Dataset Information

The map problem: a comparison of genetic and sequence-based physical maps.

ABSTRACT: The genetic order of autosomal genome-scan markers from Marshfield panels 9 and 10 were compared with their physical order, on the basis of the assembled nonredundant human genome sequence from the Human Genome Project-Santa Cruz (HGP-sc; October 2000 and April 2001 releases) and Celera (CEL; February 2001 release) databases. The genetic order of 96% of the markers on the Marshfield map for panel 10 is supported by a likelihood ratio of > or = 3 (odds ratio of 1,000:1). Inconsistencies with the genetic panel 10 map were found for 5% and 2% of the markers in the CEL and HGP-sc sequences, respectively. These inconsistencies consisted of both positional and chromosomal-assignment disagreements. For the majority of these inconsistent markers, the genetic order was supported by a likelihood ratio of > or = 3, and the physical order in the other assembly matched the genetic order. The majority of the inconsistencies between the physical- and genetic-map order point to errors in the physical-map order. A Web site is made available that displays inconsistencies for genetic markers from Marshfield panels 9 and 10 between their genetic-map positions and sequence-based physical-map positions, as well as inconsistencies between their sequence-based physical position. This Web site also contains genetic-map distances, physical-map positions from the Celera and Human Genome Project sequence, and likelihood-ratio support for the genetic maps.

SUBMITTER: DeWan AT

PROVIDER: S-EPMC384881 | biostudies-literature | 2002 Jan

REPOSITORIES: biostudies-literature

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The map problem: a comparison of genetic and sequence-based physical maps.

DeWan Andrew T AT Parrado Antonio R AR Matise Tara C TC Leal Suzanne M SM

American journal of human genetics 20011109 1

The genetic order of autosomal genome-scan markers from Marshfield panels 9 and 10 were compared with their physical order, on the basis of the assembled nonredundant human genome sequence from the Human Genome Project-Santa Cruz (HGP-sc; October 2000 and April 2001 releases) and Celera (CEL; February 2001 release) databases. The genetic order of 96% of the markers on the Marshfield map for panel 10 is supported by a likelihood ratio of > or = 3 (odds ratio of 1,000:1). Inconsistencies with the ...[more]

PMID: 11706388

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Dataset Information

The map problem: a comparison of genetic and sequence-based physical maps.

Publications

The map problem: a comparison of genetic and sequence-based physical maps.

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