Targeted capture and massively parallel sequencing of 12 human exomes - PubMed (original) (raw)
. 2009 Sep 10;461(7261):272-6.
doi: 10.1038/nature08250. Epub 2009 Aug 16.
Emily H Turner, Peggy D Robertson, Steven D Flygare, Abigail W Bigham, Choli Lee, Tristan Shaffer, Michelle Wong, Arindam Bhattacharjee, Evan E Eichler, Michael Bamshad, Deborah A Nickerson, Jay Shendure
Affiliations
- PMID: 19684571
- PMCID: PMC2844771
- DOI: 10.1038/nature08250
Targeted capture and massively parallel sequencing of 12 human exomes
Sarah B Ng et al. Nature. 2009.
Abstract
Genome-wide association studies suggest that common genetic variants explain only a modest fraction of heritable risk for common diseases, raising the question of whether rare variants account for a significant fraction of unexplained heritability. Although DNA sequencing costs have fallen markedly, they remain far from what is necessary for rare and novel variants to be routinely identified at a genome-wide scale in large cohorts. We have therefore sought to develop second-generation methods for targeted sequencing of all protein-coding regions ('exomes'), to reduce costs while enriching for discovery of highly penetrant variants. Here we report on the targeted capture and massively parallel sequencing of the exomes of 12 humans. These include eight HapMap individuals representing three populations, and four unrelated individuals with a rare dominantly inherited disorder, Freeman-Sheldon syndrome (FSS). We demonstrate the sensitive and specific identification of rare and common variants in over 300 megabases of coding sequence. Using FSS as a proof-of-concept, we show that candidate genes for Mendelian disorders can be identified by exome sequencing of a small number of unrelated, affected individuals. This strategy may be extendable to diseases with more complex genetics through larger sample sizes and appropriate weighting of non-synonymous variants by predicted functional impact.
Figures
Figure 1. Minor allele frequency and coding indel length distributions
(a) The distribution of minor allele frequencies is shown for previously annotated versus novel cSNPs. (b) The distribution of minor allele frequencies is shown for synonymous versus nonsynonymous cSNPs. (c) The distribution of minor allele frequencies (by proportion, rather than count) is shown for synonymous cSNPs (n = 21,201) versus nonsynonymous cSNPs predicted to be benign (n = 13,295), possibly damaging (n = 3,368), or probably damaging (n = 2,227) by PolyPhen. (d) The distribution of lengths of coding insertion-deletion variants is shown (average numbers per exome). Error bars indicate s.d.
Figure 2. Direct identification of the causal gene for a monogenic disorder by exome sequencing
Boxes list the number of genes with 1+ nonsynonymous cSNP, splice-site SNP, or coding indel (“NS/SS/I”) meeting specified filters. Columns show the effect of requiring that 1+ NS/SS/I variants be observed in each of 1 to 4 affected individuals. Rows show the effect of excluding from consideration variants found in dbSNP, the 8 HapMap exomes, or both. Column 5 models limited genetic heterogeneity or data incompleteness by relaxing criteria such that variants need only be observed in any 3 of 4 exomes for a gene to qualify.
Similar articles
- Molecular genetic studies of complex phenotypes.
Marian AJ. Marian AJ. Transl Res. 2012 Feb;159(2):64-79. doi: 10.1016/j.trsl.2011.08.001. Epub 2011 Aug 31. Transl Res. 2012. PMID: 22243791 Free PMC article. Review. - The complete genome of an individual by massively parallel DNA sequencing.
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A, He W, Chen YJ, Makhijani V, Roth GT, Gomes X, Tartaro K, Niazi F, Turcotte CL, Irzyk GP, Lupski JR, Chinault C, Song XZ, Liu Y, Yuan Y, Nazareth L, Qin X, Muzny DM, Margulies M, Weinstock GM, Gibbs RA, Rothberg JM. Wheeler DA, et al. Nature. 2008 Apr 17;452(7189):872-6. doi: 10.1038/nature06884. Nature. 2008. PMID: 18421352 - Concurrent exome-targeted next-generation sequencing and single nucleotide polymorphism array to identify the causative genetic aberrations of isolated Mayer-Rokitansky-Küster-Hauser syndrome.
Chen MJ, Wei SY, Yang WS, Wu TT, Li HY, Ho HN, Yang YS, Chen PL. Chen MJ, et al. Hum Reprod. 2015 Jul;30(7):1732-42. doi: 10.1093/humrep/dev095. Epub 2015 Apr 29. Hum Reprod. 2015. PMID: 25924657 - Exome resequencing combined with linkage analysis identifies novel PTH1R variants in primary failure of tooth eruption in Japanese.
Yamaguchi T, Hosomichi K, Narita A, Shirota T, Tomoyasu Y, Maki K, Inoue I. Yamaguchi T, et al. J Bone Miner Res. 2011 Jul;26(7):1655-61. doi: 10.1002/jbmr.385. J Bone Miner Res. 2011. PMID: 21404329 - Massively Parallel Sequencing for Rare Genetic Disorders: Potential and Pitfalls.
McInerney-Leo AM, Duncan EL. McInerney-Leo AM, et al. Front Endocrinol (Lausanne). 2021 Feb 19;11:628946. doi: 10.3389/fendo.2020.628946. eCollection 2020. Front Endocrinol (Lausanne). 2021. PMID: 33679611 Free PMC article. Review.
Cited by
- Kinship analysis and pedigree reconstruction by RAD sequencing in cattle.
Xu Y, Wang W, Huang J, Xu M, Wang B, Wu Y, Xie Y, Jian J. Xu Y, et al. GigaByte. 2024 Jul 18;2024:1-15. doi: 10.46471/gigabyte.131. eCollection 2024. GigaByte. 2024. PMID: 39071179 Free PMC article. - Advances and prospects of biomarkers for immune checkpoint inhibitors.
Yamaguchi H, Hsu JM, Sun L, Wang SC, Hung MC. Yamaguchi H, et al. Cell Rep Med. 2024 Jul 16;5(7):101621. doi: 10.1016/j.xcrm.2024.101621. Epub 2024 Jun 20. Cell Rep Med. 2024. PMID: 38906149 Free PMC article. Review. - Adaptive and Innate Immunity Are Key Drivers of Age at Onset of Multiple Sclerosis.
Misicka E, Huang Y, Loomis S, Sadhu N, Fisher E, Gafson A, Runz H, Tsai E, Jia X, Herman A, Bronson PG, Bhangale T, Briggs FB. Misicka E, et al. Neurol Genet. 2024 May 29;10(3):e200159. doi: 10.1212/NXG.0000000000200159. eCollection 2024 Jun. Neurol Genet. 2024. PMID: 38817245 Free PMC article. - Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders.
Hiatt SM, Lawlor JMJ, Handley LH, Latner DR, Bonnstetter ZT, Finnila CR, Thompson ML, Boston LB, Williams M, Nunez IR, Jenkins J, Kelley WV, Bebin EM, Lopez MA, Hurst ACE, Korf BR, Schmutz J, Grimwood J, Cooper GM. Hiatt SM, et al. medRxiv [Preprint]. 2024 Mar 26:2024.03.22.24304633. doi: 10.1101/2024.03.22.24304633. medRxiv. 2024. PMID: 38585854 Free PMC article. Preprint. - Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus.
Yeo NK, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Yeo NK, et al. Front Genet. 2024 Mar 4;15:1341272. doi: 10.3389/fgene.2024.1341272. eCollection 2024. Front Genet. 2024. PMID: 38501057 Free PMC article. Review.
References
- Cohen JC, et al. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science. 2004;305(5685):869–872. - PubMed
- Frazer KA, Murray SS, Schork NJ, Topol EJ. Human genetic variation and its contribution to complex traits. Nature reviews. 2009;10(4):241–251. - PubMed
- Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26(10):1135–1145. - PubMed
- Toydemir RM, et al. Mutations in embryonic myosin heavy chain (MYH3) cause Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Nature genetics. 2006;38(5):561–565. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
- R01 HL094976/HL/NHLBI NIH HHS/United States
- HHMI/Howard Hughes Medical Institute/United States
- R21 HG004749/HG/NHGRI NIH HHS/United States
- R01 HL094976-01/HL/NHLBI NIH HHS/United States
- R21 HG004749-01/HG/NHGRI NIH HHS/United States
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical
Research Materials