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Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes
Open accessAbstract
A Deep Look Into Our Genes: Recent debates have focused on the degree of genetic variation and its impact upon health at the genomic level in humans (see the Perspective by Casals and Bertranpetit ). Tennessen et al. (p. 64 , published online 17 May), looking at all of the protein-coding genes in the human genome, and Nelson et al. (p. 100 , published online 17 May), looking at genes that encode drug targets, address this question through deep sequencing efforts on samples from multiple individuals. The findings suggest that most human variation is rare, not shared between populations, and that rare variants are likely to play a role in human health.
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“This allele is common in African populations [40].”
From Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes (2013) · cites this paper as [40]
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“we used the transition:transversion mutation ratio as a figure of merit, and compared this figure to a value of 2.3, which is the ratio for missense mutations observed in large-scale genomic analyses [34,35].”
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Self-citationA framework for variation discovery and genotyping using next-generation DNA sequencing data
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Analysis of protein-coding genetic variation in 60,706 humans
Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587
Self-citationAn integrated map of genetic variation from 1,092 human genomes
The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711
Self-citationA general framework for estimating the relative pathogenicity of human genetic variants
Kircher, M., Witten, D. M., Jain, P., O'Roak, B. J., Cooper, G. M., & Shendure, J. (2014) · Nature Genetics · doi:10.1038/ng.2892 · Cited by 6,183
Predicting Functional Effect of Human Missense Mutations Using PolyPhen‐2
Adzhubei, I., Jordan, D. M., & Sunyaev, S. R. (2013) · Current Protocols in Human Genetics · doi:10.1002/0471142905.hg0720s76 · Cited by 3,705
Self-citationREVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
Ioannidis, N. M., Rothstein, J. H., Pejaver, V., Middha, S., McDonnell, S. K., Baheti, S., Musolf, A., Li, Q., Holzinger, E., Karyadi, D., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.08.016 · Cited by 2,908
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Metadata
- Authors
- Tennessen, J. A., Bigham, A. W., O’Connor, T. D., Fu, W., Kenny, E. E., Gravel, S., McGee, S., Do, R., Liu, X., Jun, G., Kang, H. M., Jordan, D., Leal, S. M., Gabriel, S., Rieder, M. J., Abecasis, G., Altshuler, D., Nickerson, D. A., Boerwinkle, E., Sunyaev, S., Bustamante, C. D., Bamshad, M. J., Akey, J. M., Broad, G. O., Seattle, G. O., & on behalf of the NHLBI Exome Sequencing Project
- Affiliations
- University of Washington (US)
- Stanford University (US)
- Broad Institute (US)
- The University of Texas Health Science Center at Houston (US)
- University of Michigan (US)
- Brigham and Women's Hospital (US)
- Baylor College of Medicine (US)
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.
- Corresponding author
- Tennessen, Jacob A.
- Bigham, Abigail W.
- O’Connor, Timothy D.
- Bamshad, Michael J.
- Akey, Joshua M.
- ORCID
- Tennessen, Jacob A.
- Bigham, Abigail W.
- O’Connor, Timothy D.
- Kenny, Eimear E.
- Gravel, Simon
- McGee, Sean
- Do, Ron
- Liu, Xiaoming
- Jun, Goo
- Kang, Hyun Min
- Jordan, Daniel
- Leal, Suzanne M.
- Gabriel, Stacey
- Rieder, Mark J.
- Altshuler, David
- Nickerson, Deborah A.
- Boerwinkle, Eric
- Sunyaev, Shamil
- Bustamante, Carlos D.
- Bamshad, Michael J.
- Akey, Joshua M.
- Venue
- Science
- Published
- 2012-07-06
- Volume
- 337
- Issue
- 6090
- Pages
- 64-69
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3708544
- OpenAlex
- W1987754412
- Cited by
- 1,613
- References
- 46
- Citations by year
- 2026: 22 · 2025: 44 · 2024: 43 · 2023: 43 · 2022: 57 · 2021: 83 · 2020: 72 · 2019: 106 · 2018: 105 · 2017: 123 · 2016: 175 · 2015: 202 · 2014: 222 · 2013: 240 · 2012: 71
- FWCI
- 139.36
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (1rc2hl103010-01)
- National Heart, Lung, and Blood Institute (RC2HL102925, RC2HL102926, RC2HL102923, RC2HL-103010, RC2HL102924)
- National Human Genome Research Institute (R01HG003229, U01HG006513)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- rare coding variants, single nucleotide variants, functional impact of variants, population-specific variants, purifying selection, population growth, European ancestry, African ancestry, variant discovery
- MeSH terms
- Black or African American, Disease, Female, Gene Frequency, Humans, Male, Population Growth, Selection, Genetic, Genetic Variation, Genome, Human, Evolution, Molecular, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, White People, Genetic Association Studies, High-Throughput Nucleotide Sequencing, Exome
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