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Enhanced genetic maps from family-based disease studies: Population-specific comparisons

He, C and Weeks, DE and Buyske, S and Abecasis, GR and Stewart, WC and Matise, TC (2011) Enhanced genetic maps from family-based disease studies: Population-specific comparisons. BMC Medical Genetics, 12.

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Abstract

Background: Accurate genetic maps are required for successful and efficient linkage mapping of disease genes. However, most available genome-wide genetic maps were built using only small collections of pedigrees, and therefore have large sampling errors. A large set of genetic studies genotyped by the NHLBI Mammalian Genotyping Service (MGS) provide appropriate data for generating more accurate maps.Results: We collected a large sample of uncleaned genotype data for 461 markers generated by the MGS using the Weber screening sets 9 and 10. This collection includes genotypes for over 4,400 pedigrees containing over 17,000 genotyped individuals from different populations. We identified and cleaned numerous relationship and genotyping errors, as well as verified the marker orders. We used this dataset to test for population-specific genetic maps, and to re-estimate the genetic map distances with greater precision; standard errors for all intervals are provided. The map-interval sizes from the European (or European descent), Chinese, and Hispanic samples are in quite good agreement with each other. We found one map interval on chromosome 8p with a statistically significant size difference between the European and Chinese samples, and several map intervals with significant size differences between the African American and Chinese samples. When comparing Palauan with European samples, a statistically significant difference was detected at the telomeric region of chromosome 11p. Several significant differences were also identified between populations in chromosomal and genome lengths.Conclusions: Our new population-specific screening set maps can be used to improve the accuracy of disease-mapping studies. As a result of the large sample size, the average length of the 95% confidence interval (CI) for a 10 cM map interval is only 2.4 cM, which is considerably smaller than on previously published maps. © 2011 He et al; licensee BioMed Central Ltd.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
He, C
Weeks, DEweeks@pitt.eduWEEKS0000-0001-9410-7228
Buyske, S
Abecasis, GR
Stewart, WC
Matise, TC
Date: 19 January 2011
Date Type: Publication
Journal or Publication Title: BMC Medical Genetics
Volume: 12
DOI or Unique Handle: 10.1186/1471-2350-12-15
Schools and Programs: Graduate School of Public Health > Biostatistics
Graduate School of Public Health > Human Genetics
Refereed: Yes
Date Deposited: 16 Nov 2016 18:48
Last Modified: 02 Feb 2019 14:56
URI: http://d-scholarship.pitt.edu/id/eprint/30191

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