ArticleBMC genomics2013
MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout.
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 62 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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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.
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Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it, 127 citations in OpenAlex.
- Improved high-throughput MHC typing for non-model species using long-read sequencing.Molecular ecology resources · 2022Pooled it
- Regional Lassa virus lineages select for divergent MHC-I repertoires in Mastomys natalensis rodents.PLoS pathogens · 2026Article
- MHC class II genes influence the gut microbiota of wild golden snub-nosed monkeys.BMC microbiology · 2026Article
- Adaptive Genetic Variation in Black-and-White Snub-Nosed Monkeys (Ecology and evolution · 2026Article
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- Article
- Balancing selection shapes population differentiation of major histocompatibility complex genes in wild golden snub-nosed monkeys.Current zoology · 2024Article
- Moderate Genetic Diversity of MHC Genes in an Isolated Small Population of Black-and-White Snub-Nosed Monkeys (Animals : an open access journal from MDPI · 2024Article
- 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
- Pathogenic selection promotes adaptive immune variations against serious bottlenecks in early invasions of bullfrogs.iScience · 2023Article
- Article
- Extensive MHC class IIβ diversity across multiple loci in the small-spotted catshark (Scyliorhinus canicula).Scientific reports · 2023Article
- Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals.Scientific reports · 2022Article
- Sequence Diversity and Differences at the Highly Duplicated MHC-I Gene Reflect Viral Susceptibility in Sympatric Pinniped Species.The Journal of heredity · 2022Article
- 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
- Polymorphism and varying selection within the MHC class I of four Anas species.Immunogenetics · 2021Article
- Southern introgression increases adaptive immune gene variability in northern range margin populations of Fire-bellied toad.Ecology and evolution · 2021Article
- Predicting gene phenotype by multi-label multi-class model based on essential functional features.Molecular genetics and genomics : MGG · 2021Article
- Major histocompatibility complex class II DR and DQ evolution and variation in wild capuchin monkey species (Cebinae).PloS one · 2021Article
- The Rhodamine Isothiocyanate Analogue as a Quorum Sensing Inhibitor Has the Potential to Control Microbially-Induced Biofouling.Marine drugs · 2020Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used in many different research fields ranging from human medical, molecular evolutionary to functional biodiversity studies. Correct assessment of the individual allelic diversity pattern and the underlying structural sequence variation is the basic requirement to address the functional importance of MHC variability. Next-generation sequencing (NGS) technologies are likely to replace traditional genotyping methods to a great extent in the near future but first empirical studies strongly indicate the need for a rigorous quality control pipeline. Strict approaches for data validation and allele calling to distinguish true alleles from artefacts are required.
resultsWe developed the analytical methodology and validated a data processing procedure which can be applied to any organism. It allows the separation of true alleles from artefacts and the evaluation of genotyping reliability, which in addition to artefacts considers for the first time the possibility of allelic dropout due to unbalanced amplification efficiencies across alleles. Finally, we developed a method to assess the confidence level per genotype a-posteriori, which helps to decide which alleles and individuals should be included in any further downstream analyses. The latter method could also be used for optimizing experiment designs in the future.
conclusionsCombining our workflow with the study of amplification efficiency offers the chance for researchers to evaluate enormous amounts of NGS-generated data in great detail, improving confidence over the downstream analyses and subsequent 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.