;98:1001–10.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu X, Petrovski S, Xie P, Ruzzo EK, Lu Y-F, McSweeney KM, Ben-Zeev B, Nissenkorn A, Anikster Y, Oz-Levi D, Dhindsa RS, Hitomi Y, Schoch K, Spillmann RC, Heimer G, Marek-Yagel D, Tzadok M, Han Y, Worley G, Goldstein J, Jiang Y-H, Lancet D, Pras E, Shashi V, McHale D, Need AC, Goldstein DB. Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Genet Med. 2015;17:774–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Homsy J, Zaidi S, Shen Y, Ware JS, Samocha KE, Karczewski KJ, DePalma SR, McKean D, Wakimoto H, Gorham J, Jin SC, Deanfield J, Giardini A, Porter GA, Kim R, Bilguvar K, López-Giráldez F, Tikhonova I, Mane S, Romano-Adesman A, Qi H, Vardarajan B, Ma L, Daly M, Roberts AE, Russell MW, Mital S, Newburger JW, Gaynor JW, Breitbart RE, et al. De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies. Science. 2015;350:1262–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fromer M, Pocklington AJ, Kavanagh DH, Williams HJ, Dwyer S, Gormley P, Georgieva L, Rees E, Palta P, Ruderfer DM, Carrera N, Humphreys I, Johnson JS, Roussos P, Barker DD, Banks E, Milanova V, Grant SG, Hannon E, Rose SA, Chambert K, Mahajan M, Scolnick EM, Moran JL, Kirov G, Palotie A, McCarroll SA, Holmans P, Sklar P, Owen MJ, et al. De novo mutations in schizophrenia implicate synaptic networks. Nature. 2014;506:179–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iossifov I, O’Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee Y, Grabowska E, Dalkic E, Wang Z, Marks S, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014;515:216–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gussow AB, Petrovski S, Wang Q, Allen AS, Goldstein DB. The intolerance to functional genetic variation of protein domains predicts the localization of pathogenic mutations within genes. Genome Biol. 2016;17:9.
Article
PubMed
PubMed Central
Google Scholar
Smith T, Ho G, Christodoulou J, Price EA, Onadim Z, Gauthier-Villars M, Dehainault C, Houdayer C, Parfait B, van Minkelen R, Lohman D, Eyre-Walker A. Extensive Variation in the Mutation Rate Between and Within Human Genes Associated with Mendelian Disease. Hum Mutat. 2016;37:488–94.
Article
CAS
PubMed
Google Scholar
Neale BM, Kou Y, Liu L, Ma’ayan A, Samocha KE, Sabo A, Lin C-F, Stevens C, Wang L-S, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature. 2012;485:242–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Samocha KE, Robinson EB, Sanders SJ, Stevens C, Sabo A, McGrath LM, Kosmicki JA, Rehnström K, Mallick S, Kirby A, Wall DP, MacArthur DG, Gabriel SB, DePristo M, Purcell SM, Palotie A, Boerwinkle E, Buxbaum JD, Cook EH, Gibbs RA, Schellenberg GD, Sutcliffe JS, Devlin B, Roeder K, Neale BM, Daly MJ. A framework for the interpretation of de novo mutation in human disease. Nat Genet. 2014;46:944–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12:745–55.
Article
CAS
PubMed
Google Scholar
Aggarwala V, Voight BF. An expanded sequence context model broadly explains variability in polymorphism levels across the human genome. Nat Genet. 2016;48:349–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Consortium EA, Lek M, Karczewski K, Minikel E, Samocha K, Banks E, Fennell T, O’Donnell-Luria A, Ware J, Hill A, Cummings B, Tukiainen T, Birnbaum D, Kosmicki J, Duncan L, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Cooper D, DePristo M, Do R, Flannick J, Fromer M, Gauthier L, Goldstein J, Gupta N, Howrigan D, Kiezun A, Kurki M, et al. Analysis of Protein-Coding Genetic Variation in 60,706 Humans. Cold Spring Harbor Labs Journals; 2015. doi: 10.1038/ng.3511.
Lohmann DR, Brandt B, Höpping W, Passarge E, Horsthemke B. The spectrum of RB1 germ-line mutations in hereditary retinoblastoma. Am J Hum Genet. 1996;58:940–9.
CAS
PubMed
PubMed Central
Google Scholar
Mancini D, Singh S, Ainsworth P, Rodenhiser D. Constitutively methylated CpG dinucleotides as mutation hot spots in the retinoblastoma gene (RB1). Am J Hum Genet. 1997;61:80–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uddin M, Tammimies K, Pellecchia G, Alipanahi B, Hu P, Wang Z, Pinto D, Lau L, Nalpathamkalam T, Marshall CR, Blencowe BJ, Frey BJ, Merico D, Yuen RKC, Scherer SW. Brain-expressed exons under purifying selection are enriched for de novo mutations in autism spectrum disorder. Nat Genet. 2014;46:742–7.
Article
CAS
PubMed
Google Scholar
Hodgkinson A, Eyre-Walker A. Variation in the mutation rate across mammalian genomes. Nat Rev Genet. 2011;12:756–66.
Article
CAS
PubMed
Google Scholar
He X, Sanders SJ, Liu L, De Rubeis S, Lim ET, Sutcliffe JS, Schellenberg GD, Gibbs RA, Daly MJ, Buxbaum JD, State MW, Devlin B, Roeder K, Sanders S, Murtha M, Gupta A, Murdoch J, Raubeson M, Neale B, Kou Y, Liu L, Ma’ayan A, Samocha K, O’Roak B, Vives L, Girirajan S, Karakoc E, Krumm N, Iossifov I, Ronemus M, et al. Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes. PLoS Genet. 2013;9:e1003671.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gallie BL, Campbell C, Devlin H, Duckett A, Squire JA. Developmental basis of retinal-specific induction of cancer by RB mutation. Cancer Res. 1999;59(7 Suppl):1731s–5s.
CAS
PubMed
Google Scholar
Knudson AG. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A. 1971;68:820–3.
Article
PubMed
PubMed Central
Google Scholar
Valverde JR, Alonso J, Palacios I, Pestaña Á. RB1 gene mutation up-date, a meta-analysis based on 932 reported mutations available in a searchable database. BMC Genet. 2005;6:53.
Richter S, Vandezande K, Chen N, Zhang K, Sutherland J, Anderson J, Han L, Panton R, Branco P, Gallie B. Sensitive and Efficient Detection of RB1 Gene Mutations Enhances Care for Families with Retinoblastoma. Am J Hum Genet. 2003;72:253–69.
Article
CAS
PubMed
Google Scholar
Mort M, Ivanov D, Cooper DN, Chuzhanova NA. A meta-analysis of nonsense mutations causing human genetic disease. Hum Mutat. 2008;29:1037–47.
Article
CAS
PubMed
Google Scholar
Hogg A, Bia B, Onadim Z, Cowell JK. Molecular mechanisms of oncogenic mutations in tumors from patients with bilateral and unilateral retinoblastoma. Proc Natl Acad Sci U S A. 1993;90:7351–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang K, Nowak I, Rushlow D, Gallie BL, Lohmann DR. Patterns of missplicing caused by RB1 gene mutations in patients with retinoblastoma and association with phenotypic expression. Hum Mutat. 2008;29:475–84.
Article
CAS
PubMed
Google Scholar
Otterson GA, Chen W, Coxon AB, Khleif SN, Kaye FJ. Incomplete penetrance of familial retinoblastoma linked to germ-line mutations that result in partial loss of RB function. Proc Natl Acad Sci U S A. 1997;94:12036–40.
Article
CAS
PubMed
PubMed Central
Google Scholar
Onadim Z, Hogg A, Baird PN, Cowell JK. Oncogenic point mutations in exon 20 of the RB1 gene in families showing incomplete penetrance and mild expression of the retinoblastoma phenotype. Proc Natl Acad Sci U S A. 1992;89:6177–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lohmann D, Brandt B, Hopping W, Passarge E, Horsthemke B. Distinct RB1 gene mutations with low penetrance in hereditary retinoblastoma. Hum Genet. 1994;94(4):349–54.
Lee JO, Russo AA, Pavletich NP. Structure of the retinoblastoma tumour-suppressor pocket domain bound to a peptide from HPV E7. Nature. 1998;391:859–65.
Article
CAS
PubMed
Google Scholar
Sánchez-Sánchez F, Ramírez-Castillejo C, Weekes DB, Beneyto M, Prieto F, Nájera C, Mittnacht S. Attenuation of disease phenotype through alternative translation initiation in low-penetrance retinoblastoma. Hum Mutat. 2007;28:159–67.
Article
PubMed
Google Scholar
Brogna S, Wen J. Nonsense-mediated mRNA decay (NMD) mechanisms. Nat Struct Mol Biol. 2009;16:107–13.
Article
CAS
PubMed
Google Scholar
Hwang DG, Green P. Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A. 2004;101:13994–4001.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fokkema IFAC, Taschner PEM, Schaafsma GCP, Celli J, Laros JFJ, den Dunnen JT. LOVD v. 2.0: the next generation in gene variant databases. Hum Mutat. 2011;32:557–63.
Article
CAS
PubMed
Google Scholar
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dudley JT, Kim Y, Liu L, Markov GJ, Gerold K, Chen R, Butte AJ, Kumar S. Human genomic disease variants: a neutral evolutionary explanation. Genome Res. 2012;22:1383–94.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nichols KE, Houseknecht MD, Godmilow L, Bunin G, Shields C, Meadows A, Ganguly A. Sensitive multistep clinical molecular screening of 180 unrelated individuals with retinoblastoma detects 36 novel mutations in the RB1 gene. Hum Mutat. 2005;25:566–74.
Article
CAS
PubMed
Google Scholar
Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A, Wong WSW, Sigurdsson G, Walters GB, Steinberg S, Helgason H, Thorleifsson G, Gudbjartsson DF, Helgason A, Magnusson OT, Thorsteinsdottir U, Stefansson K. Rate of de novo mutations and the importance of father’s age to disease risk. Nature. 2012;488:471–5.
Article
CAS
PubMed
PubMed Central
Google Scholar