An SNP linkage scan identifies significant Crohn's disease loci on chromosomes 13q13.3 and, in Jewish families, on 1p35.2 and 3q29. Shugart, Y., Y., Silverberg, M., S., Duerr, R., H., Taylor, K., D., Wang, M., Zarfas, K., Schumm, L., P., Bromfield, G., Steinhart, A., H., Griffiths, A., M., Kane, S., V., Barmada, M., M., Rotter, J., I., Mei, L., Bernstein, C., N., Bayless, T., M., Langelier, D., Cohen, A., Bitton, A., Rioux, J., D., Cho, J., H., & Brant, S., R. Genes and immunity, 9(2):161-7, 3, 2008.
An SNP linkage scan identifies significant Crohn's disease loci on chromosomes 13q13.3 and, in Jewish families, on 1p35.2 and 3q29. [link]Website  abstract   bibtex   
Inflammatory bowel disease (IBD) is a complex genetic disorder of two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC), with increased risk in Ashkenazi Jews. Twelve genome-wide linkage screens have identified multiple loci, but these screens have been of modest size and have used low-density microsatellite markers. We, therefore, performed a high-density single-nucleotide polymorphism (SNP) genome-wide linkage study of 993 IBD multiply affected pedigrees (25% Jewish ancestry) that contained 1709 IBD-affected relative pairs, including 919 CD-CD pairs and 312 UC-UC pairs. We identified a significant novel CD locus on chromosome 13p13.3 (peak logarithm of the odds (LOD) score=3.98) in all pedigrees, significant linkage evidence on chromosomes 1p35.1 (peak LOD score=3.5) and 3q29 (peak LOD score=3.19) in Jewish CD pedigrees, and suggestive loci for Jewish IBD on chromosome 10q22 (peak LOD score=2.57) and Jewish UC on chromosome 2q24 (peak LOD score=2.69). Nominal or greater linkage evidence was present for most previously designated IBD loci (IBD1-9), notably, IBD1 for CD families at chromosome 16q12.1 (peak LOD score=4.86) and IBD6 in non-Jewish UC families at chromosome 19p12 (peak LOD score=2.67). This study demonstrates the ability of high information content adequately powered SNP genome-wide linkage studies to identify loci not observed in multiple microsatellite-based studies in smaller cohorts.
@article{
 title = {An SNP linkage scan identifies significant Crohn's disease loci on chromosomes 13q13.3 and, in Jewish families, on 1p35.2 and 3q29.},
 type = {article},
 year = {2008},
 identifiers = {[object Object]},
 keywords = {Chromosomes,Colitis,Crohn Disease,Crohn Disease: epidemiology,Crohn Disease: genetics,Female,Genetic Linkage,Genetic Linkage: genetics,Genetic Markers,Genetic Markers: genetics,Human,Humans,Jews,Jews: genetics,Lod Score,Male,Pair 1,Pair 13,Pair 13: genetics,Pair 1: genetics,Pair 3,Pair 3: genetics,Pedigree,Polymorphism,Quantitative Trait Loci,Quantitative Trait Loci: genetics,Single Nucleotide,Single Nucleotide: genetics,Ulcerative,Ulcerative: epidemiology,Ulcerative: genetics},
 pages = {161-7},
 volume = {9},
 websites = {http://www.ncbi.nlm.nih.gov/pubmed/18246054,http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC3858857},
 month = {3},
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 accessed = {2013-08-24},
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 last_modified = {2018-01-08T01:10:48.205Z},
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 abstract = {Inflammatory bowel disease (IBD) is a complex genetic disorder of two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC), with increased risk in Ashkenazi Jews. Twelve genome-wide linkage screens have identified multiple loci, but these screens have been of modest size and have used low-density microsatellite markers. We, therefore, performed a high-density single-nucleotide polymorphism (SNP) genome-wide linkage study of 993 IBD multiply affected pedigrees (25% Jewish ancestry) that contained 1709 IBD-affected relative pairs, including 919 CD-CD pairs and 312 UC-UC pairs. We identified a significant novel CD locus on chromosome 13p13.3 (peak logarithm of the odds (LOD) score=3.98) in all pedigrees, significant linkage evidence on chromosomes 1p35.1 (peak LOD score=3.5) and 3q29 (peak LOD score=3.19) in Jewish CD pedigrees, and suggestive loci for Jewish IBD on chromosome 10q22 (peak LOD score=2.57) and Jewish UC on chromosome 2q24 (peak LOD score=2.69). Nominal or greater linkage evidence was present for most previously designated IBD loci (IBD1-9), notably, IBD1 for CD families at chromosome 16q12.1 (peak LOD score=4.86) and IBD6 in non-Jewish UC families at chromosome 19p12 (peak LOD score=2.67). This study demonstrates the ability of high information content adequately powered SNP genome-wide linkage studies to identify loci not observed in multiple microsatellite-based studies in smaller cohorts.},
 bibtype = {article},
 author = {Shugart, Y Y and Silverberg, M S and Duerr, R H and Taylor, K D and Wang, M-H and Zarfas, K and Schumm, L. Philip and Bromfield, G and Steinhart, A H and Griffiths, A M and Kane, S V and Barmada, M M and Rotter, J I and Mei, L and Bernstein, C N and Bayless, T M and Langelier, D and Cohen, A and Bitton, A and Rioux, J D and Cho, J H and Brant, S R},
 journal = {Genes and immunity},
 number = {2}
}

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