ArticleBMC genomics2014
A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B.
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 17 papers.
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Who cites it
17 citing papers in PubMed.
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- Genomic analysis of human noroviruses using combined Illumina-Nanopore data.Virus evolution · 2021Article
- High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing.Frontiers in genetics · 2020Article
- Epimutations in Developmental Genes Underlie the Onset of Domestication in Farmed European Sea Bass.Molecular biology and evolution · 2019Article
- Next-generation sequencing identifies contribution of both class I and II HLA genes on susceptibility of multiple sclerosis in Japanese.Journal of neuroinflammation · 2019Article
- Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population.Nature genetics · 2019Article
- Quantification of massively parallel sequencing libraries - a comparative study of eight methods.Scientific reports · 2018Article
- Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination.Epigenetics · 2018Article
- Article
- The impact of next-generation sequencing technologies on HLA research.Journal of human genetics · 2015Review
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundHuman leukocyte antigen (HLA) is a group of genes that are extremely polymorphic among individuals and populations and have been associated with more than 100 different diseases and adverse drug effects. HLA typing is accordingly an important tool in clinical application, medical research, and population genetics. We have previously developed a phase-defined HLA gene sequencing method using MiSeq sequencing.
resultsHere we report a simple, high-throughput, and cost-effective sequencing method that includes normalized library preparation and adjustment of DNA molar concentration. We applied long-range PCR to amplify HLA-B for 96 samples followed by transposase-based library construction and multiplex sequencing with the MiSeq sequencer. After sequencing, we observed low variation in read percentages (0.2% to 1.55%) among the 96 demultiplexed samples. On this basis, all the samples were amenable to haplotype phasing using our phase-defined sequencing method. In our study, a sequencing depth of 800x was necessary and sufficient to achieve full phasing of HLA-B alleles with reliable assignment of the allelic sequence to the 8 digit level.
conclusionsOur HLA sequencing method optimized for 96 multiplexing samples is highly time effective and cost effective and is especially suitable for automated multi-sample library preparation and sequencing.
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