A Scalable Method for Efficient Stem Cell Donor HLA Genotype Match Determination

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F49777513%3A23520%2F14%3A43923175" target="_blank" >RIV/49777513:23520/14:43923175 - isvavai.cz</a>

Výsledek na webu

<a href="http://www.europment.org/library/2014/prague/bypaper/EEED-BIO/EEED-BIO-04.pdf" target="_blank" >http://www.europment.org/library/2014/prague/bypaper/EEED-BIO/EEED-BIO-04.pdf</a>

DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

A Scalable Method for Efficient Stem Cell Donor HLA Genotype Match Determination

Popis výsledku v původním jazyce

Finding suitable stem cell donors comprises three independent processes: donor pool HLA typing, donor HLA haplotype inference, and search for donor HLA genotype matches. For practical and technical reasons, these processes are often decoupled leading to informational losses along the way. A method is presented that eliminates some of the technical challenges by considering all three steps together. The method relies on two practical assumptions: there exists a set of common haplotypes and the matched target is typed at high resolution. Under these two assumptions, sufficient statistical HLA analysis of a stem cell donor pool is performed to identify donors that most likely match a given genotype. The presented common haplotype Expected-Maximization (chEM) method is scalable in the number of loci, the number of alleles, and typing ambiguity, overcoming the known curse of dimensionality for the problem of HLA haplotype inference. The practical value is demonstrated on real world data provided by the Czech National Marrow Donor Registry. It is shown the chEM method significantly reduces the field of potential matches when compared to an existing match algorithm.

Název v anglickém jazyce

A Scalable Method for Efficient Stem Cell Donor HLA Genotype Match Determination

Popis výsledku anglicky

Finding suitable stem cell donors comprises three independent processes: donor pool HLA typing, donor HLA haplotype inference, and search for donor HLA genotype matches. For practical and technical reasons, these processes are often decoupled leading to informational losses along the way. A method is presented that eliminates some of the technical challenges by considering all three steps together. The method relies on two practical assumptions: there exists a set of common haplotypes and the matched target is typed at high resolution. Under these two assumptions, sufficient statistical HLA analysis of a stem cell donor pool is performed to identify donors that most likely match a given genotype. The presented common haplotype Expected-Maximization (chEM) method is scalable in the number of loci, the number of alleles, and typing ambiguity, overcoming the known curse of dimensionality for the problem of HLA haplotype inference. The practical value is demonstrated on real world data provided by the Czech National Marrow Donor Registry. It is shown the chEM method significantly reduces the field of potential matches when compared to an existing match algorithm.

Druh

D - Stať ve sborníku

CEP obor

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OECD FORD obor

20205 - Automation and control systems

Projekt

<a href="/cs/project/TA01010342" target="_blank" >TA01010342: Výzkum a vývoj pokročilých IT technologií podpory vyhledávání dárce pro transplantaci kostní dřeně</a><br>

Návaznosti

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

Rok uplatnění

2014

Kód důvěrnosti údajů

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

Název statě ve sborníku

Energy, Environment, Biology and Biomedicine

ISBN

978-1-61804-232-3

ISSN

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e-ISSN

neuvedeno

Počet stran výsledku

5

Strana od-do

28-32

Název nakladatele

Neuveden

Místo vydání

Neuvedeno

Místo konání akce

Prague

Datum konání akce

2. 4. 2014

Typ akce podle státní příslušnosti

WRD - Celosvětová akce

Kód UT WoS článku

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