ArticleBMC genomics2014
Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population.
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 6 papers.
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Who cites it
6 citing papers in PubMed.
- Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project.BMC genomics · 2018Article
- An efficient and tunable parameter to improve variant calling for whole genome and exome sequencing data.Genes & genomics · 2018Article
- The comparison of the performance of four whole genome amplification kits on ion proton platform in copy number variation detection.Bioscience reports · 2017Article
- ReliableGenome: annotation of genomic regions with high/low variant calling concordance.Bioinformatics (Oxford, England) · 2017Article
- Coverage Analysis of Lists of Genes involved in Heterogeneous Genetic Diseases following Benchtop Exome Sequencing using the Ion Proton.Journal of genetics · 2016Article
- Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
27 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundValidation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.
resultsHere, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%.
conclusionsOur results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
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