Guidelines for investigating causality of sequence variants in human disease

Nature

Volumn 508, Issue 7497, 2014, Pages 469-476

  MacArthur, D G ^a,b   Manolio, T A ^c   Dimmock, D P ^d   Rehm, H L ^e,f   Shendure, J ^g   Abecasis, G R ^h   Adams, D R ^c   Altman, R B ⁱ   Antonarakis, S E ^j,k   Ashley, E A ^l   Barrett, J C ^m   Biesecker, L G ^c   Conrad, D F ⁿ   Cooper, G M ^o   Cox, N J ^p   Daly, M J ^a,b   Gerstein, M B ^q   Goldstein, D B ^r   Hirschhorn, J N ^b,s   Leal, S M ^t   Pennacchio, L A ^u,v   Stamatoyannopoulos, J A ^g   Sunyaev, S R ^f,w   Valle, D ^x   Voight, B F ^y   Winckler, W ^b,z   Gunter, C ^o,aa   more..

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^d MEDICAL COLLEGE OF WISCONSIN   (United States)

^e LABORATORY FOR MOLECULAR MEDICINE   (United States)

^f HARVARD MEDICAL SCHOOL   (United States)

^g UNIVERSITY OF WASHINGTON   (United States)

^h UNIVERSITY OF MICHIGAN   (United States)

ⁱ STANFORD UNIVERSITY   (United States)

^j UNIVERSITY OF GENEVA MEDICAL SCHOOL   (Switzerland)

^k Institute of Genetics and Genomics of Geneva (iGE3)   (Switzerland)

^l STANFORD UNIVERSITY MEDICAL CENTER   (United States)

^m WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

ⁿ WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^o HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

^p UNIVERSITY OF CHICAGO   (United States)

^q YALE UNIVERSITY   (United States)

^r DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^s BOSTON CHILDREN S HOSPITAL   (United States)

^t BAYLOR COLLEGE OF MEDICINE   (United States)

^u LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^v U S DEPARTMENT OF ENERGY   (United States)

^w BRIGHAM AND WOMEN S HOSPITAL   (United States)

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

^y UNIVERSITY OF PENNSYLVANIA   (United States)

^z NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^aa MARCUS AUTISM CENTER   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ASSESSMENT METHOD; DISEASE PREVALENCE; GENETIC VARIATION; GENOME; GENOMICS; HEALTH RISK; PATHOGENICITY; RESOURCE DEVELOPMENT;

DISEASES; GENE SEQUENCE; GENOME; HUMAN; PATHOGENICITY; PRACTICE GUIDELINE; PRIORITY JOURNAL; REVIEW;

DISEASE; FALSE POSITIVE REACTIONS; GENES; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GUIDELINES AS TOPIC; HUMANS; INFORMATION DISSEMINATION; PUBLISHING; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; TRANSLATIONAL MEDICAL RESEARCH;

EID: 84899476119     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature13127     Document Type: Review

References (59)

1. Bell, C. J. et al. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci. Transl. Med. 3, 65ra4 (2011).
2. Xue, Y. et al. Deleterious-and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing. Am. J. Hum. Genet. 91, 1022-1032 (2012).
3. Norton, N. et al. Evaluating pathogenicity of rare variants from dilated cardiomyopathy in the exome era. Circ Cardiovasc Genet 5, 167-174 (2012).
4. Weng, L. et al. Lack of MEF2A mutations in coronary artery disease. J. Clin. Invest. 115, 1016-1020 (2005).
5. Hunt, K. A. et al. Rare and functional SIAE variants are not associated with autoimmune disease risk in up to 66,924 individuals of European ancestry. Nature Genet. 44, 3-5 (2012).
6. Allen, A. S. et al. De novo mutations in epileptic encephalopathies. Nature 501, 217-221 (2013).
7. Manolio, T. A. et al. Finding the missing heritability of complex diseases. Nature 461, 747-753 (2009).
8. Bamshad, M. J. et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nature Rev. Genet. 12, 745-755 (2011).
9. Kiezun, A. et al. Exome sequencing and the genetic basis of complex traits. Nature Genet. 44, 623-630 (2012).
10. Pasaniuc, B. et al. Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nature Genet. 44, 631-635 (2012).
11. Li, B., Wang, G. & Leal, S. M. SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits. Bioinformatics 28, 2703-2704 (2012).
12. Johnston, J. J. et al. The phenotype of a germline mutation in PIGA: the gene somaticallymutated in paroxysmal nocturnal hemoglobinuria. Am. J. Hum. Genet. 90, 295-300 (2012).
13. Zuk, O. et al. Searching for missing heritability: designing rare variant association studies. Proc. Natl Acad. Sci USA 111, E445-E464 (2014).
14. Chanock, S. J. et al. Replicating genotype-phenotype associations. Nature 447, 655-660 (2007).
15. O'Connor, T. D. et al. Fine-scale patterns of population stratification confound rare variant association tests. PLoS ONE 8, e65834 (2013).
16. Mathieson, I. & McVean, G. Differential confounding of rare and common variants in spatially structured populations. Nature Genet. 44, 243-246 (2012).
17. Goldstein, D. B. et al. Sequencing studies in human genetics: design and interpretation. Nature Rev. Genet. 14, 460-470 (2013).
18. de Ligt, J. et al. Diagnostic exome sequencing in persons with severe intellectual disability. N. Engl. J. Med. 367, 1921-1929 (2012).
19. Rauch, A. et al. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380, 1674-1682 (2012).
20. Sanders, S. J. et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237-241 (2012).
21. O'Roak, B. J. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246-250 (2012).
22. Neale, B. M. et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485, 242-245 (2012).
23. Iossifov, I. et al. De novo gene disruptions in children on the autistic spectrum. Neuron 74, 285-299 (2012).
24. O'Roak, B. J. et al. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 1619-1622 (2012).
25. Lander, E. & Kruglyak, L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nature Genet. 11, 241-247 (1995).
26. Harrow, J. et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012).
27. Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775-1789 (2012).
28. Ng, S. B. et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nature Genet. 42, 790-793 (2010).
29. Lemaire, M. et al. Recessive mutations in DGKE cause atypical hemolytic-uremic syndrome. Nature Genet. 45, 531-536 (2013).
30. Albers, C. A. et al. Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nature Genet. 44, 435-439 (2012).
31. Zaidi, S. et al. De novo mutations in histone-modifying genes in congenital heart disease. Nature 498, 220-223 (2013).
32. Lage, K. et al. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc. Natl Acad. Sci. USA 105, 20870-20875 (2008).
33. Franke, L. et al. Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am. J. Hum. Genet. 78, 1011-1025 (2006).
34. Boulding, H. & Webber, C. Large-scale objective association of mouse phenotypes with human symptoms through structural variation identified in patients with developmental disorders. Hum. Mutat. 33, 874-883 (2012).
35. Webber, C. et al. Forging links between human mental retardation- associated CNVs and mouse gene knockout models. PLoS Genet. 5, e1000531 (2009).
36. Reed, D. R., Lawler, M. P. & Tordoff, M. G. Reduced body weight is a common effect of gene knockout in mice. BMC Genet. 9, 4 (2008).
37. Giallourakis, C., Henson, C., Reich,M., Xie, X. & Mootha, V. K. Disease gene discovery throughintegrativegenomics.Annu.Rev.GenomicsHum.Genet. 6,381-406(2005).
38. Tennessen, J. A. et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64-69 (2012).
39. Veltman, J. A. & Brunner, H. G. De novo mutations in human genetic disease. Nature Rev. Genet. 13, 565-575 (2012).
40. Bustamante, C. D. et al. Natural selection on protein-coding genes in the human genome. Nature 437, 1153-1157 (2005).
41. MacArthur, D. G. et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823-828 (2012).
42. Cooper, G. M. & Shendure, J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Rev. Genet. 12, 628-640 (2011).
43. Adzhubei, I. A. et al. A method and server for predicting damaging missense mutations. Nature Methods 7, 248-249 (2010).
44. Cooper, G. M. et al. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nature Methods 7, 250-251 (2010).
45. Kondrashov, A. S., Sunyaev, S. & Kondrashov, F. A. Dobzhansky-Muller incompatibilities in protein evolution.Proc.NatlAcad. Sci.USA99,14878- 14883(2002).
46. The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
47. Patwardhan, R. P. et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nature Biotechnol. 30, 265-270 (2012).
48. Cooper, G. M. et al. A copy number variation morbidity map of developmental delay. Nature Genet. 43, 838-846 (2011).
49. Bick, A. G. et al. Burden of rare sarcomere gene variants in the Framingham and Jackson Heart Study cohorts. Am. J. Hum. Genet. 91, 513-519 (2012).
50. Flannick, J. et al. Assessing the phenotypic effects in the general population of rare variants in genes for a dominant Mendelian form of diabetes. Nature Genet. 1380-1385 (2013).
51. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010); corrigendum, 473, 544 (2011).
52. Editorial. Share alike. Nature 490, 143-144 (2012).
53. Fokkema, I. F. et al. LOVD v.2.0: the next generation in gene variant databases. Hum. Mutat. 32, 557-563 (2011).
54. Firth, H. V. et al. DECIPHER: Database of Chromosomal Imbalance and Phenotype inHumans Using Ensembl Resources.Am. J.Hum. Genet. 84, 524-533 (2009).
55. Walport, M.&Brest, P.Sharing research data toimprove public health. Lancet 377, 537-539 (2011).
56. Global Alliance for Genomics and Health. Creating a global alliance to enable responsible sharing of genomic and clinical data. http:// genomicsandhealth.org/files/public/White%20Paper%20June%203%20final.pdf (2013).
57. Richards, C. S. et al. ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007. Genet. Med. 10, 294-300 (2008).
58. Gargis, A. S. et al. Assuring the quality of next-generation sequencing in clinical laboratory practice. Nature Biotechnol. 30, 1033-1036 (2012).
59. Rehm, H. L. et al. ACMG Clinical Laboratory Standards for Next Generation Sequencing. Genet. Med. (in the press) (2013).