PMID- 19933168
OWN - NLM
STAT- MEDLINE
DCOM- 20100329
LR  - 20211020
IS  - 1460-2083 (Electronic)
IS  - 0964-6906 (Print)
IS  - 0964-6906 (Linking)
VI  - 19
IP  - 4
DP  - 2010 Feb 15
TI  - Novel sequence feature variant type analysis of the HLA genetic association in 
      systemic sclerosis.
PG  - 707-19
LID - 10.1093/hmg/ddp521 [doi]
AB  - We describe a novel approach to genetic association analyses with proteins 
      sub-divided into biologically relevant smaller sequence features (SFs), and their 
      variant types (VTs). SFVT analyses are particularly informative for study of 
      highly polymorphic proteins such as the human leukocyte antigen (HLA), given the 
      nature of its genetic variation: the high level of polymorphism, the pattern of 
      amino acid variability, and that most HLA variation occurs at functionally 
      important sites, as well as its known role in organ transplant rejection, 
      autoimmune disease development and response to infection. Further, combinations 
      of variable amino acid sites shared by several HLA alleles (shared epitopes) are 
      most likely better descriptors of the actual causative genetic variants. In a 
      cohort of systemic sclerosis patients/controls, SFVT analysis shows that a 
      combination of SFs implicating specific amino acid residues in peptide binding 
      pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk.
FAU - Karp, David R
AU  - Karp DR
AD  - Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX 
      75390-8884, USA. david.karp@utsouthwestern.edu
FAU - Marthandan, Nishanth
AU  - Marthandan N
FAU - Marsh, Steven G E
AU  - Marsh SG
FAU - Ahn, Chul
AU  - Ahn C
FAU - Arnett, Frank C
AU  - Arnett FC
FAU - Deluca, David S
AU  - Deluca DS
FAU - Diehl, Alexander D
AU  - Diehl AD
FAU - Dunivin, Raymond
AU  - Dunivin R
FAU - Eilbeck, Karen
AU  - Eilbeck K
FAU - Feolo, Michael
AU  - Feolo M
FAU - Guidry, Paula A
AU  - Guidry PA
FAU - Helmberg, Wolfgang
AU  - Helmberg W
FAU - Lewis, Suzanna
AU  - Lewis S
FAU - Mayes, Maureen D
AU  - Mayes MD
FAU - Mungall, Chris
AU  - Mungall C
FAU - Natale, Darren A
AU  - Natale DA
FAU - Peters, Bjoern
AU  - Peters B
FAU - Petersdorf, Effie
AU  - Petersdorf E
FAU - Reveille, John D
AU  - Reveille JD
FAU - Smith, Barry
AU  - Smith B
FAU - Thomson, Glenys
AU  - Thomson G
FAU - Waller, Matthew J
AU  - Waller MJ
FAU - Scheuermann, Richard H
AU  - Scheuermann RH
LA  - eng
GR  - P50 AR054144-020001/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-010001/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-02/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-040001/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-04S1/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-03S1/AR/NIAMS NIH HHS/United States
GR  - N01-AI40076/AI/NIAID NIH HHS/United States
GR  - P50 AR054144-04/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-05/AR/NIAMS NIH HHS/United States
GR  - UL1 RR024148-02/RR/NCRR NIH HHS/United States
GR  - P50 AR054144/AR/NIAMS NIH HHS/United States
GR  - N01-AR02251/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-025826/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-019001/AR/NIAMS NIH HHS/United States
GR  - P50-AR054144/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-01/AR/NIAMS NIH HHS/United States
GR  - UL1 RR024148-010004/RR/NCRR NIH HHS/United States
GR  - UL1 RR024982/RR/NCRR NIH HHS/United States
GR  - UL1 RR024148-027759/RR/NCRR NIH HHS/United States
GR  - UL1 RR024148/RR/NCRR NIH HHS/United States
GR  - P50 AR054144-030001/AR/NIAMS NIH HHS/United States
GR  - UL1-RR024982/RR/NCRR NIH HHS/United States
GR  - UL1-RR024148/RR/NCRR NIH HHS/United States
GR  - UL1 RR024148-01/RR/NCRR NIH HHS/United States
GR  - R01 AR055258/AR/NIAMS NIH HHS/United States
GR  - P50 AR054144-03/AR/NIAMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20091118
PL  - England
TA  - Hum Mol Genet
JT  - Human molecular genetics
JID - 9208958
RN  - 0 (HLA Antigens)
RN  - 0 (HLA-DR Antigens)
RN  - 0 (HLA-DRB1 Chains)
SB  - IM
MH  - *Genetic Variation
MH  - HLA Antigens/chemistry/*genetics
MH  - HLA-DR Antigens/chemistry/genetics
MH  - HLA-DRB1 Chains
MH  - Humans
MH  - Molecular Conformation
MH  - Scleroderma, Systemic/*genetics
PMC - PMC2807365
EDAT- 2009/11/26 06:00
MHDA- 2010/03/30 06:00
PMCR- 2011/02/15
CRDT- 2009/11/26 06:00
PHST- 2009/11/26 06:00 [entrez]
PHST- 2009/11/26 06:00 [pubmed]
PHST- 2010/03/30 06:00 [medline]
PHST- 2011/02/15 00:00 [pmc-release]
AID - ddp521 [pii]
AID - 10.1093/hmg/ddp521 [doi]
PST - ppublish
SO  - Hum Mol Genet. 2010 Feb 15;19(4):707-19. doi: 10.1093/hmg/ddp521. Epub 2009 Nov 
      18.