ArticleHeredity2018
A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra).
Article in Heredity, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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
20 citing papers in PubMed, 2 syntheses or guidelines pooled it, 34 citations in OpenAlex.
- Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species.Molecular ecology · 2022Pooled it
- Improved high-throughput MHC typing for non-model species using long-read sequencing.Molecular ecology resources · 2022Pooled it
- Animal Species and Identity Testing: Developments, Challenges, and Applications to Non-Human Forensics.Genes · 2025Review
- Article
- Using bioinformatics to investigate functional diversity: a case study of MHC diversity in koalas.Immunogenetics · 2024Article
- High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure.Genes · 2023Article
- Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil.Frontiers in plant science · 2023Review
- Reconstruction of Acinetobacter johnsonii ICE_NC genome using hybrid de novo genome assemblies and identification of the 12α-hydroxysteroid dehydrogenase gene.Journal of applied microbiology · 2022Article
- A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics.Molecular ecology resources · 2022Article
- Discriminating Clonotypes of Influenza A Virus Genes by Nanopore Sequencing.International journal of molecular sciences · 2021Article
- Long-Read Genome Assemblies Reveal Extraordinary Variation in the Number and Structure of MHC Loci in Birds.Genome biology and evolution · 2021Article
- Rapid Characterization of Complex Killer Cell Immunoglobulin-Like Receptor (KIR) Regions Using Cas9 Enrichment and Nanopore Sequencing.Frontiers in immunology · 2021Article
- Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.Wellcome open research · 2021Article
- MHC Genotyping by SSCP and Amplicon-Based NGS Approach in Chamois.Animals : an open access journal from MDPI · 2020Article
- Precise and Cost-Effective Nanopore Sequencing for Post-GWAS Fine-Mapping and Causal Variant Identification.iScience · 2020Article
- Targeted short read sequencing and assembly of re-arrangements and candidate gene loci provide megabase diplotypes.Nucleic acids research · 2019Article
- Review
- Is reliance on an inaccurate genome sequence sabotaging your experiments?PLoS pathogens · 2019Article
- Assessment of low-coverage nanopore long read sequencing for SNP genotyping in doubled haploid canola (Brassica napus L.).Scientific reports · 2019Article
- Long-read genotyping with SLANG (Simple Long-read loci Assembly of Nanopore data for Genotyping).Applications in plant sciencesArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.