Current Bioinformatics

Yi-Ping Phoebe Chen
Department of Computer Science and Information Technology
La Trobe University
Melbourne
Australia

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MASS KIR Analyzer: An In Silico Approach for Analyzing the Killer Immunoglobulin Receptor Gene Content and its Diversity

Author(s): Manmohan Pandey, Aditya Narayan Sarangi, Swayam Prakash, Suraksha Agrawal.

Abstract:

Introduction: This is a first study where user friendly software (MASS KIR Analyzer) has been presented to analyze the Killer Immunoglobulin-like receptors (KIR) gene content diversity. The main objective of this software is to generate error free KIR genotyping data.

Materials and Methods: The MASSKIR Analyzer accepts KIR genotyping data in binary format. It has the potential to determine KIR genotype, haplotype and linkage group frequencies and assignment of genotypic ID for each KIR profile as suggested by the Allele Frequency Net database. The software includes linkage disequilibrium analysis based on Lewontin, Mattiuz and Cramer’s V statistic’s principle. Genotype, haplotype and linkage group modules of the software were validated based on KIR genotyping data (n=12,481) available at the Allele Frequency Net database. Genetic distance and heatmap modules of the software were validated based on KIR data (n=976) from the Human Genome Diversity Project-Centre d'Etude du Polymorphisme Humain (HGDP-CEPH) database.

Results: The MASS KIR Analyzer software detected 225 genotypic errors in the KIR dataset reported to the Allele Frequency Net database. The Linkage Disequilibrium analysis revealed negative linkage disequilibrium between KIR3DS1-3DL1(p=<0.001) and KIR2DL2-2DL1(p=<0.001) genes and positive linkage disequilibrium between KIR2DS2-2DL2 (p=<0.001) genes. Genetic distances calculated for the HGDP-CEPH KIR populations, revealed similar results in lieu of published data for clustered heatmap. This validated proper functioning of the software for KIR data analysis.

Conclusion: The MASSKIR Analyzer is a promising software for KIR biologists and may significantly improve the KIR genotyping without errors.

Keywords: Genetic distance, killer immunoglobuliN-like receptors (KIR), KIR genotype, KIR haplotype, KIR linkage group, linkage disequilibrium.

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Article Details

VOLUME: 10
ISSUE: 3
Year: 2015
Page: [292 - 298]
Pages: 7
DOI: 10.2174/1574893609999140918200855
Price: $58