ArticlePLoS computational biology2012
Efficiency and power as a function of sequence coverage, SNP array density, and imputation.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population.Scientific reports · 2023Article
- Medium-coverage DNA sequencing in the design of the genetic association study.European journal of human genetics : EJHG · 2020Article
- Low-, high-coverage, and two-stage DNA sequencing in the design of the genetic association study.Genetic epidemiology · 2017Article
- Whole-exome sequencing of over 4100 men of African ancestry and prostate cancer risk.Human molecular genetics · 2016Article
- Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'.European journal of human genetics : EJHG · 2014Article
- Fast and accurate imputation of summary statistics enhances evidence of functional enrichment.Bioinformatics (Oxford, England) · 2014Article
- Article
- The inflammatory gene pathway is not a major contributor to polycystic ovary snydrome.The Journal of clinical endocrinology and metabolism · 2014Article
- Identification and validation of loss of function variants in clinical contexts.Molecular genetics & genomic medicine · 2014Article
- De novo transcriptome assembly and novel microsatellite marker information in Capsicum annuum varieties Saengryeg 211 and Saengryeg 213.Botanical studies · 2013Article
- Absence of GenomicInternational journal of molecular medical science · 2013Article
- AbCD: arbitrary coverage design for sequencing-based genetic studies.Bioinformatics (Oxford, England) · 2013Article
- Imputation of exome sequence variants into population- based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project.American journal of human genetics · 2012Article
- Article
- Exome sequencing and complex disease: practical aspects of rare variant association studies.Human molecular genetics · 2012Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
High coverage whole genome sequencing provides near complete information about genetic variation. However, other technologies can be more efficient in some settings by (a) reducing redundant coverage within samples and (b) exploiting patterns of genetic variation across samples. To characterize as many samples as possible, many genetic studies therefore employ lower coverage sequencing or SNP array genotyping coupled to statistical imputation. To compare these approaches individually and in conjunction, we developed a statistical framework to estimate genotypes jointly from sequence reads, array intensities, and imputation. In European samples, we find similar sensitivity (89%) and specificity (99.6%) from imputation with either 1× sequencing or 1 M SNP arrays. Sensitivity is increased, particularly for low-frequency polymorphisms (MAF < 5%), when low coverage sequence reads are added to dense genome-wide SNP arrays--the converse, however, is not true. At sites where sequence reads and array intensities produce different sample genotypes, joint analysis reduces genotype errors and identifies novel error modes. Our joint framework informs the use of next-generation sequencing in genome wide association studies and supports development of improved methods for genotype calling.
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