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A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis.

Thomas R, Duke SE, Karlsson EK, Evans A, Ellis P, Lindblad-Toh K, Langford CF, Breen M - Cytogenet. Genome Res. (2008)

Bottom Line: The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species.We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy.This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Raleigh, NC 27606, USA.

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FISH analysis of clones from CFA10. (A) The chromosome location of five differentially labeled clones from the previously reported 10 Mb resolution dog BAC set (Thomas et al., 2007), starting with the most centromeric clone. The text color indicates the fluorochrome with which each clone was labeled for FISH analysis, and the Mb position on CFA10 is shown after the corresponding BAC address. To the left is the CFA10 ideogram, and to the right, three examples of these five probes hybridized to CFA10 at increasingly later stages of metaphase. Accurate assignment of clones at 10 Mb resolution is clearly possible in early metaphase, and probe order is easily ascertained. (B) Five probes at intervals of approximately 1 Mb, starting from the second clone in the previous 10 Mb set (326H08). In metaphase (Bi) these five probes at 1 Mb intervals can be accurately assigned to a chromosome band, but their relative order cannot be readily resolved due to extensive chromosome contraction. Accurate ordering is thus reliant on interphase mapping (Bii).
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Figure 1: FISH analysis of clones from CFA10. (A) The chromosome location of five differentially labeled clones from the previously reported 10 Mb resolution dog BAC set (Thomas et al., 2007), starting with the most centromeric clone. The text color indicates the fluorochrome with which each clone was labeled for FISH analysis, and the Mb position on CFA10 is shown after the corresponding BAC address. To the left is the CFA10 ideogram, and to the right, three examples of these five probes hybridized to CFA10 at increasingly later stages of metaphase. Accurate assignment of clones at 10 Mb resolution is clearly possible in early metaphase, and probe order is easily ascertained. (B) Five probes at intervals of approximately 1 Mb, starting from the second clone in the previous 10 Mb set (326H08). In metaphase (Bi) these five probes at 1 Mb intervals can be accurately assigned to a chromosome band, but their relative order cannot be readily resolved due to extensive chromosome contraction. Accurate ordering is thus reliant on interphase mapping (Bii).

Mentions: Initial (phase I) FISH analysis of our original selected panel of 2122 BAC clones resulted in successful placement of 1941 clones (91.5%) to the expected, unique chromosome location in full concordance with their position in the dog genome assembly, satisfying our criteria for use as downstream cytogenetic markers. Results of FISH analysis are summarized in Table 1, and Fig. 1 demonstrates our FISH analysis approach, using combinations of BAC clones positioned at intervals of 10 Mb and 1 Mb on dog chromosome 10 (Canis familiaris, CFA). Of the 181 clones that were rejected since they did not meet the necessary standard, 108 (60%) mapped to the expected chromosome location but showed hybridization signals at additional genomic sites that would confound downstream analysis. These included 106 clones that showed one or more secondary signals that had no obvious association with the observed primary signal. Two further clones mapped to the centromeres of all chromosomes.


A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis.

Thomas R, Duke SE, Karlsson EK, Evans A, Ellis P, Lindblad-Toh K, Langford CF, Breen M - Cytogenet. Genome Res. (2008)

FISH analysis of clones from CFA10. (A) The chromosome location of five differentially labeled clones from the previously reported 10 Mb resolution dog BAC set (Thomas et al., 2007), starting with the most centromeric clone. The text color indicates the fluorochrome with which each clone was labeled for FISH analysis, and the Mb position on CFA10 is shown after the corresponding BAC address. To the left is the CFA10 ideogram, and to the right, three examples of these five probes hybridized to CFA10 at increasingly later stages of metaphase. Accurate assignment of clones at 10 Mb resolution is clearly possible in early metaphase, and probe order is easily ascertained. (B) Five probes at intervals of approximately 1 Mb, starting from the second clone in the previous 10 Mb set (326H08). In metaphase (Bi) these five probes at 1 Mb intervals can be accurately assigned to a chromosome band, but their relative order cannot be readily resolved due to extensive chromosome contraction. Accurate ordering is thus reliant on interphase mapping (Bii).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2874680&req=5

Figure 1: FISH analysis of clones from CFA10. (A) The chromosome location of five differentially labeled clones from the previously reported 10 Mb resolution dog BAC set (Thomas et al., 2007), starting with the most centromeric clone. The text color indicates the fluorochrome with which each clone was labeled for FISH analysis, and the Mb position on CFA10 is shown after the corresponding BAC address. To the left is the CFA10 ideogram, and to the right, three examples of these five probes hybridized to CFA10 at increasingly later stages of metaphase. Accurate assignment of clones at 10 Mb resolution is clearly possible in early metaphase, and probe order is easily ascertained. (B) Five probes at intervals of approximately 1 Mb, starting from the second clone in the previous 10 Mb set (326H08). In metaphase (Bi) these five probes at 1 Mb intervals can be accurately assigned to a chromosome band, but their relative order cannot be readily resolved due to extensive chromosome contraction. Accurate ordering is thus reliant on interphase mapping (Bii).
Mentions: Initial (phase I) FISH analysis of our original selected panel of 2122 BAC clones resulted in successful placement of 1941 clones (91.5%) to the expected, unique chromosome location in full concordance with their position in the dog genome assembly, satisfying our criteria for use as downstream cytogenetic markers. Results of FISH analysis are summarized in Table 1, and Fig. 1 demonstrates our FISH analysis approach, using combinations of BAC clones positioned at intervals of 10 Mb and 1 Mb on dog chromosome 10 (Canis familiaris, CFA). Of the 181 clones that were rejected since they did not meet the necessary standard, 108 (60%) mapped to the expected chromosome location but showed hybridization signals at additional genomic sites that would confound downstream analysis. These included 106 clones that showed one or more secondary signals that had no obvious association with the observed primary signal. Two further clones mapped to the centromeres of all chromosomes.

Bottom Line: The emergence of high quality genome assemblies for several model organisms provides exciting opportunities to develop novel genome-integrated molecular cytogenetic resources that now permit a comparative approach to evaluating the relevance of tumor-associated chromosome aberrations, both within and between species.We have used the clone set to develop a genome-wide microarray for comparative genomic hybridization (aCGH) analysis, and demonstrate its application in detection of tumor-associated DNA copy number aberrations (CNAs) including single copy deletions and amplifications, regional aneuploidy and whole chromosome aneuploidy.This cytogenetically validated, genome integrated BAC clone panel has enormous potential for aiding gene discovery through a comparative approach to molecular oncology.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biomedical Sciences, College of Veterinary Medicine, Raleigh, NC 27606, USA.

Show MeSH
Related in: MedlinePlus