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Integration of animal linkage and BAC contig maps using overgo hybridization

Romanov, Michael N, Price, Jennifer A, Dodgson, Jerry B (2003) Integration of animal linkage and BAC contig maps using overgo hybridization. Cytogenetic and Genome Research, 102 (1-4). pp. 277-281. ISSN 1424-8581. E-ISSN 1424-859X. (doi:10.1159/000075763) (Access to this publication is currently restricted. You may be able to access a copy if URLs are provided) (KAR id:37564)

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Abstract

The alignment of genome linkage maps, defined primarily by segregation of sequence-tagged site (STS) markers, with BAC contig physical maps and full genome sequences requires high throughput mechanisms to identify BAC clones that contain specific STS. A powerful technique for this purpose is multi-dimensional hybridization of "overgo" probes. The probes are chosen from available STS sequence data by selecting unique probe sequences that have a common melting temperature. We have hybridized sets of 216 overgo probes in subset pools of 36 overgos at a time to filter-spotted chicken BAC clone arrays. A four-dimensional pooling strategy, including one degree of redundancy, has been employed. This requires 24 hybridizations to completely assign BACs for all 216 probes. Results to date are consistent with about a 10% failure rate in overgo probe design and a 15-20% false negative detection rate within a group of 216 markers. Three complete rounds of overgo hybridization, each to sets of about 39,000 BACs (either BamHI or EcoRI partial digest inserts) generated a total of 1853 BAC alignments for 517 mapped chicken genome STS markers. These data are publicly available, and they have been used in the assembly of a first generation BAC contig map of the chicken genome.

Item Type: Article
DOI/Identification number: 10.1159/000075763
Uncontrolled keywords: chicken genome; genes
Subjects: Q Science > QH Natural history > QH426 Genetics
S Agriculture > SF Animal culture
Divisions: Divisions > Division of Natural Sciences > Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 12 Dec 2013 17:07 UTC
Last Modified: 16 Nov 2021 10:14 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/37564 (The current URI for this page, for reference purposes)
Romanov, Michael N: https://orcid.org/0000-0003-3584-4644
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