Comparing strategies to fine-map the association of common SNPs at chromosome 9p21 with type 2 diabetes and myocardial infarction
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Noncoding variants at human chromosome 9p21 near CDKN2A and CDKN2B are associated with type 2 diabetes, myocardial infarction, aneurysm, vertical cup disc ratio and at least five cancers. Here we compare approaches to more comprehensively assess genetic variation in the region. We carried out targeted sequencing at high coverage in 47 individuals and compared the results to pilot data from the 1000 Genomes Project. We imputed variants into type 2 diabetes and myocardial infarction cohorts directly from targeted sequencing, from a genotyped reference panel derived from sequencing and from 1000 Genomes Project low-coverage data. Polymorphisms with frequency >5% were captured well by all strategies. Imputation of intermediate-frequency polymorphisms required a higher density of tag SNPs in disease samples than is available on first-generation genome-wide association study (GWAS) arrays. Our association analyses identified more comprehensive sets of variants showing equivalent statistical association with type 2 diabetes or myocardial infarction, but did not identify stronger associations than the original GWAS signals.
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Due to improved imputation, most minor alleles down to 5% frequency can now be inferred with high accuracy if the reference panel is appropriately matched for population structure.
“Due to improved methods for imputation, most minor alleles down to 5% frequency can now be inferred with high accuracy, if the reference panel is appropriately matched for population structure129.”
From Rare and common variants: twenty arguments (2012) · cites this paper as [129]
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The Chromosome 9p21 CVD- and T2D-Associated Regions in a Norwegian Population (The HUNT2 Survey)
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Quick, “Imputation-free” meta-analysis with proxy-SNPs
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Gene-Based Rare Allele Analysis Identified a Risk Gene of Alzheimer’s Disease
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The Molecular Biology and Genetics of Aneurysms
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Quick, "Imputation-free" meta-analysis with
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Fine-Mapping of Type 2 Diabetes Loci
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- Authors
- The Myocardial Infarction Genetics Consortium, Shea, J., Agarwala, V., Philippakis, A. A., Maguire, J., Banks, E., DePristo, M., Thomson, B., Guiducci, C., Onofrio, R. C., Kathiresan, S., Gabriel, S., Burtt, N. P., Daly, M. J., Groop, L., & Altshuler, D.
- Affiliations
- Broad Institute (US)
- Lund University (SE)
- Corresponding author
- Altshuler, David
- ORCID
- Venue
- Nature Genetics
- Published
- 2011-07-24
- Volume
- 43
- Issue
- 8
- Pages
- 801-805
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC4096898
- OpenAlex
- W2023742867
- Cited by
- 87
- References
- 32
- Citations by year
- 2024: 3 · 2023: 1 · 2021: 3 · 2020: 2 · 2019: 1 · 2018: 3 · 2017: 2 · 2016: 12 · 2015: 12 · 2014: 11 · 2013: 8 · 2012: 25
- FWCI
- 9.58
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Lund University Publications (Lund University) (submittedVersion)
- Funders
- National Heart, Lung, and Blood Institute (R01HL087676)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- chromosome 9p21, type 2 diabetes, myocardial infarction, CDKN2A, CDKN2B, fine mapping, targeted sequencing, imputation, non-coding variants, tag SNPs, 1000 Genomes Project, genetic association
- MeSH terms
- Chromosome Mapping, Chromosomes, Human, Pair 9, Diabetes Mellitus, Type 2, Haplotypes, Humans, Myocardial Infarction, Genetic Variation, Genome, Human, Polymorphism, Single Nucleotide, Genome-Wide Association Study
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