Construction and analysis of sequence-based integrated maps
Construction and analysis of sequence-based integrated maps
The “finished” human genome sequence, transition from positional cloning of major genes by linkage to genes which predispose to common disorder by linkage disequilibrium, and wealth of genomic information available on the internet have prompted revision of the location database (LDB). An automated bioinformatic method of producing sequence-based integrated maps has been developed and used to create maps of all autosomal chromosomes. As a result, the location database (LDB2000) contains a more comprehensive set of markers that are classified by type and represented by HUGO approved symbols where possible or the next most appropriate symbol. The alias system has been improved and sequence based information has been incorporated so that physical locations are relative to the nearest base-pair. The presentation and interrogation of the database via the website has also been updated. As a result, the location database (LDB2000) has a continuing role in disease gene mapping, the understanding of chromosome organisation and recombination.
Given the correct order and more informative data, the resolution and accuracy of the linkage maps has been improved so that recombination hot-spots are resolved with more confidence. These maps identify regional differences in recombination so that the genome can be subdivided into recombination hot and cold spots leading to speculation that recombination may be influenced by sequence characteristics. Four sequence features (G+C content, SINEs, LINEs and GT/CA repeats) were found to explain 17% of the variance with sex-averaged rates of recombination. The distribution and intensity of recombination is markedly different between the sexes with females having a recombination rate that is 1.65 times higher than males although there are regions of the genome, such as telomeres, where the recombination rate is particularly high in men and low in women and vice versa. This demonstrates that, in the absence of any known sex-specific sequence differences, other epigenetic factors such as replication timing, chromatin structure and histone modification contribute to the determination of recombination rate where the sequence is essentially the same.
University of Southampton
Tapper, William
b261d71e-497e-4aea-862a-d2bb397af7c3
2004
Tapper, William
b261d71e-497e-4aea-862a-d2bb397af7c3
Tapper, William
(2004)
Construction and analysis of sequence-based integrated maps.
University of Southampton, Doctoral Thesis.
Record type:
Thesis
(Doctoral)
Abstract
The “finished” human genome sequence, transition from positional cloning of major genes by linkage to genes which predispose to common disorder by linkage disequilibrium, and wealth of genomic information available on the internet have prompted revision of the location database (LDB). An automated bioinformatic method of producing sequence-based integrated maps has been developed and used to create maps of all autosomal chromosomes. As a result, the location database (LDB2000) contains a more comprehensive set of markers that are classified by type and represented by HUGO approved symbols where possible or the next most appropriate symbol. The alias system has been improved and sequence based information has been incorporated so that physical locations are relative to the nearest base-pair. The presentation and interrogation of the database via the website has also been updated. As a result, the location database (LDB2000) has a continuing role in disease gene mapping, the understanding of chromosome organisation and recombination.
Given the correct order and more informative data, the resolution and accuracy of the linkage maps has been improved so that recombination hot-spots are resolved with more confidence. These maps identify regional differences in recombination so that the genome can be subdivided into recombination hot and cold spots leading to speculation that recombination may be influenced by sequence characteristics. Four sequence features (G+C content, SINEs, LINEs and GT/CA repeats) were found to explain 17% of the variance with sex-averaged rates of recombination. The distribution and intensity of recombination is markedly different between the sexes with females having a recombination rate that is 1.65 times higher than males although there are regions of the genome, such as telomeres, where the recombination rate is particularly high in men and low in women and vice versa. This demonstrates that, in the absence of any known sex-specific sequence differences, other epigenetic factors such as replication timing, chromatin structure and histone modification contribute to the determination of recombination rate where the sequence is essentially the same.
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Published date: 2004
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Local EPrints ID: 465310
URI: http://eprints.soton.ac.uk/id/eprint/465310
PURE UUID: 36ec2873-68d8-479a-b287-615ae85d6337
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Date deposited: 05 Jul 2022 00:37
Last modified: 23 Jul 2022 01:13
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Author:
William Tapper
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