Linked Life Data

16451599

Source:http://linkedlifedata.com/resource/pubmed/id/16451599

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:dateCreated
2010-1-19
pubmed:abstractText
Recent studies have suggested that a high-density single nucleotide polymorphism (SNP) marker set could provide equivalent or even superior information compared with currently used microsatellite (STR) marker sets for gene mapping by linkage. The focus of this study was to compare results obtained from linkage analyses involving extended pedigrees with STR and single-nucleotide polymorphism (SNP) marker sets. We also wanted to compare the performance of current linkage programs in the presence of high marker density and extended pedigree structures. One replicate of the Genetic Analysis Workshop 14 (GAW14) simulated extended pedigrees (n = 50) from New York City was analyzed to identify the major gene D2. Four marker sets with varying information content and density on chromosome 3 (STR [7.5 cM]; SNP [3 cM, 1 cM, 0.3 cM]) were analyzed to detect two traits, the original affection status, and a redefined trait more closely correlated with D2. Multipoint parametric and nonparametric linkage analyses (NPL) were performed using programs GENEHUNTER, MERLIN, SIMWALK2, and S.A.G.E. SIBPAL. Our results suggested that the densest SNP map (0.3 cM) had the greatest power to detect linkage for the original trait (genetic heterogeneity), with the highest LOD score/NPL score and mapping precision. However, no significant improvement in linkage signals was observed with the densest SNP map compared with STR or SNP-1 cM maps for the redefined affection status (genetic homogeneity), possibly due to the extremely high information contents for all maps. Finally, our results suggested that each linkage program had limitations in handling the large, complex pedigrees as well as a high-density SNP marker set.
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-11731797, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-11921081, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-15060841, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-15154113, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-15514889, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-15818627, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-6587361, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-8056435, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-8317490, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-8651310, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-8651312, http://linkedlifedata.com/resource/pubmed/commentcorrection/16451599-9288093
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:issn
1471-2156
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
6 Suppl 1
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
S14
pubmed:dateRevised
2010-9-20
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
Linkage analysis of the GAW14 simulated dataset with microsatellite and single-nucleotide polymorphism markers in large pedigrees.
pubmed:affiliation
Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA. royang@mail.nih.gov
pubmed:publicationType
Journal Article