New tools for mendelian disease gene identification: PhenoDB variant analysis module; and genematcher, a web-based tool for linking investigators with an interest in the same gene

Human Mutation

Volumn 36, Issue 4, 2015, Pages 425-431

  Sobreira, Nara ^a   Schiettecatte, François ^b   Boehm, Corinne ^a   Valle, David ^a   Hamosh, Ada ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b FS Consulting   (United States)

Author keywords

Mendelian disease; Mutation; Next generation sequencing; Whole exome sequencing; Whole genome sequencing

Indexed keywords

ARTICLE; AUTOSOMAL DOMINANT INHERITANCE; EXOME; GENE; GENE IDENTIFICATION; GENE MUTATION; GENEMATCHER; GENETIC DISORDER; GENETIC VARIABILITY; HUMAN; MENDELIAN DISEASE; PHENODB; PHENOTYPE; PRIORITY JOURNAL; WEB BROWSER; BIOLOGY; COMPUTER PROGRAM; GENETIC ASSOCIATION STUDY; GENETIC DATABASE; GENETIC DISEASES, INBORN; GENETIC VARIATION; GENETICS; GENOMICS; INTERNET; PROCEDURES;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENETIC ASSOCIATION STUDIES; GENETIC DISEASES, INBORN; GENETIC VARIATION; GENOMICS; INTERNET; PHENOTYPE; SOFTWARE; WEB BROWSER;

EID: 84925851486     PISSN: 10597794     EISSN: 10981004     Source Type: Journal    
DOI: 10.1002/humu.22769     Document Type: Article

References (22)

1. Amberger J, Bocchini C, Hamosh A. 2011. A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®). Hum Mutat 32:564-567.
2. Beaulieu CL, Majewski J, Schwartzentruber J, Samuels ME, Fernandez BA, Bernier FP, Brudno M, Knoppers B, Marcadier J, Dyment D, Adam S, Bulman DE, et al. 2014. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project. Am J Hum Genet 94:809-817.
3. Boycott KM, Vanstone MR, Bulman DE, MacKenzie AE. 2013. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat Rev Genet 14:681-691.
4. Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, McGuire AL, Nussbaum RL, O'Daniel JM, Ormond KE, Rehm HL, Watson MS, Williams MS, Biesecker LG, American College of Medical Genetics and Genomics. 2013. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med 15:565-574.
5. Gripp KW, Robbins KM, Sobreira NL, Witmer PD, Bird LM, Avela K, Makitie O, Alves D, Hogue JS, Zackai EH, Doheny KF, Stabley DL, Sol-Church K. 2015. Truncating mutations in the last exon of NOTCH3 cause lateral meningocele syndrome. Am J Med Genet A 167:271-281.
6. Hamosh A, Sobreira N, Hoover-Fong J, Sutton VR, Boehm C, Schiettecatte F, Valle D. 2013. PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features. Hum Mutat 34:566-571.
7. Hoover-Fong J, Sobreira N, Jurgens J, Modaff P, Blout C, Moser A, Kim OH, Cho TJ, Cho SY, Kim SJ, Jin DK, Kitoh H, et al. 2014. Mutations in PCYT1A, encoding a key regulator of phosphatidylcholine metabolism, cause spondylometaphyseal dysplasia with cone-rod dystrophy. Am J Hum Genet 94:105-112.
8. Jacob HJ, Abrams K, Bick DP, Brodie K, Dimmock DP, Farrell M, Geurts J, Harris J, Helbling D, Joers BJ, Kliegman R, Kowalski G, et al. 2013. Genomics in clinical practice: lessons from the front lines. Sci Transl Med 5:194cm5.
9. Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. 2014. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46:310-315.
10. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, et al. 2014. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res 42:D966-D974.
11. 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, et al. 2014. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA 312:1880-1887.
12. Meloni VA, Guilherme RS, Oliveira MM, Migliavacca M, Takeno SS, Sobreira NL, deFatima Faria Soares M, deMello CB, Melaragno MI. 2014. Cytogenomic delineation and clinical follow-up of two siblings with an 8.5 Mb 6q24.2-q25.2 deletion inherited from a paternal insertion. 2014. Am J Med Genet A 164A:2378-2384.
13. Migliavacca MP, Sobreira NL, Antonialli GP, Oliveira MM, Melaragno MI, Casteels I, deRavel T, Brunoni D, Valle D, Perez AB. 2014. Sclerocornea in a patient with van den Ende-Gupta syndrome homozygous for a SCARF2 microdeletion. Am J Med Genet A 164A:1170-1174.
14. Moldenhauer Minillo R, Sobreira N, deFatima de Faria Soares M, Jurgens J, Ling H, Hetrick KN, Doheny KF, Valle D, Brunoni D, Alvarez Perez AB. 2014. Novel deletion of SERPINF1 causes autosomal recessive osteogenesis imperfecta type VI in two Brazilian families. Mol Syndromol 5:268-275.
15. Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, Huff CD, Shannon PT, Jabs EW, Nickerson DA, Shendure J, Bamshad MJ. 2010. Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42:30-35.
16. Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB. 2013. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet 9:e1003709.
17. Sobreira NL, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, Stevens EL, Ge D, Shianna KV, Smith JP, Maia JM, Gumbs CE, Pevsner J, et al. 2010. Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene. PLoS Genet 6:e1000991.
18. Sobreira N, Modaff P, Steel G, You J, Nanda S, Hoover-Fong J, Valle D, Pauli RM. 2015. An anadysplasia-like, spontaneously remitting spondylometaphyseal dysplasia secondary to lamin B receptor (LBR) gene mutations: further definition of the phenotypic heterogeneity of LBR-bone dysplasias. Am J Med Genet A 167A:159-163.
19. The 1000 Genomes Project Consortium. 2012. An integrated map of genetic variation from 1092 human genomes. Nature 491:56-65.
20. Wang K, Li M, Hakonarson H. 2010. ANNOVAR: functional annotation of genetic variants from next-generation sequencing data. Nucleic Acids Res 38:e164.
21. Yang Y, Muzny DM, Reid JG, Bainbridge MN, Willis A, Ward PA, Braxton A, Beuten J, Xia F, Niu Z, Hardison M, Person R, et al. 2013. Clinical whole-exome sequencing for the diagnosis of mendelian disorders. N Engl J Med 369:1502-1511.
22. Yang Y, Muzny DM, Xia F, Niu Z, Person R, Ding Y, Ward P, Braxton A, Wang M, Buhay C, Veeraraghavan N, Hawes A, et al. 2014. Molecular findings among patients referred for clinical whole-exome sequencing. JAMA 312:1870-1879.