The impact of reference sequence for KIR alleles identification

Kód výsledku v 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>

Výsledek na webu

<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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Jazyk výsledku

angličtina

Název v původním jazyce

The impact of reference sequence for KIR alleles identification

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

The impact of reference sequence for KIR alleles identification

Popis výsledku anglicky

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.

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

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

Projekt

<a href="/cs/project/LM2023055" target="_blank" >LM2023055: Česká národní infrastruktura pro biologická data</a><br>

Návaznosti

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

Rok uplatnění

2025

Kód důvěrnosti údajů

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