ArticleBMC genomics2021
Comparing low-pass sequencing and genotyping for trait mapping in pharmacogenetics.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed, 78 citations in OpenAlex.
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- Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.Genetics, selection, evolution : GSE · 2025Article
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- Genotype imputation from low-coverage data for medical and population genetic analyses.Genome research · 2025Article
- Single-variant genome-wide association study and regional heritability mapping of protein efficiency and performance traits in Large White pigs.Genetics, selection, evolution : GSE · 2025Article
- Genetic Architecture of Immune Cell DNA Methylation in the Rhesus Macaque.Molecular ecology · 2025Article
- A Breast Cancer Polygenic Risk Score Validation in 15,490 Brazilians Using Exome Sequencing.Diagnostics (Basel, Switzerland) · 2025Article
- Genotype inference from aggregated chromatin accessibility data reveals genetic regulatory mechanisms.Genome biology · 2025Article
- A cost-effective, high-throughput, highly accurate genotyping method for outbred populations.G3 (Bethesda, Md.) · 2025Article
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- A genome-wide association study of neonatal metabolites.Cell genomics · 2024Article
- Human milk variation is shaped by maternal genetics and impacts the infant gut microbiome.Cell genomics · 2024Article
- Unraveling the genomic diversity and admixture history of captive tigers in the United States.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLow pass sequencing has been proposed as a cost-effective alternative to genotyping arrays to identify genetic variants that influence multifactorial traits in humans. For common diseases this typically has required both large sample sizes and comprehensive variant discovery. Genotyping arrays are also routinely used to perform pharmacogenetic (PGx) experiments where sample sizes are likely to be significantly smaller, but clinically relevant effect sizes likely to be larger.
resultsTo assess how low pass sequencing would compare to array based genotyping for PGx we compared a low-pass assay (in which 1x coverage or less of a target genome is sequenced) along with software for genotype imputation to standard approaches. We sequenced 79 individuals to 1x genome coverage and genotyped the same samples on the Affymetrix Axiom Biobank Precision Medicine Research Array (PMRA). We then down-sampled the sequencing data to 0.8x, 0.6x, and 0.4x coverage, and performed imputation. Both the genotype data and the sequencing data were further used to impute human leukocyte antigen (HLA) genotypes for all samples. We compared the sequencing data and the genotyping array data in terms of four metrics: overall concordance, concordance at single nucleotide polymorphisms in pharmacogenetics-related genes, concordance in imputed HLA genotypes, and imputation r
conclusionsThese results indicate that low-pass sequencing to a depth above 0.4x coverage attains higher power for association studies when compared to the PMRA and should be considered as a competitive alternative to genotyping arrays for trait mapping in pharmacogenetics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.