ArticlePloS one2014
Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 41 citations in OpenAlex.
- Climate factors and selection shape MHC class II diversity in a montane wild sheep (Ovis ammon).Immunogenetics · 2026Article
- AmpliSAS and AmpliHLA: Web Server and Local Tools for MHC Typing of Non-model Species and Human Using NGS Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Diversifying selection and climatic effects on major histocompatibility complex class II gene diversity in the greater horseshoe bat.Evolutionary applications · 2023Article
- Performance Comparison of Different Approaches in Genotyping MHC-DRB: The Contrast between Single-Locus and Multi-Locus Species.Animals : an open access journal from MDPI · 2022Article
- Distinct evolutionary trajectories of MHC class I and class II genes in Old World finches and buntings.Heredity · 2021Article
- What evolutionary processes maintain MHC IIꞵ diversity within and among populations of stickleback?Molecular ecology · 2021Article
- Article
- Lack of evidence for selection favouring MHC haplotypes that combine high functional diversity.Heredity · 2018Article
- Genotyping strategy matters when analyzing hypervariable major histocompatibility complex-Experience from a passerine bird.Ecology and evolution · 2018Article
- Characterization of MHC class I in a long distance migratory wader, the Icelandic black-tailed godwit.Immunogenetics · 2017Article
- Frequency dependence limits divergent evolution by favouring rare immigrants over residents.Nature · 2017Article
- Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications.BMC genomics · 2016Article
- PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches.PloS one · 2016Article
- Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota.The ISME journal · 2015Article
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Genes of the vertebrate major histocompatibility complex (MHC) are of great interest to biologists because of their important role in immunity and disease, and their extremely high levels of genetic diversity. Next generation sequencing (NGS) technologies are quickly becoming the method of choice for high-throughput genotyping of multi-locus templates like MHC in non-model organisms. Previous approaches to genotyping MHC genes using NGS technologies suffer from two problems:1) a "gray zone" where low frequency alleles and high frequency artifacts can be difficult to disentangle and 2) a similar sequence problem, where very similar alleles can be difficult to distinguish as two distinct alleles. Here were present a new method for genotyping MHC loci--Stepwise Threshold Clustering (STC)--that addresses these problems by taking full advantage of the increase in sequence data provided by NGS technologies. Unlike previous approaches for genotyping MHC with NGS data that attempt to classify individual sequences as alleles or artifacts, STC uses a quasi-Dirichlet clustering algorithm to cluster similar sequences at increasing levels of sequence similarity. By applying frequency and similarity based criteria to clusters rather than individual sequences, STC is able to successfully identify clusters of sequences that correspond to individual or similar alleles present in the genomes of individual samples. Furthermore, STC does not require duplicate runs of all samples, increasing the number of samples that can be genotyped in a given project. We show how the STC method works using a single sample library. We then apply STC to 295 threespine stickleback (Gasterosteus aculeatus) samples from four populations and show that neighboring populations differ significantly in MHC allele pools. We show that STC is a reliable, accurate, efficient, and flexible method for genotyping MHC that will be of use to biologists interested in a variety of downstream applications.
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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.