HLAminer

Derivation of HLA class I and II predictions from shotgun sequence datasets

Project Description

HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads.

 

It has been used successfully to predict expressed HLA genes in the large TCGA (The Cancer Genome Atlas) cancer cohort. 

HLAminer uses TASR as its main assembly engine, which in turn is derived from SSAKE, the first de novo genome assembler published. A manuscript describing the methodology is published in the peer-reviewed journal Genome Medicine.

 

About the author: www.renewarren.ca

 

Targeted assembly: The HLA prediction by targeted assembly of short sequence reads performs targeted de novo assembly of HLA NGS reads and align them to reference HLA alleles from the IMGT/HLA sequence repository using commodity hardware with standard specifications (2GB RAM, 2GHz). This short clip shows the process: https://www.youtube.com/watch?v=j-g8Geh5ST8

 Read alignment: The HLA prediction from direct read alignment method is conceptually simpler and faster to execute, since paired reads are aligned up-front to reference HLA alleles. However, the HLA allele detection sensitivity and specificity from this method is currently (100nt paired reads) lower than from targeted HLA assembly.

 *Alignments from both methods are processed by HLAminer to derive HLA class I and II predictions by scoring and evaluating the probability of each candidate allele bearing alignments.

 

If you use HLAminer in your research, please cite:

 

Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, Holt RA.  2012. Derivation of HLA types from shotgun sequence datasets. Genome Med. 4:95.