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HLA Assignment specifications

Information


Unique identifier OMICS_15046
Name HLA Assignment
Interface Web user interface
Restrictions to use None
Input data The measured CD8+ T cell ELISpot reactivities from a set of donors with known HLA class I alleles.
Output data The donor's individual HLA alleles to be responsible for the observed reactivities.
Computer skills Basic
Stability No
Maintained No

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This tool is not available anymore.

Information


Unique identifier OMICS_15046
Name HLA Assignment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The measured CD8+ T cell ELISpot reactivities from a set of donors with known HLA class I alleles.
Output data The donor's individual HLA alleles to be responsible for the observed reactivities.
Operating system Windows
Computer skills Advanced
Stability No
Maintained No

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Publication for HLA Assignment

HLA Assignment in publications

 (3)
PMCID: 5733459
PMID: 29326702
DOI: 10.3389/fimmu.2017.01815

[…] or the consensus could be drawn only at the one-field resolution level (i.e., low-resolution assignment). as an example, there were three samples with a deviant majority vote result and a discordant hla assignment with omixon target (table ). the discordant assignment could not be explained by low coverage or sequencing depth, as both alleles had an average coverage range of 97–100 and average […]

PMCID: 3909933
PMID: 24460756
DOI: 10.1186/1471-2164-15-63

[…] association to an eag, and the percentage of reads in an exon which contribute to the final result in this specific exon. each parameter has two predefined thresholds allowing classification of the hla assignment’s quality. if a parameter exceeds the upper threshold, it scores 1, whereas if it falls below the lower threshold, it scores 0 and between the two thresholds the score is linearly […]

PMCID: 3756051
PMID: 24015196
DOI: 10.1371/journal.pone.0071888

[…] with hla annotations were compared. next, it was discovered that certain hla subtypes associated mutations were enriched in sequence sets from drug exposed individuals that are devoid of l90m. from hla assignment data, the frequency of occurrence of l90m were measured. the influence of antiretroviral choice was explored to determine if bias was introduced resulting in lower observed frequency […]


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HLA Assignment institution(s)
Microsoft Research, Redmond, WA, USA; Partners AIDS Research Center, Massachusetts General Hospital, Charlestown, MA, USA
HLA Assignment funding source(s)
This work has been funded in whole or in part by US National Institutes of Health contracts N01-Al-15422 and R01-A1-067077.

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