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Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders.

Zangerl B, Johnson JL, Pillardy J, Sun Q, André C, Galibert F, Acland GM, Aguirre GD - Mol. Vis. (2009)

Bottom Line: Unique map positions could be assigned for 99% of the mapped clones, of which only 29% showed significant homology to known RefSeq sequences.A comparison between RH map and sequence assembly indicated some areas of discrepancy.Several of the EST clones were located within areas of conserved synteny to human retinal disease loci.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. bzangerl@vet.upenn.edu

ABSTRACT

Purpose: To identify the genomic location of previously uncharacterized canine retina-expressed expressed sequence tags (ESTs), and thus identify potential candidate genes for heritable retinal disorders.

Methods: A set of over 500 retinal canine ESTs were mapped onto the canine genome using the RHDF(5000-2) radiation hybrid (RH) panel, and the resulting map positions were compared to their respective localization in the CanFam2 assembly of the canine genome sequence.

Results: Unique map positions could be assigned for 99% of the mapped clones, of which only 29% showed significant homology to known RefSeq sequences. A comparison between RH map and sequence assembly indicated some areas of discrepancy. Retinal expressed genes were not concentrated in particular areas of the canine genome, and also were located on the canine Y chromosome (CFAY). Several of the EST clones were located within areas of conserved synteny to human retinal disease loci.

Conclusions: RH mapping of canine retinal ESTs provides insight into the location of potential candidate genes for hereditary retinal disorders, and, by comparison with the assembled canine genome sequence, highlights inconsistencies with the current assembly. Regions of conserved synteny between the canine and the human genomes allow this information to be extrapolated to identify potential positional candidate genes for mapped human retinal disorders. Furthermore, these ESTs can help identify novel or uncharacterized genes of significance for better understanding of retinal morphology, physiology, and pathology.

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Related in: MedlinePlus

Quality control for retinal clones on the RHDF5000–2 panel. A total of 555 retinal clones were amplified from 118 cell lines representing the RHDF5000–2 panel. For each locus, we assessed both, the overall number of cell lines that could unambiguously be scored, and the number of cell lines amplifying the respective EST, for quality. Half of the loci were scored in each individual line with the balance of loci missing only few scores (A). The respective retention frequency resulting from amplification scores, on average, was 0.22 and showed a distribution that is similar to previously published data [12] using this panel (B). The good quality performance of EST amplification resulted in highly supported linkage to known markers (C) with most of the LOD scores above 10.
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f1: Quality control for retinal clones on the RHDF5000–2 panel. A total of 555 retinal clones were amplified from 118 cell lines representing the RHDF5000–2 panel. For each locus, we assessed both, the overall number of cell lines that could unambiguously be scored, and the number of cell lines amplifying the respective EST, for quality. Half of the loci were scored in each individual line with the balance of loci missing only few scores (A). The respective retention frequency resulting from amplification scores, on average, was 0.22 and showed a distribution that is similar to previously published data [12] using this panel (B). The good quality performance of EST amplification resulted in highly supported linkage to known markers (C) with most of the LOD scores above 10.

Mentions: From the initial set of 1,418 ESTs with no detected homology to previously known sequences, amplification was attempted for a subset of 1,147 markers. Of these, 998 (87%) amplified a unique PCR product from canine genomic DNA without optimization, and 711 (62%) amplified a consistent and distinctive product from the RHDF5000–2 panel cell lines (Table 1). Roughly half of the ESTs tested could be scored satisfactorily for each of the 118 cell lines (Figure 1A). The overall presence of each EST marker on the panel (Figure 1B) was similar to previously published results (e.g., average retention frequency 22% in [12]). Furthermore, linkage to at least one other marker present in the RHDF5000–2 panel was found; this was supported by most two-point LOD scores higher than 10 (Figure 1C, Appendix 3).


Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders.

Zangerl B, Johnson JL, Pillardy J, Sun Q, André C, Galibert F, Acland GM, Aguirre GD - Mol. Vis. (2009)

Quality control for retinal clones on the RHDF5000–2 panel. A total of 555 retinal clones were amplified from 118 cell lines representing the RHDF5000–2 panel. For each locus, we assessed both, the overall number of cell lines that could unambiguously be scored, and the number of cell lines amplifying the respective EST, for quality. Half of the loci were scored in each individual line with the balance of loci missing only few scores (A). The respective retention frequency resulting from amplification scores, on average, was 0.22 and showed a distribution that is similar to previously published data [12] using this panel (B). The good quality performance of EST amplification resulted in highly supported linkage to known markers (C) with most of the LOD scores above 10.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2683029&req=5

f1: Quality control for retinal clones on the RHDF5000–2 panel. A total of 555 retinal clones were amplified from 118 cell lines representing the RHDF5000–2 panel. For each locus, we assessed both, the overall number of cell lines that could unambiguously be scored, and the number of cell lines amplifying the respective EST, for quality. Half of the loci were scored in each individual line with the balance of loci missing only few scores (A). The respective retention frequency resulting from amplification scores, on average, was 0.22 and showed a distribution that is similar to previously published data [12] using this panel (B). The good quality performance of EST amplification resulted in highly supported linkage to known markers (C) with most of the LOD scores above 10.
Mentions: From the initial set of 1,418 ESTs with no detected homology to previously known sequences, amplification was attempted for a subset of 1,147 markers. Of these, 998 (87%) amplified a unique PCR product from canine genomic DNA without optimization, and 711 (62%) amplified a consistent and distinctive product from the RHDF5000–2 panel cell lines (Table 1). Roughly half of the ESTs tested could be scored satisfactorily for each of the 118 cell lines (Figure 1A). The overall presence of each EST marker on the panel (Figure 1B) was similar to previously published results (e.g., average retention frequency 22% in [12]). Furthermore, linkage to at least one other marker present in the RHDF5000–2 panel was found; this was supported by most two-point LOD scores higher than 10 (Figure 1C, Appendix 3).

Bottom Line: Unique map positions could be assigned for 99% of the mapped clones, of which only 29% showed significant homology to known RefSeq sequences.A comparison between RH map and sequence assembly indicated some areas of discrepancy.Several of the EST clones were located within areas of conserved synteny to human retinal disease loci.

View Article: PubMed Central - PubMed

Affiliation: Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. bzangerl@vet.upenn.edu

ABSTRACT

Purpose: To identify the genomic location of previously uncharacterized canine retina-expressed expressed sequence tags (ESTs), and thus identify potential candidate genes for heritable retinal disorders.

Methods: A set of over 500 retinal canine ESTs were mapped onto the canine genome using the RHDF(5000-2) radiation hybrid (RH) panel, and the resulting map positions were compared to their respective localization in the CanFam2 assembly of the canine genome sequence.

Results: Unique map positions could be assigned for 99% of the mapped clones, of which only 29% showed significant homology to known RefSeq sequences. A comparison between RH map and sequence assembly indicated some areas of discrepancy. Retinal expressed genes were not concentrated in particular areas of the canine genome, and also were located on the canine Y chromosome (CFAY). Several of the EST clones were located within areas of conserved synteny to human retinal disease loci.

Conclusions: RH mapping of canine retinal ESTs provides insight into the location of potential candidate genes for hereditary retinal disorders, and, by comparison with the assembled canine genome sequence, highlights inconsistencies with the current assembly. Regions of conserved synteny between the canine and the human genomes allow this information to be extrapolated to identify potential positional candidate genes for mapped human retinal disorders. Furthermore, these ESTs can help identify novel or uncharacterized genes of significance for better understanding of retinal morphology, physiology, and pathology.

Show MeSH
Related in: MedlinePlus