Name: ImmunogeneticDataTools

Owner: NMDP/Be The Match Bioinformatics Research

Description: Immunogenetic Data Tools related to HLA, GLStrings, Linkage Disequilibrium

Created: 2014-11-27 03:58:23.0

Updated: 2017-03-28 22:22:02.0

Pushed: 2017-04-08 03:20:54.0

Homepage: null

Size: 13912

Language: Java

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Immunogenetic Data Tools

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Use Cases and Implementations
1. HLA Linkage Disequilibrium

Linkage disequilibrium is the non-random association of alleles at two or more loci, that descend from a single ancestral chromosome. The particular linkages referenced here are relevant in the context of HLA and immunogenetics.

HLA typing using Next Generation Sequencing (NGS) is becoming common practice in research and clinical lab settings. HLA typing miss-call occurs when DNA sequences from one of the alleles drop out.

HLA Linkage Disequilibrium Validation software was developed to identify common linkages between HLA-B and HLA-C, and HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1 and HLA-DQB1. This information is useful when HLA typing from NGS is reviewed. The software not only validates known linkages, but also sends warning messages when unusual linkage was found.

The software user can find stronger evidences of the accuracy of his/her HLA typing results when common linkages are found. Also the user can focus on reviewing the unusual HLA linkages whether these are true or likely generated from DNA sequencing drop-outs.

The results of the software should be used for supporting the evidence, but not used to correct any HLA typing without confirmatory experiments.

Input: Genotype(s) - expressed as GL String

Output: Linked alleles by locus, a frequency and any additional notes, accompanied by GL String and Id (either assigned or generated)

Future Goals:

Using the software:

As of release .7, the ability to download the software package and make use of command line tools is available.

From the Releases section of GitHub you may grab the snapshot of the latest release. E.g: ld-tools-0.0.1-SNAPSHOT-bin.zip from release .7 at Releases

After un-zipping the software, you may run ./ld-tools-0.0.1-SNAPSHOT/bin/analyze-gl-strings -h for instructions on how to run the software.

Basic Installation Process from source code:

If you prefer to compile / package the software from source, follow these instructions…

Running a Test Data Set:



2011 NMDP Frequency Install Instructions:

2011 NMDP Frequency Re-Formatting Instructions:

This work is supported by the National Institutes of Health's National Center for Advancing Translational Sciences, Grant Number U24TR002306. This work is solely the responsibility of the creators and does not necessarily represent the official views of the National Institutes of Health.