Linked Life Data

11528504

Source:http://linkedlifedata.com/resource/pubmed/id/11528504

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
8
pubmed:dateCreated
2001-8-30
pubmed:abstractText
We present a dense STR/linkage disequilibrium(LD)/gene map between the RING3 and HLA-B loci, reference allelic sizes on the most prevalent HLA haplotypes and their allelic frequencies in pedigree founders. This resource will facilitate LD, evolution and gene mapping studies, including comparisons of HLA and STR haplotypes and identification of HLA recombinants. The map was constructed by testing novel and previously reported STRs using a panel of 885 individuals in 211 families and 60 DNA samples from cell lines and bone marrow donors homozygous in the HLA-A, -B and -DR loci selected from over 15 000 entries into the registry of Swedish bone marrow donors. We have also analysed the variability of STR alleles/haplotypes on the most prevalent HLA haplotypes to identify STRs useful for fine mapping of disease genes in the region previously implicated in susceptibility to many disorders. The analysis of 40 HLA-A*01, B*0801, DRB1*03011, DQB1*0201 haplotypes in homozygous donors showed a surprising stability in 23 STRs between the class II recombination hot spot and HLA-B, with the average of 1.9% (16/838) variant alleles. However, 40% variant alleles were found at the D6S2670 locus in intron 19 of the tenascin-X gene both in the families and homozygous donors. The nucleotide sequence analysis of this STR showed a complex polymorphism consisting of tetra- (CTTT)(8-18) and penta-nucleotide (CTTTT)(1-2) repeats, separated by an intervening non-polymorphic sequence of 42 bp. The HLA-A1, B*0801, DRB1*03011, DQB1*0201 haplotypes had five (CTTT)(14-18)/(CTTTT)(2) variants with a predominant (CTTT)(16) allele, implicating the tetranucleotide component as the source of this ancestral haplotype diversification, which may be due to the location of D6S2670 in the region of the highest GC content in the human MHC.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1018-4813
pubmed:author
pubmed:issnType
Print
pubmed:volume
9
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
590-8
pubmed:dateRevised
2011-11-17
pubmed:meshHeading
pubmed-meshheading:11528504-Centromere, pubmed-meshheading:11528504-Chromosome Mapping, pubmed-meshheading:11528504-Gene Order, pubmed-meshheading:11528504-Genetic Markers, pubmed-meshheading:11528504-Genetic Variation, pubmed-meshheading:11528504-HLA-A1 Antigen, pubmed-meshheading:11528504-HLA-B8 Antigen, pubmed-meshheading:11528504-HLA-DQ Antigens, pubmed-meshheading:11528504-HLA-DQ beta-Chains, pubmed-meshheading:11528504-HLA-DR Antigens, pubmed-meshheading:11528504-HLA-DR3 Antigen, pubmed-meshheading:11528504-HLA-DRB1 Chains, pubmed-meshheading:11528504-Haplotypes, pubmed-meshheading:11528504-Humans, pubmed-meshheading:11528504-Linkage Disequilibrium, pubmed-meshheading:11528504-Major Histocompatibility Complex, pubmed-meshheading:11528504-Protein-Serine-Threonine Kinases, pubmed-meshheading:11528504-Tandem Repeat Sequences
pubmed:year
2001
pubmed:articleTitle
Short tandem repeat (STR) haplotypes in HLA: an integrated 50-kb STR/linkage disequilibrium/gene map between the RING3 and HLA-B genes and identification of STR haplotype diversification in the class III region.
pubmed:affiliation
Department of Biosciences at NOVUM, Karolinska Institute, S-14157 Huddinge, Sweden. igvo@cbt.ki.se
pubmed:publicationType
Journal Article