A spectral approach integrating functional genomic annotations for coding and noncoding variants

Nature Genetics

Volumn 48, Issue 2, 2016, Pages 214-220

  Ionita Laza, Iuliana ^a   Mccallum, Kenneth ^a   Xu, Bin ^a   Buxbaum, Joseph D ^b  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTISM; CONTROLLED STUDY; DATA BASE; DE NOVO MUTATION; DISEASE ASSESSMENT; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE MAPPING; GENE MUTATION; GENETIC ANALYSIS; GENETIC CODE; GENETIC DISORDER; GENETIC VARIABILITY; HUMAN; INTELLECTUAL IMPAIRMENT; LENNOX GASTAUT SYNDROME; MENDELIAN DISEASE; MUTATION; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS; SCHIZOPHRENIA; SINGLE NUCLEOTIDE POLYMORPHISM; GENETIC PREDISPOSITION; HUMAN GENOME;

GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; HUMANS; MUTATION; QUANTITATIVE TRAIT LOCI;

EID: 84956688641     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3477     Document Type: Article

References (47)

1. Mardis, E.R. The impact of next-generation sequencing technology on genetics. Trends Genet. 24, 133-141 (2008
2. Metzker, M.L. Sequencing technologies-The next generation. Nat. Rev. Genet. 11, 31-46 (2010
3. Zhang, J., Chiodini, R., Badr, A., & Zhang, G. The impact of next-generation sequencing on genomics. J. Genet. Genomics 38, 95-109 (2011
4. Adzhubei I.A., et al A method and server for predicting damaging missense mutations. Nat. Methods 7, 248-249 (2010
5. Davydov E.V., et al. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput. Biol. 6, e1001025 (2010
6. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489 57-74 (2012
7. Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature 518 317-330 (2015
8. GTEx Consortium. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science 348 648-660 (2015
9. Capanu M., et al. The use of hierarchical models for estimating relative risks of individual genetic variants: an application to a study of melanoma. Stat. Med. 27, 1973-1992 (2008
10. Capanu, M., & Begg, C.B. Hierarchical modeling for estimating relative risks of rare genetic variants: properties of the pseudo-likelihood method. Biometrics 67, 371-380 (2011
11. Kichaev G., et al. Integrating functional data to prioritize causal variants in statistical fine-mapping studies. PLoS Genet. 10, e1004722 (2014
12. Ionita-Laza, I., Capanu, M., De Rubeis, S., McCallum, K., & Buxbaum, J.D. Identification of rare causal variants in sequence-based studies: methods and applications to VPS13B, a gene involved in Cohen syndrome and autism. PLoS Genet. 10, e1004729 (2014
13. Ng S.B., et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790-793 (2010
14. Bamshad M.J., et al. Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet. 12, 745-755 (2011
15. Meyer K.B., et al. Fine-scale mapping of the FGFR2 breast cancer risk locus: putative functional variants differentially bind FOXA1 and E2F1. Am. J. Hum. Genet. 93, 1046-1060 (2013
16. Pickrell, J.K. Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am. J. Hum. Genet. 94, 559-573 (2014
17. Gusev A., et al. Partitioning heritability of regulatory and cell-Type-specific variants across 11 common diseases. Am. J. Hum. Genet. 95, 535-552 (2014
18. Kircher M., et al A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46, 310-315 (2014
19. Ritchie, G.R.S., Dunham, I., Zeggini, E., & Flicek, P. Functional annotation of noncoding sequence variants. Nat. Methods 11, 294-296 (2014
20. Gulko, B., Hubisz, M.J., Gronau, I., & Siepel, A A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat. Genet. 47, 276-283 (2015
21. Liu, X., Jian, X., & Boerwinkle, E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat. 34, E2393-E2402 (2013
22. Iossifov I., et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216-221 (2014
23. Iossifov I., et al. De novo gene disruptions in children on the autistic spectrum. Neuron 74, 285-299 (2012
24. Neale B.M., et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485, 242-245 (2012
25. O'Roak B.J., et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246-250 (2012
26. Sanders S.J., et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237-241 (2012
27. Fromer M., et al. De novo mutations in schizophrenia implicate synaptic networks. Nature 506, 179-184 (2014
28. Gulsuner S., et al. Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell 154, 518-529 (2013
29. Girard S.L., et al. Increased exonic de novo mutation rate in individuals with schizophrenia. Nat. Genet. 43, 860-863 (2011
30. McCarthy S.E., et al. De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. Mol. Psychiatry 19, 652-658 (2014
31. Xu B., et al. De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat. Genet. 44, 1365-1369 (2012
32. Epi4K Consortium & Epilepsy Phenome/Genome Project. De novo mutations in epileptic encephalopathies. Nature 501 217-221 (2013
33. de Ligt J., et al. Diagnostic exome sequencing in persons with severe intellectual disability. N. Engl. J. Med. 367, 1921-1929 (2012
34. 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
35. Darnell J.C., et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 146, 247-261 (2011
36. Dong S., et al. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Rep. 9, 16-23 (2014
37. Farh K.K., et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 518, 337-343 (2015
38. Lappalainen T., et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013
39. Forbes S.A., et al. COSMIC: exploring the world?s knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811 (2015
40. Trynka G., et al. Chromatin marks identify critical cell types for fine mapping complex trait variants. Nat. Genet. 45, 124-130 (2013
41. Ye C.J., et al. Intersection of population variation and autoimmunity genetics in human T cell activation. Science 345, 1254665 (2014
42. Ko A., et al. Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. Nat. Commun. 5, 3983 (2014
43. Gudbjartsson D.F., et al. Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47, 435-444 (2015
44. O'Rawe J., et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 5, 28 (2013
45. Lam H.Y., et al. Performance comparison of whole-genome sequencing platforms. Nat. Biotechnol. 30, 78-82 (2012
46. Fang H., et al. Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med. 6, 89 (2014
47. Parisi, F., Strino, F., Nadler, B., & Kluger, Y. Ranking and combining multiple predictors without labeled data. Proc. Natl. Acad. Sci. USA 111, 1253-1258 (2014