title: SKDM human leukocyte antigen (HLA) tool: A comprehensive HLA and disease associations analysis software.
abstract: The immensely polymorphic and gene-rich landscape of the major histocompatibility complex on chromosome 6 necessitates a thorough and consistent investigation of its constituting elements. The human leukocyte antigens (HLAs) are an example of such polymorphic elements, implicated in many immune-based diseases. So far, analyses of HLA molecules in the context of diseases have been ad hoc, frequently incomplete, and extremely cumbersome. SKDM provides a comprehensive and automated workflow for detecting and dissecting HLA associations in diseases. We created a Java application to consistently perform our proposed method of analysis of HLAs in case-control datasets. The SKDM HLA tool can test for HLA allele differences between two populations and, by retrieving amino acid sequences, evaluates each polymorphic amino acid residue or a pocket of amino acids as an independent variant. Once primary associations are identified, the program examines zygosity and tests for strongest association, interaction, and linkage disequilibrium among amino acid epitopes of the same HLA molecule or between HLA isotypes. A summary of the analysis is output in plain language. The software and a user's manual are freely available at http://sourceforge.net/projects/skdm.
authors.affiliation: Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, and Department of Pediatrics, University of Pennsylvania, School of Medicine, Philadelphia, PA, USA.
authors.forename: Stathis
authors.initials: S
authors.lastname: Kanterakis
authors.forename: Eleni
authors.initials: E
authors.lastname: Magira
authors.forename: Kenneth D
authors.initials: KD
authors.lastname: Rosenman
authors.forename: Milton
authors.initials: M
authors.lastname: Rossman
authors.forename: Keyur
authors.initials: K
authors.lastname: Talsania
authors.forename: Dimitri S
authors.initials: DS
authors.lastname: Monos
mesh_terms: D000483:Alleles; D020022:Genetic Predisposition to Disease; D006680:HLA Antigens / Q000235:genetics*; D006801:Humans; D012984:Software
chemical_list: D006680:HLA Antigens