ArticleBMC genomics2013
Phase-defined complete sequencing of the HLA genes by next-generation sequencing.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- HLA-B*39:01:01 is a novel risk factor for antithyroid drug-induced agranulocytosis in Japanese population.The pharmacogenomics journal · 2021Pooled it
- HLA associations, somatic loss of HLA expression, and clinical outcomes in immune aplastic anemia.Blood · 2021Trial
- HLA genotyping in Japanese patients with multiple myeloma receiving bortezomib: An exploratory biomarker study of JCOG1105 (JCOG1105A1).Cancer science · 2021Trial
- High-Resolution Eight-Digit Human Leukocyte Antigen-A, -B, -C, and -DRB1 Allele and Haplotype Frequencies in South Koreans Using Next-Generation Sequencing.Annals of laboratory medicine · 2026Article
- Toward a More Complete High-Resolution Human Leukocyte Antigen Reference for Koreans.Annals of laboratory medicine · 2026Article
- Frequencies of HLA-B alleles in Indonesian Malay Ethnic.Heliyon · 2024Article
- Advancements in HLA Typing Techniques and Their Impact on Transplantation Medicine.Medical principles and practice : international journal of the Kuwait University, Health Science Centre · 2024Review
- Association of HLA-A*11:01, -A*24:02, and -B*18:01 with Prostate Cancer Risk: A Case-Control Study.International journal of molecular sciences · 2023Article
- Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.Nature protocols · 2023Review
- Whole blood transcriptome profiling identifies gene expression subnetworks and a key gene characteristic of the rare type of osteomyelitis.Biochemistry and biophysics reports · 2022Article
- A Single-Center Experience on HLA Typing with 11 Loci Next Generation Sequencing in Korean Patients with Hematologic Disease.Diagnostics (Basel, Switzerland) · 2022Article
- Article
- Identification of 8-Digit HLA-A, -B, -C, and -DRB1 Allele and Haplotype Frequencies in Koreans Using the One Lambda AllType Next-Generation Sequencing Kit.Annals of laboratory medicine · 2021Article
- Genome wide association study of HTLV-1-associated myelopathy/tropical spastic paraparesis in the Japanese population.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- High-Throughput Sequencing to Investigate Associations Between HLA Genes and Metamizole-Induced Agranulocytosis.Frontiers in genetics · 2020Article
- High-Resolution HLA Typing of HLA-A, -B, -C, -DRB1, and -DQB1 in Kinh Vietnamese by Using Next-Generation Sequencing.Frontiers in genetics · 2020Article
- Next-generation sequencing identifies contribution of both class I and II HLA genes on susceptibility of multiple sclerosis in Japanese.Journal of neuroinflammation · 2019Article
- Rare variant phasing using paired tumor:normal sequence data.BMC bioinformatics · 2019Article
- Inverse PCR to perform long-distance haplotyping: main applications to improve preimplantation genetic diagnosis in hemophilia.European journal of human genetics : EJHG · 2019Article
- Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population.Nature genetics · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe human leukocyte antigen (HLA) region, the 3.8-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, mostly autoimmune diseases. Due to the complex nature of HLA genes, there are difficulties in elucidating complete HLA gene sequences especially HLA gene haplotype structures by the conventional sequencing method. We propose a novel, accurate, and cost-effective method for generating phase-defined complete sequencing of HLA genes by using indexed multiplex next generation sequencing.
resultsA total of 33 HLA homozygous samples, 11 HLA heterozygous samples, and 3 parents-child families were subjected to phase-defined HLA gene sequencing. We applied long-range PCR to amplify six HLA genes (HLA-A, -C, -B, DRB1, -DQB1, and -DPB1) followed by transposase-based library construction and multiplex sequencing with the MiSeq sequencer. Paired-end reads (2 × 250 bp) derived from the sequencer were aligned to the six HLA gene segments of UCSC hg19 allowing at most 80 bases mismatch. For HLA homozygous samples, the six amplicons of an individual were pooled and simultaneously sequenced and mapped as an individual-tagging method. The paired-end reads were aligned to corresponding genes of UCSC hg19 and unambiguous, continuous sequences were obtained. For HLA heterozygous samples, each amplicon was separately sequenced and mapped as a gene-tagging method. After alignments, we detected informative paired-end reads harboring SNVs on both forward and reverse reads that are used to separate two chromosomes and to generate two phase-defined sequences in an individual. Consequently, we were able to determine the phase-defined HLA gene sequences from promoter to 3'-UTR and assign up to 8-digit HLA allele numbers, regardless of whether the alleles are rare or novel. Parent-child trio-based sequencing validated our sequencing and phasing methods.
conclusionsOur protocol generated phased-defined sequences of the entire HLA genes, resulting in high resolution HLA typing and new allele detection.
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