ISCID News Editor
Moderator
Member # 1417
|
posted 03. January 2006 09:46
Source: Nature Genetics
Letter
Nature Genetics 38, 82 - 85 (2006)
Published online: 4 December 2005; | doi:10.1038/ng1695
Common deletions and SNPs^ are in linkage disequilibrium in the human genome^
David A Hinds, Andrew P Kloek1, Michael Jen, Xiyin Chen & Kelly A Frazer
These authors contributed equally to this work.
Correspondence should be addressed to Kelly A Frazer kelly_frazer@perlegen.com
From Paragraph 11
Our platform enables us to evaluate most unique sequences in the human genome^ : we can amplify nearly 94% of all human sequences and examine even short stretches ( 60 bp) of relatively non-redundant sequence flanked by repetitive elements. Thus, we have effectively queried a representative fraction of the nonrepetitive sequence in the human genome and consider that the properties of the set of intermediate-length deletions identified in our study are representative of deletions in typical genomic contexts. Notably, unusual local sequence structures exist across the genome that create regions of genomic instability and result in recurrent rearrangements. For example, large (>10 kb) insertion/deletion polymorphisms associated with local duplications (sharing >95% identity and separated by 50 kb to 10 Mb) result from recurrent events [references in original]. These large rearrangements are responsible for several known human disorders and may complicate the interpretation of SNP-based association studies... [Single Nucleotide Polymorphisms]
Paragraph 12
The set of common intermediate-length deletions identified here has linkage disequilibrium patterns similar to SNPs, indicating that these polymorphisms share a similar evolutionary history and suggesting that most intermediate-length deletions, like SNPs, arose once in human history. High linkage disequilibrium with nearby SNPs suggests that most of these deletions are effectively assayed^ by proxy in SNP-based association studies, consistent with previous results for short insertion/deletion polymorphisms. On the basis of the fraction of the genome examined and the technical limits of our study, we estimate there are several thousand intermediate insertion/deletion polymorphisms in the human genome, suggesting that they represent an important component of common genetic variation and are likely to contribute to phenotypic variation in complex traits.
Read full letter from researchers at Nature Genetics
[Emphases added by ISCID News Editor]
[Link-underlined terms with ^ indicate linked entry in ISCID Encyclopedia of Science and Philosophy as added by ISCID News Editor]
[ 03. January 2006, 09:47: Message edited by: ISCID News Editor ]
IP: Logged
|
Printer-friendly view of this topic