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United States Department of Agriculture

Agricultural Research Service

Research Project: RESOURCE DEVELOPMENT FACILITATING BOVINE GENOME SEQUENCE USE TO IMPROVE CATTLE PRODUCTION EFFICIENCY, PRODUCT QUALITY & ENVIRONMENTAL IMPACT Title: A Multiway Analysis for Identifying High Integrity Bovine BACs

Authors
item Ratnakumar, Abhirami -
item Barris, Wesley -
item Mcwilliam, Sean -
item Brauning, Rudiger -
item Mcewan, John -
item Snelling, Warren
item Dalrymple, Brian -

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 23, 2009
Publication Date: January 23, 2009
Repository URL: http://biomedcentral.com/content/pdf/1471-2164-10-46.pdf
Citation: Ratnakumar, A., Barris, W., McWilliam, S., Brauning, R., McEwan, J.C., Snelling, W.M., Dalrymple, B.P. 2009. A Multiway Analysis for Identifying High Integrity Bovine BACs. Biomed Central (BMC) Genomics. 10:46 (13 pp).

Interpretive Summary: Large genomics projects such as that undertaken by the International Bovine BAC Mapping Consortium (IBBMC) require work on a common set of biological samples to be distributed across several laboratories. Despite automated pipelines and other steps to ensure integrity of samples, such as bacterial artificial chromosome (BAC) clones, various errors may occur in processing and distribution so sample identity can become inconsistent. This research developed BAC fingerprint map and end sequence-based rules to determine BAC clones that may have been misidentified. Error rate among clones with complete data included in the IBBMC project appears to be less than 5%; problematic clones were identified for removal from further research. The methodology developed is applicable to checking integrity of BAC-based datasets used for genomic sequence assembly.

Technical Abstract: In large genomics projects involving many different types of analyses of bacterial artificial chromosomes (BACs), such as fingerprinting, end sequencing (BES) and full BAC sequencing there are many opportunities for the identities of BACs to become confused. However, by comparing the results from the different analyses, inconsistencies can be identified and a set of high integrity BACs preferred for future research can be defined. The location of each bovine BAC in the BAC fingerprint-based genome map and in the genome assembly were compared based on the reported BESs, and for a smaller number of BACs the full sequence. Inconsistencies between BES-based and fingerprint map positions identified thirty-one plates from the CHORI-240 library that appear to have suffered substantial systematic problems during the end-sequencing of the BACs. No systematic problems were identified in the fingerprinting of the BACs. Our analysis shows that ~95% of the bovine CHORI-240 library clones with both a BAC fingerprint and two BESs mapping to the genome in the expected orientations (~27% of all BACs) have consistent locations in the BAC fingerprint map and the genome assembly. We have developed a broadly applicable methodology for checking the integrity of BAC-based datasets even where only incomplete and partially assembled genomic sequence is available.

Last Modified: 12/19/2014
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