Green ED, Guyer MS: Charting a course for genomic medicine from base pairs to bedside. Nature. 2011, 470: 204-213. 10.1038/nature09764.
Article
CAS
PubMed
Google Scholar
McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA, Hirschhorn JN: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008, 9: 356-369. 10.1038/nrg2344.
Article
CAS
PubMed
Google Scholar
Van Karnebeek CD, Sly WS, Ross CJ, Salvarinova R, Yaplito-Lee J, Santra S, Shyr C, Horvath GA, Eydoux P, Lehman AM, Bernard V, Newlove T, Ukpeh H, Chakrapani A, Preece MA, Ball S, Pitt J, Vallance HD, Coulter-Mackie M, Nguyen H, Zhang L-H, Bhavsar AP, Sinclair G, Waheed A, Wasserman WW, Stockler-Ipsiroglu S: Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood. Am J Hum Genet. 2014, 94: 453-461. 10.1016/j.ajhg.2014.01.006.
Article
CAS
PubMed
PubMed Central
Google Scholar
Montserrat Moliner A, Waligóra J: The European union policy in the field of rare diseases. Public Health Genomics. 2013, 16: 268-277. 10.1159/000355930.
Article
CAS
PubMed
Google Scholar
Carter CO: Monogenic disorders. J Med Genet. 1977, 14: 316-320. 10.1136/jmg.14.5.316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Baird PA, Anderson TW, Newcombe HB, Lowry RB: Genetic disorders in children and young adults: a population study. Am J Hum Genet. 1988, 42: 677-693.
CAS
PubMed
PubMed Central
Google Scholar
Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE: Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet. 2013, 14: 681-691. 10.1038/nrg3555.
Article
CAS
PubMed
Google Scholar
McKusick VA: Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet. 2007, 80: 588-604. 10.1086/514346.
Article
CAS
PubMed
PubMed Central
Google Scholar
Aymé S, Urbero B, Oziel D, Lecouturier E, Biscarat AC: Information on rare diseases: the Orphanet project. Rev Médecine Interne Fondée Par Société Natl Francaise Médecine Interne. 1998, 19 (Suppl 3): 376S-377S. 10.1016/S0248-8663(98)90021-2.
Article
Google Scholar
Samuels ME: Saturation of the human phenome. Curr Genomics. 2010, 11: 482-499. 10.2174/138920210793175886.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cooper DN, Chen J-M, Ball EV, Howells K, Mort M, Phillips AD, Chuzhanova N, Krawczak M, Kehrer-Sawatzki H, Stenson PD: Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics. Hum Mutat. 2010, 31: 631-655. 10.1002/humu.21260.
Article
CAS
PubMed
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: 745-755. 10.1038/nrg3031.
Article
CAS
PubMed
Google Scholar
Gilissen C, Hoischen A, Brunner HG, Veltman JA: Unlocking Mendelian disease using exome sequencing. Genome Biol. 2011, 12: 228-10.1186/gb-2011-12-9-228.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ku C-S, Naidoo N, Pawitan Y: Revisiting Mendelian disorders through exome sequencing. Hum Genet. 2011, 129: 351-370. 10.1007/s00439-011-0964-2.
Article
PubMed
Google Scholar
Rabbani B, Mahdieh N, Hosomichi K, Nakaoka H, Inoue I: Next-generation sequencing: impact of exome sequencing in characterizing Mendelian disorders. J Hum Genet. 2012, 57: 621-632. 10.1038/jhg.2012.91.
Article
CAS
PubMed
Google Scholar
Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z: A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014, 15: 256-278. 10.1093/bib/bbs086.
Article
PubMed
Google Scholar
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29: 308-311. 10.1093/nar/29.1.308.
Article
CAS
PubMed
PubMed Central
Google Scholar
Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA: A map of human genome variation from population-scale sequencing. Nature. 2010, 467: 1061-1073. 10.1038/nature09534.
Article
PubMed
Google Scholar
A haplotype map of the human genome. Nature. 2005, 437: 1299-1320. 10.1038/nature04226.
Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu F, Yang H, Zeng C, Gao Y, Hu H, Hu W, Li C, Lin W, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q, et al: A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007, 449: 851-861. 10.1038/nature06258.
Article
CAS
PubMed
Google Scholar
Kumar P, Henikoff S, Ng PC: Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009, 4: 1073-1081. 10.1038/nprot.2009.86.
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: 248-249. 10.1038/nmeth0410-248.
Article
CAS
PubMed
PubMed Central
Google Scholar
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner M-M, Hunt T, et al: A systematic survey of loss-of-function variants in human protein-coding genes. Science. 2012, 335: 823-828. 10.1126/science.1215040.
Article
CAS
PubMed
PubMed Central
Google Scholar
Adzhubei I, Jordan DM, Sunyaev SR: Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet Editor Board Jonathan Haines Al. 2013, Chapter 7:Unit7.20
Google Scholar
Gill N, Singh S, Aseri TC: Computational disease gene prioritization: an appraisal. J Comput Biol J Comput Mol Cell Biol. 2014, 21: 456-465. 10.1089/cmb.2013.0158.
Article
CAS
Google Scholar
Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB: Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 2013, 9: e1003709-10.1371/journal.pgen.1003709.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, Bruford EA EA: Genenames.org: the HGNC resources in 2013. Nucleic Acids Res. 2013, 41 (Database issue): D545-D552. 10.1093/nar/gks1066.
CAS
PubMed
Google Scholar
Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN: The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Hum Genet. 2014, 133: 1-9. 10.1007/s00439-013-1358-4.
Article
CAS
PubMed
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM: A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012, 6: 80-92. 10.4161/fly.19695.
Article
CAS
Google Scholar
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, et al: Ensembl 2014. Nucleic Acids Res. 2014, 42 (Database issue): D749-D755. 10.1093/nar/gkt1196.
Article
CAS
PubMed
Google Scholar
Piton A, Redin C, Mandel J-L: XLID-causing mutations and associated genes challenged in light of data from large-scale human exome sequencing. Am J Hum Genet. 2013, 93: 368-383. 10.1016/j.ajhg.2013.06.013.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cheung WA, Ouellette BFF, Wasserman WW: Compensating for literature annotation bias when predicting novel drug-disease relationships through Medical Subject Heading Over-representation Profile (MeSHOP) similarity. BMC Med Genomics. 2013, 6 (Suppl 2): S3-10.1186/1755-8794-6-S2-S3.
Article
PubMed
PubMed Central
Google Scholar
Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GCM, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park S-M, Riggs ER, Scott RH, Sisodiya S, et al: The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014, 42 (Database issue): D966-D974. 10.1093/nar/gkt1026.
Article
PubMed
Google Scholar
R Foundation for Statistical Computing. 2008
Van Karnebeek CDM, Shevell M, Zschocke J, Moeschler JB, Stockler S: The metabolic evaluation of the child with an intellectual developmental disorder: diagnostic algorithm for identification of treatable causes and new digital resource. Mol Genet Metab. 2014, 111: 428-438. 10.1016/j.ymgme.2014.01.011.
Article
CAS
PubMed
Google Scholar
Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J: A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014, 46: 310-315. 10.1038/ng.2892.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW: De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature. 2012, 485: 237-241. 10.1038/nature10945.
Article
CAS
PubMed
PubMed Central
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: 242-245. 10.1038/nature11011.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, Coe BP, Levy R, Ko A, Lee C, Smith JD, Turner EH, Stanaway IB, Vernot B, Malig M, Baker C, Reilly B, Akey JM, Borenstein E, Rieder MJ, Nickerson DA, Bernier R, Shendure J, Eichler EE: Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature. 2012, 485: 246-250. 10.1038/nature10989.
Article
PubMed
PubMed Central
Google Scholar
Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee Y-H, Narzisi G, Leotta A, Kendall J, Grabowska E, Ma B, Marks S, Rodgers L, Stepansky A, Troge J, Andrews P, Bekritsky M, Pradhan K, Ghiban E, Kramer M, Parla J, Demeter R, Fulton LL, Fulton RS, Magrini VJ, Ye K, Darnell JC, Darnell RB, et al: De novo gene disruptions in children on the autistic spectrum. Neuron. 2012, 74: 285-299. 10.1016/j.neuron.2012.04.009.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, McMillin MJ, Gildersleeve HI, Beck AE, Tabor HK, Cooper GM, Mefford HC, Lee C, Turner EH, Smith JD, Rieder MJ, Yoshiura K-I, Matsumoto N, Ohta T, Niikawa N, Nickerson DA, Bamshad MJ, Shendure J: Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat Genet. 2010, 42: 790-793. 10.1038/ng.646.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen W-H, Zhao X-M, van Noort V, Bork P: Human monogenic disease genes have frequently functionally redundant paralogs. PLoS Comput Biol. 2013, 9: e1003073-10.1371/journal.pcbi.1003073.
Article
CAS
PubMed
PubMed Central
Google Scholar
Diss G, Ascencio D, Deluna A, Landry CR: Molecular mechanisms of paralogous compensation and the robustness of cellular networks. J Exp Zoolog B Mol Dev Evol. 2014, 322: 488-499. 10.1002/jez.b.22555.
Article
Google Scholar
Castellana S, Mazza T: Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools. Brief Bioinform. 2013, 14: 448-459. 10.1093/bib/bbt013.
Article
CAS
PubMed
Google Scholar
Stearns FW: One hundred years of pleiotropy: a retrospective. Genetics. 2010, 186: 767-773. 10.1534/genetics.110.122549.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yamaguchi T, Sharma P, Athanasiou M, Kumar A, Yamada S, Kuehn MR: Mutation of SENP1/SuPr-2 reveals an essential role for desumoylation in mouse development. Mol Cell Biol. 2005, 25: 5171-5182. 10.1128/MCB.25.12.5171-5182.2005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yu L, Ji W, Zhang H, Renda MJ, He Y, Lin S, Cheng E, Chen H, Krause DS, Min W: SENP1-mediated GATA1 deSUMOylation is critical for definitive erythropoiesis. J Exp Med. 2010, 207: 1183-1195. 10.1084/jem.20092215.
Article
CAS
PubMed
PubMed Central
Google Scholar
Van Nguyen T, Angkasekwinai P, Dou H, Lin F-M, Lu L-S, Cheng J, Chin YE, Dong C, Yeh ETH: SUMO-specific protease 1 is critical for early lymphoid development through regulation of STAT5 activation. Mol Cell. 2012, 45: 210-221. 10.1016/j.molcel.2011.12.026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moreau Y, Tranchevent L-C: Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nat Rev Genet. 2012, 13: 523-536. 10.1038/nrg3253.
Article
CAS
PubMed
Google Scholar
Micale L, Augello B, Maffeo C, Selicorni A, Zucchetti F, Fusco C, De Nittis P, Pellico MT, Mandriani B, Fischetto R, Boccone L, Silengo M, Biamino E, Perria C, Sotgiu S, Serra G, Lapi E, Neri M, Ferlini A, Cavaliere ML, Chiurazzi P, Monica MD, Scarano G, Faravelli F, Ferrari P, Mazzanti L, Pilotta A, Patricelli MG, Bedeschi MF, Benedicenti F, et al: Molecular Analysis, Pathogenic Mechanisms, and Readthrough Therapy on a Large Cohort of Kabuki Syndrome Patients. Hum Mutat. 2014, 35: 841-850. 10.1002/humu.22547.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schulz Y, Freese L, Mänz J, Zoll B, Völter C, Brockmann K, Bögershausen N, Becker J, Wollnik B, Pauli S: CHARGE and Kabuki syndromes: a phenotypic and molecular link. Hum Mol Genet. 2014, 23: 4396-4405. 10.1093/hmg/ddu156.
Article
CAS
PubMed
Google Scholar
Harlalka GV, Baple EL, Cross H, Kühnle S, Cubillos-Rojas M, Matentzoglu K, Patton MA, Wagner K, Coblentz R, Ford DL, Mackay DJG, Chioza BA, Scheffner M, Rosa JL, Crosby AH: Mutation of HERC2 causes developmental delay with Angelman-like features. J Med Genet. 2013, 50: 65-73. 10.1136/jmedgenet-2012-101367.
Article
CAS
PubMed
Google Scholar
Cheon CK, Sohn YB, Ko JM, Lee YJ, Song JS, Moon JW, Yang BK, Ha IS, Bae EJ, Jin H-S, Jeong S-Y: Identification of KMT2D and KDM6A mutations by exome sequencing in Korean patients with Kabuki syndrome. J Hum Genet. 2014, 59: 321-325. 10.1038/jhg.2014.25.
Article
CAS
PubMed
Google Scholar
Puffenberger EG, Jinks RN, Wang H, Xin B, Fiorentini C, Sherman EA, Degrazio D, Shaw C, Sougnez C, Cibulskis K, Gabriel S, Kelley RI, Morton DH, Strauss KA: A homozygous missense mutation in HERC2 associated with global developmental delay and autism spectrum disorder. Hum Mutat. 2012, 33: 1639-1646. 10.1002/humu.22237.
Article
CAS
PubMed
Google Scholar
Böhm J, Leshinsky-Silver E, Vassilopoulos S, Le Gras S, Lerman-Sagie T, Ginzberg M, Jost B, Lev D, Laporte J: Samaritan myopathy, an ultimately benign congenital myopathy, is caused by a RYR1 mutation. Acta Neuropathol (Berl). 2012, 124: 575-581. 10.1007/s00401-012-1007-3.
Article
Google Scholar
MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C: Guidelines for investigating causality of sequence variants in human disease. Nature. 2014, 508: 469-476. 10.1038/nature13127.
Article
CAS
PubMed
PubMed Central
Google Scholar
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D: Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005, 15: 1034-1050. 10.1101/gr.3715005.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A: Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010, 20: 110-121. 10.1101/gr.097857.109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jung J-Y, DeLuca TF, Nelson TH, Wall DP: A literature search tool for intelligent extraction of disease-associated genes. J Am Med Inform Assoc JAMIA. 2014, 21: 399-405. 10.1136/amiajnl-2012-001563.
Article
PubMed
Google Scholar
Xu R, Li L, Wang Q: Towards building a disease-phenotype knowledge base: extracting disease-manifestation relationship from literature. Bioinforma Oxf Engl. 2013, 29: 2186-2194. 10.1093/bioinformatics/btt359.
Article
CAS
Google Scholar
Yu W, Gwinn M, Clyne M, Yesupriya A, Khoury MJ: A navigator for human genome epidemiology. Nat Genet. 2008, 40: 124-125. 10.1038/ng0208-124.
Article
CAS
PubMed
Google Scholar
Kocot KM, Citarella MR, Moroz LL, Halanych KM: PhyloTreePruner: A Phylogenetic Tree-Based Approach for Selection of Orthologous Sequences for Phylogenomics. Evol Bioinforma Online. 2013, 9: 429-435. 10.4137/EBO.S12813.
CAS
Google Scholar
Altenhoff AM, Dessimoz C: Inferring orthology and paralogy. Methods Mol Biol Clifton NJ. 2012, 855: 259-279. 10.1007/978-1-61779-582-4_9.
Article
CAS
Google Scholar
Pryszcz LP, Huerta-Cepas J, Gabaldón T: MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score. Nucleic Acids Res. 2011, 39: e32-10.1093/nar/gkq953.
Article
CAS
PubMed
Google Scholar