#RLW 2013

File description:


HLAminer_GenomeMedicine2012_additionalfiles.tar.gz

Contains supplemental material associated with the CRC dataset and supporting
data presented in Warren et al 2012 (Genome Medicine 4:95) available for
download (public access) at: http://genomemedicine.com/content/4/12/95


The tar ball comprises these additional files:

Additional File 1:  HLAminer performance. HLA allele group and protein coding
allele predictions derived from targeted read assembly or direct read
alignment of simulated 100nt RNA-Seq, WGS and exon capture datasets were
compared to original, spiked-in, HLA sequences and performance metrics
(sensitivity, specificity and ambiguity) evaluated.  HLAminer predictions also
obtained from targeted assembly of colorectal cancer (CRC), lymphoma (DLBCL),
1000 Genomes and ovarian cancer  patient tumor and/or matched normal shotgun
datasets and compared to PCR-based HLA types to calculate performance metrics.

Additional File 2:  HLA class I allele predictions obtained by running
HLAminer on the RNA-Seq data of 16 CRC patients compared to those obtained by
PCR.

Additional File 3:  HLA class I allele predictions obtained by running
HLAminer on 1000 Genomes low-coverage WGS data from 20 HapMap subjects
compared to PCR-based predictions from Erlich and colleagues (2011) [9].


SRP0010181_CRC_info.txt

Description of the sample libraries for the CRC NGS sequence data submitted
to the Sequence Read Archive at accession SRP0010181