A gene feature enumeration approach for describing HLA allele polymorphism

Mack, Steven J.

doi:10.1016/j.humimm.2015.09.016

Cited by 18 publications

(10 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Field-1 is the allelic lineage or group that is shared by all allele variants in that group; field-2 defines a DNA variation that leads to an amino acid difference (non-synonymous DNA substitution) in the allele group defined by field-1; field-3 indicates the synonymous DNA substitution in the coding region of the allelic group; and field-4 refers to differences in the non-coding regions of the allelic group. ( 42 ). HLA exonic sequencing is limited to the field-3 level of allelic resolution, whereas HLA genomic coding and non-coding sequencing extends the allelic resolution up to the field-4 level.…”

Section: Methodsmentioning

confidence: 99%

Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform

Suzuki

Ranade

Osaki³

et al. 2018

Front. Immunol.

View full text Add to dashboard Cite

Although NGS technologies fuel advances in high-throughput HLA genotyping methods for identification and classification of HLA genes to assist with precision medicine efforts in disease and transplantation, the efficiency of these methods are impeded by the absence of adequately-characterized high-frequency HLA allele reference sequence databases for the highly polymorphic HLA gene system. Here, we report on producing a comprehensive collection of full-length HLA allele sequences for eight classical HLA loci found in the Japanese population. We augmented the second-generation short read data generated by the Ion Torrent technology with long amplicon spanning consensus reads delivered by the third-generation SMRT sequencing method to create reference grade high-quality sequences of HLA class I and II gene alleles resolved at the genomic coding and non-coding level. Forty-six DNAs were obtained from a reference set used previously to establish the HLA allele frequency data in Japanese subjects. The samples included alleles with a collective allele frequency in the Japanese population of more than 99.2%. The HLA loci were independently amplified by long-range PCR using previously designed HLA-locus specific primers and subsequently sequenced using SMRT and Ion PGM sequencers. The mapped long and short-reads were used to produce a reference library of consensus HLA allelic sequences with the help of the reference-aware software tool LAA for SMRT Sequencing. A total of 253 distinct alleles were determined for 46 healthy subjects. Of them, 137 were novel alleles: 101 SNVs and/or indels and 36 extended alleles at a partial or full-length level. Comparing the HLA sequences from the perspective of nucleotide diversity revealed that HLA-DRB1 was the most divergent among the eight HLA genes, and that the HLA-DPB1 gene sequences diverged into two distinct groups, DP2 and DP5, with evidence of independent polymorphisms generated in exon 2. We also identified two specific intronic variations in HLA-DRB1 that might be involved in rheumatoid arthritis. In conclusion, full-length HLA allele sequencing by third-generation and second-generation technologies has provided polymorphic gene reference sequences at a genomic allelic resolution including allelic variations assigned up to the field-4 level for a stronger foundation in precision medicine and HLA-related disease and transplantation studies.

show abstract

Section: Methodsmentioning

confidence: 99%

Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform

Suzuki

Ranade

Osaki³

et al. 2018

Front. Immunol.

View full text Add to dashboard Cite

show abstract

“…Alignments were checked individually to remove divergent and badly aligned sequences. From these alignments, gene regions (corresponding to the "gene features" defined by Mack 2015, 60 and ranging from 5'UTR to 3'UTR when available) were extracted separately for each sequenced individual.…”

Section: Ngs-miseq Sequence Alignmentsmentioning

confidence: 99%

Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well‐documented population from sub‐Saharan Africa

Goeury

Creary

Brunet

et al. 2017

HLA

View full text Add to dashboard Cite

With the aim to understand how next‐generation sequencing (NGS) improves both our assessment of genetic variation within populations and our knowledge on HLA molecular evolution, we sequenced and analysed 8 HLA loci in a well‐documented population from sub‐Saharan Africa (Mandenka). The results of full‐gene NGS‐MiSeq sequencing compared with those obtained by traditional typing techniques or limited sequencing strategies showed that segregating sites located outside exon 2 are crucial to describe not only class I but also class II population diversity. A comprehensive analysis of exons 2, 3, 4 and 5 nucleotide diversity at the 8 HLA loci revealed remarkable differences among these gene regions, notably a greater variation concentrated in the antigen recognition sites of class I exons 3 and some class II exons 2, likely associated with their peptide‐presentation function, a lower diversity of HLA‐C exon 3, possibly related to its role as a KIR ligand, and a peculiar molecular diversity of HLA‐A exon 2, revealing demographic signals. Based on full‐length HLA sequences, we also propose that the most frequent DRB1 allele in the studied population, DRB1*13:04, emerged from an allelic conversion involving 3 potential alleles as donors and DRB1*11:02:01 as recipient. Finally, our analysis revealed a high occurrence of the DRB1*13:04‐DQA1*05:05:01‐DQB1*03:19 haplotype, possibly resulting from a selective sweep due to protection to Onchorcerca volvulus, a prevalent pathogen in West Africa. This study unveils highly relevant information on the molecular evolution of HLA genes in relation to their immune function, calling for similar analyses in other populations living in contrasting environments.

show abstract

“…The read lengths of third-generation single-molecule sequencing can reach 20 kb with high quality [ 37 – 39 ]. Because the genomic loci of class I and II HLA alleles are between approximately 1 kb and 17 kb [ 40 ], third-generation single-molecule sequencing can directly provide HLA allele-level resolution and should be the ultimate solution to identify novel HLA alleles [ 41 ]. Although PCR amplicon approaches have been successfully tested for HLA-A, -B and -C in third-generation sequencing [ 41 ], the potential risk of long-template PCR artifacts (i.e., chimeras, mutations and drop-off) is high [ 42 – 44 ].…”

Section: Discussionmentioning

confidence: 99%

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq)

Yang

et al. 2018

BMC Genomics

View full text Add to dashboard Cite

BackgroundHighly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine.ResultsHere, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing.ConclusionsSTC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4431-5) contains supplementary material, which is available to authorized users.

show abstract

A gene feature enumeration approach for describing HLA allele polymorphism

Cited by 18 publications

References 18 publications

Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform

Reference Grade Characterization of Polymorphisms in Full-Length HLA Class I and II Genes With Short-Read Sequencing on the ION PGM System and Long-Reads Generated by Single Molecule, Real-Time Sequencing on the PacBio Platform

Deciphering the fine nucleotide diversity of full HLA class I and class II genes in a well‐documented population from sub‐Saharan Africa

High-sensitivity HLA typing by Saturated Tiling Capture Sequencing (STC-Seq)

Contact Info

Product

Resources

About