The impact of reference sequence for KIR alleles identification

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F49777513%3A23520%2F25%3A43978274" target="_blank" >RIV/49777513:23520/25:43978274 - isvavai.cz</a>

Result on the web

<a href="https://cdn.ymaws.com/www.cttcanada.org/resource/resmgr/2025_annual_meeting/CTTCIDRC_2025_ScientificProg.pdf" target="_blank" >https://cdn.ymaws.com/www.cttcanada.org/resource/resmgr/2025_annual_meeting/CTTCIDRC_2025_ScientificProg.pdf</a>

DOI - Digital Object Identifier

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Result language

angličtina

Original language name

The impact of reference sequence for KIR alleles identification

Original language description

KIR genes are characterized as highly diverse due to KIR gene content, KIR gene copy number, or allelic polymorphism. There are several existing pipelines and tools engaged in KIR allele identification but due to their characterization, a slight change in the reference sequence may lead to a read misalignment and may considerably influence the alignment result. The impact of reference sequence on results was analysed (for NGS input data). The particular allele for the gene was chosen based on a heatmap created from synthetic sequence (IPD database). Multiple reference sequences were created, and a variation of alleles was subsequently done for each of the examined genes. The value of the heatmap was a pipeline error. The correctness of the chosen reference alleles was verified on the synthetic genotypes created based on AFND database. The reference sequence was validated on reference cell lines.

Czech name

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Czech description

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Type

O - Miscellaneous

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/LM2023055" target="_blank" >LM2023055: Czech National Infrastructure for Biological Data</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2025

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů