Crossref journal-article
Springer Science and Business Media LLC
Nature Genetics (297)
Bibliography

Kircher, M., Witten, D. M., Jain, P., O’Roak, B. J., Cooper, G. M., & Shendure, J. (2014). A general framework for estimating the relative pathogenicity of human genetic variants. Nature Genetics, 46(3), 310–315.

Authors 6
  1. Martin Kircher (first)
  2. Daniela M Witten (additional)
  3. Preti Jain (additional)
  4. Brian J O'Roak (additional)
  5. Gregory M Cooper (additional)
  6. Jay Shendure (additional)
References 59 Referenced 5,445
  1. Cooper, G.M. et al. Single-nucleotide evolutionary constraint scores highlight disease-causing mutations. Nat. Methods 7, 250–251 (2010). (10.1038/nmeth0410-250) / Nat. Methods by GM Cooper (2010)
  2. Cooper, G.M. & Shendure, J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12, 628–640 (2011). (10.1038/nrg3046) / Nat. Rev. Genet. by GM Cooper (2011)
  3. Musunuru, K. et al. From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus. Nature 466, 714–719 (2010). (10.1038/nature09266) / Nature by K Musunuru (2010)
  4. Ward, L.D. & Kellis, M. Interpreting noncoding genetic variation in complex traits and human disease. Nat. Biotechnol. 30, 1095–1106 (2012). (10.1038/nbt.2422) / Nat. Biotechnol. by LD Ward (2012)
  5. Ng, S.B. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009). (10.1038/nature08250) / Nature by SB Ng (2009)
  6. Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010). (10.1038/nmeth0410-248) / Nat. Methods by IA Adzhubei (2010)
  7. Ng, P.C. & Henikoff, S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31, 3812–3814 (2003). (10.1093/nar/gkg509) / Nucleic Acids Res. by PC Ng (2003)
  8. Cooper, G.M. et al. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 15, 901–913 (2005). (10.1101/gr.3577405) / Genome Res. by GM Cooper (2005)
  9. Siepel, A. et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005). (10.1101/gr.3715005) / Genome Res. by A Siepel (2005)
  10. Pollard, K.S., Hubisz, M.J., Rosenbloom, K.R. & Siepel, A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 20, 110–121 (2010). (10.1101/gr.097857.109) / Genome Res. by KS Pollard (2010)
  11. ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012). (10.1038/nature11247)
  12. Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge University Press, Cambridge and New York, 1983). (10.1017/CBO9780511623486)
  13. Paten, B. et al. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res. 18, 1829–1843 (2008). (10.1101/gr.076521.108) / Genome Res. by B Paten (2008)
  14. 1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012). (10.1038/nature11632)
  15. Paten, B., Herrero, J., Beal, K., Fitzgerald, S. & Birney, E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res. 18, 1814–1828 (2008). (10.1101/gr.076554.108) / Genome Res. by B Paten (2008)
  16. McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069–2070 (2010). (10.1093/bioinformatics/btq330) / Bioinformatics by W McLaren (2010)
  17. Meyer, L.R. et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 41, D64–D69 (2013). (10.1093/nar/gks1048) / Nucleic Acids Res. by LR Meyer (2013)
  18. Boyle, A.P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008). (10.1016/j.cell.2007.12.014) / Cell by AP Boyle (2008)
  19. Johnson, D.S., Mortazavi, A., Myers, R.M. & Wold, B. Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007). (10.1126/science.1141319) / Science by DS Johnson (2007)
  20. Grantham, R. Amino acid difference formula to help explain protein evolution. Science 185, 862–864 (1974). (10.1126/science.185.4154.862) / Science by R Grantham (1974)
  21. Franc, V. & Sonnenburg, S. Optimized cutting plane algorithm for large-scale risk minimization. J. Mach. Learn. Res. 10, 2157–2192 (2009). / J. Mach. Learn. Res. by V Franc (2009)
  22. Ewing, B. & Green, P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186–194 (1998). (10.1101/gr.8.3.186) / Genome Res. by B Ewing (1998)
  23. Liao, B.Y. & Zhang, J. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc. Natl. Acad. Sci. USA 105, 6987–6992 (2008). (10.1073/pnas.0800387105) / Proc. Natl. Acad. Sci. USA by BY Liao (2008)
  24. Fu, W. et al. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature 493, 216–220 (2013). (10.1038/nature11690) / Nature by W Fu (2013)
  25. Makrythanasis, P. et al. MLL2 mutation detection in 86 patients with Kabuki syndrome: a genotype-phenotype study. Clin. Genet. doi:10.1111/cge.12081 (16 January 2013). (10.1111/cge.12081)
  26. Giardine, B. et al. HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update. Hum. Mutat. 28, 206 (2007). (10.1002/humu.9479) / Hum. Mutat. by B Giardine (2007)
  27. Baker, M. One-stop shop for disease genes. Nature 491, 171 (2012). (10.1038/491171a) / Nature by M Baker (2012)
  28. Patwardhan, R.P. et al. Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 30, 265–270 (2012). (10.1038/nbt.2136) / Nat. Biotechnol. by RP Patwardhan (2012)
  29. Patwardhan, R.P. et al. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 27, 1173–1175 (2009). (10.1038/nbt.1589) / Nat. Biotechnol. by RP Patwardhan (2009)
  30. O'Roak, B.J. et al. Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nat. Genet. 43, 585–589 (2011). (10.1038/ng.835) / Nat. Genet. by BJ O'Roak (2011)
  31. O'Roak, B.J. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246–250 (2012). (10.1038/nature10989) / Nature by BJ O'Roak (2012)
  32. Sanders, S.J. et al. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485, 237–241 (2012). (10.1038/nature10945) / Nature by SJ Sanders (2012)
  33. Neale, B.M. et al. Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485, 242–245 (2012). (10.1038/nature11011) / Nature by BM Neale (2012)
  34. Iossifov, I. et al. De novo gene disruptions in children on the autistic spectrum. Neuron 74, 285–299 (2012). (10.1016/j.neuron.2012.04.009) / Neuron by I Iossifov (2012)
  35. 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). (10.1016/S0140-6736(12)61480-9) / Lancet by A Rauch (2012)
  36. de Ligt, J. et al. Diagnostic exome sequencing in persons with severe intellectual disability. N. Engl. J. Med. 367, 1921–1929 (2012). (10.1056/NEJMoa1206524) / N. Engl. J. Med. by J de Ligt (2012)
  37. Cooper, G.M. et al. A copy number variation morbidity map of developmental delay. Nat. Genet. 43, 838–846 (2011). (10.1038/ng.909) / Nat. Genet. by GM Cooper (2011)
  38. Ng, S.B. et al. Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790–793 (2010). (10.1038/ng.646) / Nat. Genet. by SB Ng (2010)
  39. Rohland, N. & Reich, D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 22, 939–946 (2012). (10.1101/gr.128124.111) / Genome Res. by N Rohland (2012)
  40. Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222–226 (2012). (10.1126/science.1224344) / Science by M Meyer (2012)
  41. Hindorff, L.A. et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106, 9362–9367 (2009). (10.1073/pnas.0903103106) / Proc. Natl. Acad. Sci. USA by LA Hindorff (2009)
  42. Nicolae, D.L. et al. Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet. 6, e1000888 (2010). (10.1371/journal.pgen.1000888) / PLoS Genet. by DL Nicolae (2010)
  43. Gerstein, M.B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91–100 (2012). (10.1038/nature11245) / Nature by MB Gerstein (2012)
  44. Schaub, M.A., Boyle, A.P., Kundaje, A., Batzoglou, S. & Snyder, M. Linking disease associations with regulatory information in the human genome. Genome Res. 22, 1748–1759 (2012). (10.1101/gr.136127.111) / Genome Res. by MA Schaub (2012)
  45. González-Pérez, A. & Lopez-Bigas, N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am. J. Hum. Genet. 88, 440–449 (2011). (10.1016/j.ajhg.2011.03.004) / Am. J. Hum. Genet. by A González-Pérez (2011)
  46. Arbiza, L. et al. Genome-wide inference of natural selection on human transcription factor binding sites. Nat. Genet. 45, 723–729 (2013). (10.1038/ng.2658) / Nat. Genet. by L Arbiza (2013)
  47. Weedon, M.N. et al. Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis. Nat. Genet. 46, 61–64 (2014). (10.1038/ng.2826) / Nat. Genet. by MN Weedon (2014)
  48. Stenson, P.D. et al. The Human Gene Mutation Database: 2008 update. Genome Med. 1, 13 (2009). (10.1186/gm13) / Genome Med. by PD Stenson (2009)
  49. MacArthur, D.G. et al. A systematic survey of loss-of-function variants in human protein-coding genes. Science 335, 823–828 (2012). (10.1126/science.1215040) / Science by DG MacArthur (2012)
  50. Tavaré, S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lect. Math. Life Sci. 17, 57–86 (1986). / Lect. Math. Life Sci. by S Tavaré (1986)
  51. Fujita, P.A. et al. The UCSC Genome Browser database: update 2011. Nucleic Acids Res. 39, D876–D882 (2011). (10.1093/nar/gkq963) / Nucleic Acids Res. by PA Fujita (2011)
  52. Rosenbloom, K.R. et al. ENCODE whole-genome data in the UCSC Genome Browser: update 2012. Nucleic Acids Res. 40, D912–D917 (2012). (10.1093/nar/gkr1012) / Nucleic Acids Res. by KR Rosenbloom (2012)
  53. Hubisz, M.J., Pollard, K.S. & Siepel, A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief. Bioinform. 12, 41–51 (2011). (10.1093/bib/bbq072) / Brief. Bioinform. by MJ Hubisz (2011)
  54. 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). (10.1371/journal.pcbi.1001025) / PLoS Comput. Biol. by EV Davydov (2010)
  55. McVicker, G., Gordon, D., Davis, C. & Green, P. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet. 5, e1000471 (2009). (10.1371/journal.pgen.1000471) / PLoS Genet. by G McVicker (2009)
  56. Hoffman, M.M. et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods 9, 473–476 (2012). (10.1038/nmeth.1937) / Nat. Methods by MM Hoffman (2012)
  57. Tennessen, J.A. et al. Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 337, 64–69 (2012). (10.1126/science.1219240) / Science by JA Tennessen (2012)
  58. Khurana, E., Fu, Y., Chen, J. & Gerstein, M. Interpretation of genomic variants using a unified biological network approach. PLoS Comput. Biol. 9, e1002886 (2013). (10.1371/journal.pcbi.1002886) / PLoS Comput. Biol. by E Khurana (2013)
  59. Liu, X., Jian, X. & Boerwinkle, E. dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions. Hum. Mutat. 32, 894–899 (2011). (10.1002/humu.21517) / Hum. Mutat. by X Liu (2011)
Dates
Type When
Created 11 years, 7 months ago (Feb. 2, 2014, 4:46 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 4:57 p.m.)
Indexed 16 hours, 13 minutes ago (Sept. 4, 2025, 9:41 a.m.)
Issued 11 years, 7 months ago (Feb. 2, 2014)
Published 11 years, 7 months ago (Feb. 2, 2014)
Published Online 11 years, 7 months ago (Feb. 2, 2014)
Published Print 11 years, 6 months ago (March 1, 2014)
Funders 0

None

@article{Kircher_2014, title={A general framework for estimating the relative pathogenicity of human genetic variants}, volume={46}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.2892}, DOI={10.1038/ng.2892}, number={3}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Kircher, Martin and Witten, Daniela M and Jain, Preti and O’Roak, Brian J and Cooper, Gregory M and Shendure, Jay}, year={2014}, month=feb, pages={310–315} }