The allogenomics approach was developed by the Suthanthiran and Campagne laboratories at the Weill Cornell Medical College.

The Allogenomics Scoring Tool is a software that estimates the allogenomics mismatch score, given genotypes for two DNA samples (Mesnard L et al, PeerJPrePrint). We have found that the allogenomics mismatch score correlates with graft function post-transplantation in two cohorts of kidney transplant recipients.  This page provides resources (software and data) associated with the manuscript.

(md5 checksum:

9b1c219573fc9d65c6a47f94039be1d3  allogenomics-1.1.7-scoring-tool.jar)

Usage

The following command line will process an input VCF file to produce scores for each transplant pair:


java -jar allogenomics-1.1.7-scoring-tool.jar -i input.vcf.gz \
 -p pairs-definition.pairs -a protein_coding.gtf \
 -t secreted+transmembrane.tsv -o secreted+transmembrane-scores.tsv
java -jar allogenomics-1.1.7-scoring-tool.jar -—help

will print usage information.

Note that the tool assumes the VCF format was produced with Goby (discover-sequence-variants mode), followed by  annotation with the Variant Effect Predictor. Other VCF format flavors may also be compatible as long as the file includes genotype information and VEP annotations in an INFO field called ‘VariantEffectPrediction’ (see example header file in VCF_files_input/headers.vcf). Goby VCF files can be generated from read files with the NYoSh Analysis Workbench (open-source) or with GobyWeb.

Citation

Exome sequencing, histoincompatibility and long-term kidney allograft function. Laurent Mesnard, Thangamani Muthukumar, Maren Burbach, Carol Li,Huimin Shang, Darshana Dadhania, John R Lee, Vijay K Sharma, Jenny Xiang,John J Friedewald, Michael M Abecassis, Manikkam Suthanthiran​, Fabien Campagne​ [PrePrints: PeerJPrePrint]