MHC genotyping by sscp and amplicon‐based ngs approach in chamois
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081766%3A_____%2F20%3A00532506" target="_blank" >RIV/68081766:_____/20:00532506 - isvavai.cz</a>
Result on the web
<a href="https://www.mdpi.com/2076-2615/10/9/1694" target="_blank" >https://www.mdpi.com/2076-2615/10/9/1694</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3390/ani10091694" target="_blank" >10.3390/ani10091694</a>
Alternative languages
Result language
angličtina
Original language name
MHC genotyping by sscp and amplicon‐based ngs approach in chamois
Original language description
Genes of the major histocompatibility complex (MHC) code for cell surface proteins essential for adaptive immunity. They show the most outstanding genetic diversity in vertebrates, which has been connected with various fitness traits and thus with the long-term persistence of populations. In this study, polymorphism of the MHC class II DRB locus was investigated in chamois with Single-Strand Conformation Polymorphism (SSCP)/Sanger genotyping and Ion Torrent S5 next-generation sequencing (NGS). From eight identified DRB variants in 28 individuals, five had already been described, and three were new, undescribed alleles. With conventional SSCP/Sanger sequencing, we were able to detect seven alleles, all of which were also detected with NGS. We found inconsistencies in the individual genotypes between the two methods, which were mainly caused by allelic dropout in the SSCP/Sanger method. Six out of 28 individuals were falsely classified as homozygous with SSCP/Sanger analysis. Overall, 25% of the individuals were identified as genotyping discrepancies between the two methods. Our results show that NGS technologies are better performing in sequencing highly variable regions such as the MHC, and they also have a higher detection capacity, thus allowing a more accurate description of the genetic composition, which is crucial for evolutionary and population genetic studies.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10613 - Zoology
Result continuities
Project
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Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2020
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Animals
ISSN
2076-2615
e-ISSN
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Volume of the periodical
10
Issue of the periodical within the volume
9
Country of publishing house
CH - SWITZERLAND
Number of pages
9
Pages from-to
1694
UT code for WoS article
000581374000001
EID of the result in the Scopus database
2-s2.0-85091114854