PMID- 18601964
OWN - NLM
STAT- MEDLINE
DCOM- 20081009
LR  - 20080818
IS  - 0198-8859 (Print)
IS  - 0198-8859 (Linking)
VI  - 69
IP  - 8
DP  - 2008 Aug
TI  - SKDM human leukocyte antigen (HLA) tool: A comprehensive HLA and disease 
      associations analysis software.
PG  - 522-5
LID - 10.1016/j.humimm.2008.05.011 [doi]
AB  - 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.
FAU - Kanterakis, Stathis
AU  - Kanterakis S
AD  - 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.
FAU - Magira, Eleni
AU  - Magira E
FAU - Rosenman, Kenneth D
AU  - Rosenman KD
FAU - Rossman, Milton
AU  - Rossman M
FAU - Talsania, Keyur
AU  - Talsania K
FAU - Monos, Dimitri S
AU  - Monos DS
LA  - eng
PT  - Journal Article
PT  - Research Support, U.S. Gov't, P.H.S.
DEP - 20080702
PL  - United States
TA  - Hum Immunol
JT  - Human immunology
JID - 8010936
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Alleles
MH  - *Genetic Predisposition to Disease
MH  - HLA Antigens/*genetics
MH  - Humans
MH  - *Software
EDAT- 2008/07/08 09:00
MHDA- 2008/10/10 09:00
CRDT- 2008/07/08 09:00
PHST- 2008/03/24 00:00 [received]
PHST- 2008/05/23 00:00 [revised]
PHST- 2008/05/29 00:00 [accepted]
PHST- 2008/07/08 09:00 [pubmed]
PHST- 2008/10/10 09:00 [medline]
PHST- 2008/07/08 09:00 [entrez]
AID - S0198-8859(08)00091-8 [pii]
AID - 10.1016/j.humimm.2008.05.011 [doi]
PST - ppublish
SO  - Hum Immunol. 2008 Aug;69(8):522-5. doi: 10.1016/j.humimm.2008.05.011. Epub 2008 
      Jul 2.