Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.

Haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase (LPL) gene was scored in three populations: African-Americans from Jackson, Mississippi (24 individuals), Finns from North Karelia, Finland (24), and non-Hispanic whites from Rochester, Minnesota (23). Earlier an...

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Main Authors: Templeton, A R, Weiss, K M, Nickerson, D A, Boerwinkle, E, Sing, C F
Format: Text
Language:English
Published: 2000
Subjects:
Online Access:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461336
http://www.ncbi.nlm.nih.gov/pubmed/11063700
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spelling ftpubmed:oai:pubmedcentral.nih.gov:1461336 2023-05-15T17:00:23+02:00 Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies. Templeton, A R Weiss, K M Nickerson, D A Boerwinkle, E Sing, C F 2000-11 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461336 http://www.ncbi.nlm.nih.gov/pubmed/11063700 en eng http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461336 http://www.ncbi.nlm.nih.gov/pubmed/11063700 Research Article Text 2000 ftpubmed 2013-08-31T01:31:52Z Haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase (LPL) gene was scored in three populations: African-Americans from Jackson, Mississippi (24 individuals), Finns from North Karelia, Finland (24), and non-Hispanic whites from Rochester, Minnesota (23). Earlier analyses had indicated that recombination was common but concentrated into a hotspot and that recurrent mutations at multiple sites may have occurred. We show that much evolutionary structure exists in the haplotype variation on either side of the recombinational hotspot. By peeling off significant recombination events from a tree estimated under the null hypothesis of no recombination, we also reveal some cladistic structure not disrupted by recombination during the time to coalescence of this variation. Additional cladistic structure is estimated to have emerged after recombination. Many apparent multiple mutational events at sites still remain after removing the effects of the detected recombination/gene conversion events. These apparent multiple events are found primarily at sites identified as highly mutable by previous studies, strengthening the conclusion that they are true multiple events. This analysis portrays the complexity of the interplay among many recombinational and mutational events that would be needed to explain the patterns of haplotype diversity in this gene. The cladistic structure in this region is used to identify four to six single-nucleotide polymorphisms (SNPs) that would provide disequilibrium coverage over much of this region. These sites may be useful in identifying phenotypic associations with variable sites in this gene. Evolutionary considerations also imply that the SNPs in the 3' region should have general utility in most human populations, but the 5' SNPs may be more population specific. Choosing SNPs at random would generally not provide adequate disequilibrium coverage of the sequenced region. Text karelia* PubMed Central (PMC)
institution Open Polar
collection PubMed Central (PMC)
op_collection_id ftpubmed
language English
topic Research Article
spellingShingle Research Article
Templeton, A R
Weiss, K M
Nickerson, D A
Boerwinkle, E
Sing, C F
Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
topic_facet Research Article
description Haplotype variation in 9.7 kb of genomic DNA sequence from the human lipoprotein lipase (LPL) gene was scored in three populations: African-Americans from Jackson, Mississippi (24 individuals), Finns from North Karelia, Finland (24), and non-Hispanic whites from Rochester, Minnesota (23). Earlier analyses had indicated that recombination was common but concentrated into a hotspot and that recurrent mutations at multiple sites may have occurred. We show that much evolutionary structure exists in the haplotype variation on either side of the recombinational hotspot. By peeling off significant recombination events from a tree estimated under the null hypothesis of no recombination, we also reveal some cladistic structure not disrupted by recombination during the time to coalescence of this variation. Additional cladistic structure is estimated to have emerged after recombination. Many apparent multiple mutational events at sites still remain after removing the effects of the detected recombination/gene conversion events. These apparent multiple events are found primarily at sites identified as highly mutable by previous studies, strengthening the conclusion that they are true multiple events. This analysis portrays the complexity of the interplay among many recombinational and mutational events that would be needed to explain the patterns of haplotype diversity in this gene. The cladistic structure in this region is used to identify four to six single-nucleotide polymorphisms (SNPs) that would provide disequilibrium coverage over much of this region. These sites may be useful in identifying phenotypic associations with variable sites in this gene. Evolutionary considerations also imply that the SNPs in the 3' region should have general utility in most human populations, but the 5' SNPs may be more population specific. Choosing SNPs at random would generally not provide adequate disequilibrium coverage of the sequenced region.
format Text
author Templeton, A R
Weiss, K M
Nickerson, D A
Boerwinkle, E
Sing, C F
author_facet Templeton, A R
Weiss, K M
Nickerson, D A
Boerwinkle, E
Sing, C F
author_sort Templeton, A R
title Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
title_short Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
title_full Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
title_fullStr Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
title_full_unstemmed Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies.
title_sort cladistic structure within the human lipoprotein lipase gene and its implications for phenotypic association studies.
publishDate 2000
url http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461336
http://www.ncbi.nlm.nih.gov/pubmed/11063700
genre karelia*
genre_facet karelia*
op_relation http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1461336
http://www.ncbi.nlm.nih.gov/pubmed/11063700
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