Fonseca NA, Rung J, Brazma A, Marioni JC. Tools for mapping high-throughput sequencing data. Bioinformatics. 2012;28:3169–77.
Article
CAS
PubMed
Google Scholar
Leung RKK, Tsui SKW. Alns: a new searchable and filterable sequence alignment format. Int J Data Min Bioinform. 2013;7:135–45.
Article
PubMed
Google Scholar
Van der Auwera GA, Carneiro MO, Hartl C, Poplin R, del Angel G, Levy-Moonshine A, Jordan T, Shakir K, Roazen D, Thibault J, Banks E, Garimella KV, Altshuler D, Gabriel S, DePristo MA. From FastQ Data to High-Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline. In: Current Protocols in Bioinformatics. 2013. 11.10.1–11.10.33.
Google Scholar
Vaser R, Adusumalli S, Leng SN, Sikic M, Ng PC. SIFT missense predictions for genomes. Nat Protoc. 2015;11:1–9.
Article
PubMed
Google Scholar
Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013, Chapter 7:Unit7.20.
Yang H, Wang K. Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc. 2015;10:1556–66.
Article
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;14:681–91.
Article
CAS
PubMed
Google Scholar
Aerts S, Lambrechts D, Maity S, Van Loo P, Coessens B, De Smet F, Tranchevent L-C, De Moor B, Marynen P, Hassan B, Carmeliet P, Moreau Y. Gene prioritization through genomic data fusion. Nat Biotechnol. 2006;24:537–44.
Article
CAS
PubMed
Google Scholar
Sifrim A, Popovic D, Tranchevent L-C, Ardeshirdavani A, Sakai R, Konings P, Vermeesch JR, Aerts J, De Moor B, Moreau Y. eXtasy: variant prioritization by genomic data fusion. Nat Methods. 2013;10:1083–4.
Article
CAS
PubMed
Google Scholar
Zemojtel T, Köhler S, Mackenroth L, Jäger M, Hecht J, Krawitz P, Graul-Neumann L, Doelken S, Ehmke N, Spielmann M, Oien NC, Schweiger MR, Krüger U, Frommer G, Fischer B, Kornak U, Flöttmann R, Ardeshirdavani A, Moreau Y, Lewis SE, Haendel M, Smedley D, Horn D, Mundlos S, Robinson PN. Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med. 2014;6:252ra123.
Article
PubMed
PubMed Central
Google Scholar
Yang H, Robinson PN, Wang K. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases. Nat Methods. 2015;12:841–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robinson PN, Kohler S, Oellrich A, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D, Project SMG. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2013;24:340–8.
Article
PubMed
Google Scholar
Smedley D, Jacobsen JOB, Jäger M, Köhler S, Holtgrewe M, Schubach M, Siragusa E, Zemojtel T, Buske OJ, Washington NL, Bone WP, Haendel MA, Robinson PN. Next-generation diagnostics and disease-gene discovery with the Exomiser. Nat. Protoc. 2015:10;2004–2015.
Singleton MV, Guthery SL, Voelkerding KV, Chen K, Kennedy B, Margraf RL, Durtschi J, Eilbeck K, Reese MG, Jorde LB, Huff CD, Yandell M. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet. 2014;94:599–610.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.
Article
CAS
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, Van Vooren S, Wapner RJ, Wilkie AOM, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BBA, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. The human phenotype ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014;42:D966–74.
Article
PubMed
Google Scholar
Kibbe WA, Arze C, Felix V, Mitraka E, Bolton E, Fu G, Mungall CJ, Binder JX, Malone J, Vasant D, Parkinson H, Schriml LM. Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 2015;43:D1071–8.
Article
PubMed
Google Scholar
Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol. 2013;14:153–65.
Article
CAS
PubMed
Google Scholar
Alemán A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Nucleic Acids Res. 2014;42:W88–93.
Article
PubMed
PubMed Central
Google Scholar
Santoni FA, Makrythanasis P, Nikolaev S, Guipponi M, Robyr D, Bottani A, Antonarakis SE. Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster. Genome Res. 2014;24:349–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013;34:E2393–402.
Article
CAS
PubMed
PubMed Central
Google Scholar
FTP Download [http://grch37.ensembl.org/info/data/ftp/]. Accessed 23 Sept 2015.
Sherry ST. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308–11.
Article
CAS
PubMed
PubMed Central
Google Scholar
dbSNP Home Page [http://www.ncbi.nlm.nih.gov/SNP/]. Accessed 1 Dec 2015.
Exome Variant Server [http://evs.gs.washington.edu/EVS/]. Accessed 25 Aug 2016.
OMIM - Online Mendelian Inheritance in Man [http://www.omim.org/]. Accessed 9 Sept 2015.
Forbes SA, Beare D, Gunasekaran P, Leung K, Bindal N, Boutselakis H, Ding M, Bamford S, Cole C, Ward S, Kok CY, Jia M, De T, Teague JW, Stratton MR, McDermott U, Campbell PJ. COSMIC: exploring the world’s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 2014;43:D805–11.
Article
PubMed
PubMed Central
Google Scholar
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database. 2011;2011:bar030.
Article
PubMed
PubMed Central
Google Scholar
The Gene Ontology Consortium. Gene ontology consortium: going forward. Nucleic Acids Res. 2014;43:D1049–56.
Article
PubMed Central
Google Scholar
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJA, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. InterPro: the integrative protein signature database. Nucleic Acids Res. 2009;37:D211–5.
Article
CAS
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012;40:D109–14.
Article
CAS
PubMed
Google Scholar
Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D’Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42:D472–7.
Article
CAS
PubMed
Google Scholar
Sales G, Calura E, Cavalieri D, Romualdi C. Graphite - a bioconductor package to convert pathway topology to gene network. BMC Bioinformatics. 2012;13:20.
Article
PubMed
PubMed Central
Google Scholar
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80.
Article
PubMed
PubMed Central
Google Scholar
GTEx Consortium. The genotype-tissue expression (GTEx) project. Nat Genet. 2013;45:580–5.
Article
Google Scholar
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.
Article
CAS
PubMed
Google Scholar
Piñero J, Queralt-Rosinach N, Bravo A, Deu-Pons J, Bauer-Mehren A, Baron M, Sanz F, Furlong LI. DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database. 2015;2015:bav028.
Article
PubMed
PubMed Central
Google Scholar
de Ligt J, Willemsen MH, van Bon BWM, Kleefstra T, Yntema HG, Kroes T, Vulto-van Silfhout AT, Koolen DA, de Vries P, Gilissen C, del Rosario M, Hoischen A, Scheffer H, de Vries BBA, Brunner HG, Veltman JA, Vissers LELM. Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med. 2012;367:1921–9.
Article
PubMed
Google Scholar
EGAS00001000287 < Studies < EMBL-EBI [https://www.ebi.ac.uk/ega/studies/EGAS00001000287]. Accessed 30 June 2016.
Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39:e118.
Article
CAS
PubMed
PubMed Central
Google Scholar
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a high fraction of the human genome to be under selective constraint using GERP. PLoS Comput Biol. 2010;6:e1001025.
Article
PubMed
PubMed Central
Google Scholar
1000 Genomes Project Consortium, 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;467:1061–73.
Article
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schwarz JM, Cooper DN, Schuelke M, Seelow D. MutationTaster2: mutation prediction for the deep-sequencing age. Nat Methods. 2014;11:361–2.
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;46:310–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Quang D, Chen Y, Xie X. DANN: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics. 2015;31:761–3.
Article
CAS
PubMed
Google Scholar
Szpiech ZA, Xu J, Pemberton TJ, Peng W, Zöllner S, Rosenberg NA, Li JZ. Long runs of homozygosity are enriched for deleterious variation. Am J Hum Genet. 2013;93:90–102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2008;4:44–57.
Article
Google Scholar
Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010;42:30–5.
Article
CAS
PubMed
Google Scholar
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, Flicek P, Cunningham F. The Ensembl variant effect predictor. Genome Biol. 2016;17:122.
Article
PubMed
PubMed Central
Google Scholar
Antanaviciute A, Watson CM, Harrison SM, Lascelles C, Crinnion L, Markham AF, Bonthron DT, Carr IM. OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. Bioinformatics. 2015;31:3822–9.
Article
CAS
PubMed
PubMed Central
Google Scholar