ArticleBMC genomics2014
Variant calling in low-coverage whole genome sequencing of a Native American population sample.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Extensive genetic interactions (epistasis) linked to alcohol use disorder in a high-risk population.Communications biology · 2026Article
- Benchmarking imputation accuracy in the presence or absence of a reference panel.Molecular biology and evolution · 2026Article
- Genetic factors associated with suicidal behaviors and alcohol use disorders in an American Indian population.Molecular psychiatry · 2024Article
- Pleiotropic loci for cannabis use disorder severity in multi-ancestry high-risk populations.Molecular and cellular neurosciences · 2023Article
- Genetic Factors Associated with Suicidal Behaviors and Alcohol Use Disorders in an American Indian Population.Research square · 2023Article
- Association of Predicted Expression and Multimodel Association Analysis of Substance Abuse Traits.Complex psychiatry · 2022Article
- A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics.Molecular ecology · 2021Article
- Long tracks of homozygosity predict the severity of alcohol use disorders in an American Indian population.Molecular psychiatry · 2021Article
- Common genetic substrates of alcohol and substance use disorder severity revealed by pleiotropy detection against GWAS catalog in two populations.Addiction biology · 2021Article
- Optimal sequencing depth design for whole genome re-sequencing in pigs.BMC bioinformatics · 2019Article
- An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity.Molecular ecology resources · 2019Article
- Genetic loci for alcohol-related life events and substance-induced affective symptoms: indexing the "dark side" of addiction.Translational psychiatry · 2019Article
- Whole genome sequence study of cannabis dependence in two independent cohorts.Addiction biology · 2018Article
- Genetic Influences on Evening Preference Overlap with Those for Bipolar Disorder in a Sample of Mexican Americans and American Indians.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2017Article
- Associations Between Genomic Variants in Alcohol Dehydrogenase Genes and Alcohol Symptomatology in American Indians and European Americans: Distinctions and Convergence.Alcoholism, clinical and experimental research · 2017Article
- Deep whole-genome sequencing of 90 Han Chinese genomes.GigaScience · 2017Article
- Genome-wide meta-analysis identifies a novel susceptibility signal at CACNA2D3 for nicotine dependence.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2017Article
- Whole genome sequence association and ancestry-informed polygenic profile of EEG alpha in a Native American population.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2017Article
- Genome-Wide Association Study of Post-Traumatic Stress Disorder in Two High-Risk Populations.Twin research and human genetics : the official journal of the International Society for Twin Studies · 2017Article
- Polygenic risk scores for cigarettes smoked per day do not generalize to a Native American population.Drug and alcohol dependence · 2016Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundThe reduction in the cost of sequencing a human genome has led to the use of genotype sampling strategies in order to impute and infer the presence of sequence variants that can then be tested for associations with traits of interest. Low-coverage Whole Genome Sequencing (WGS) is a sampling strategy that overcomes some of the deficiencies seen in fixed content SNP array studies. Linkage-disequilibrium (LD) aware variant callers, such as the program Thunder, may provide a calling rate and accuracy that makes a low-coverage sequencing strategy viable.
resultsWe examined the performance of an LD-aware variant calling strategy in a population of 708 low-coverage whole genome sequences from a community sample of Native Americans. We assessed variant calling through a comparison of the sequencing results to genotypes measured in 641 of the same subjects using a fixed content first generation exome array. The comparison was made using the variant calling routines GATK Unified Genotyper program and the LD-aware variant caller Thunder. Thunder was found to improve concordance in a coverage dependent fashion, while correctly calling nearly all of the common variants as well as a high percentage of the rare variants present in the sample.
conclusionsLow-coverage WGS is a strategy that appears to collect genetic information intermediate in scope between fixed content genotyping arrays and deep-coverage WGS. Our data suggests that low-coverage WGS is a viable strategy with a greater chance of discovering novel variants and associations than fixed content arrays for large sample association analyses.
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