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Congenital cataracts: de novo gene conversion event in CRYBB2.

Garnai SJ, Huyghe JR, Reed DM, Scott KM, Liebmann JM, Boehnke M, Richards JE, Ritch R, Pawar H - Mol. Vis. (2014)

Bottom Line: We found significant evidence of linkage to chromosome 22, under an autosomal dominant inheritance model, with a maximum logarithm of the odds (LOD) score of 3.91 (16.918 to 25.641 Mb).We did not find these changes in six unaffected family members, including the unaffected grandfather who contributed the affected haplotype, nor did we find them in the 100 Ashkenazi Jewish controls.This study highlights how linkage mapping can be complicated by de novo mutation events, as well as how sequence-analysis pipeline mapping of short reads from next-generation sequencing can be complicated by the existence of pseudogenes or other highly homologous sequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI.

ABSTRACT

Purpose: To identify the cause of congenital cataracts in a consanguineous family of Ashkenazi Jewish ancestry.

Methods: We performed genome-wide linkage analysis and whole-exome sequencing for the initial discovery of variants, and we confirmed the variants using gene-specific primers and Sanger sequencing.

Results: We found significant evidence of linkage to chromosome 22, under an autosomal dominant inheritance model, with a maximum logarithm of the odds (LOD) score of 3.91 (16.918 to 25.641 Mb). Exome sequencing identified three nonsynonymous changes in the CRYBB2 exon 5 coding sequence that are consistent with the sequence of the corresponding region of the pseudogene CRYBB2P1. The identification of these changes was complicated by possible mismapping of some mutated CRYBB2 sequences to CRYBB2P1. Sequencing with gene-specific primers confirmed that the changes--rs2330991, c.433 C>T (p.R145W); rs2330992, c.440A>G (p.Q147R); and rs4049504, c.449C>T (p.T150M)--present in all ten affected family members are located in CRYBB2 and are not artifacts of cross-reaction with CRYBB2P1. We did not find these changes in six unaffected family members, including the unaffected grandfather who contributed the affected haplotype, nor did we find them in the 100 Ashkenazi Jewish controls.

Conclusions: Our data are consistent with a de novo gene conversion event, transferring 270 base pairs at most from CRYBB2P1 to exon 5 of CRYBB2. This study highlights how linkage mapping can be complicated by de novo mutation events, as well as how sequence-analysis pipeline mapping of short reads from next-generation sequencing can be complicated by the existence of pseudogenes or other highly homologous sequences.

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Related in: MedlinePlus

Alignment of the CRYBB2 and CRYBB2P1 sequences. The blue boxes highlight three coding sequence changes consistent with the sequence of the pseudogene that were modestly represented in the exome sequence reads. Nucleotides within the exon 5 coding sequence appear inside the gray box. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.
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f5: Alignment of the CRYBB2 and CRYBB2P1 sequences. The blue boxes highlight three coding sequence changes consistent with the sequence of the pseudogene that were modestly represented in the exome sequence reads. Nucleotides within the exon 5 coding sequence appear inside the gray box. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.

Mentions: A visual inspection of the sequence data for the CRYBB2 and CRYBB3 regions using the Integrated Genomics Viewer identified three changes in CRYBB2 represented at a low level that had not been picked up by the sequence-analysis pipeline. These sequence variants convert the normal CRYBB2 exon 5 coding sequence to look like the corresponding sequence of the pseudogene CRYBB2P1 (Figure 5). When comparing exon 5 of CRYBB2 and the corresponding region of CRYBB2P1, we find 98% DNA sequence homology; the variant form of CRYBB2 exon 5 has 100% sequence homology to the corresponding region of the pseudogene.


Congenital cataracts: de novo gene conversion event in CRYBB2.

Garnai SJ, Huyghe JR, Reed DM, Scott KM, Liebmann JM, Boehnke M, Richards JE, Ritch R, Pawar H - Mol. Vis. (2014)

Alignment of the CRYBB2 and CRYBB2P1 sequences. The blue boxes highlight three coding sequence changes consistent with the sequence of the pseudogene that were modestly represented in the exome sequence reads. Nucleotides within the exon 5 coding sequence appear inside the gray box. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4225141&req=5

f5: Alignment of the CRYBB2 and CRYBB2P1 sequences. The blue boxes highlight three coding sequence changes consistent with the sequence of the pseudogene that were modestly represented in the exome sequence reads. Nucleotides within the exon 5 coding sequence appear inside the gray box. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.
Mentions: A visual inspection of the sequence data for the CRYBB2 and CRYBB3 regions using the Integrated Genomics Viewer identified three changes in CRYBB2 represented at a low level that had not been picked up by the sequence-analysis pipeline. These sequence variants convert the normal CRYBB2 exon 5 coding sequence to look like the corresponding sequence of the pseudogene CRYBB2P1 (Figure 5). When comparing exon 5 of CRYBB2 and the corresponding region of CRYBB2P1, we find 98% DNA sequence homology; the variant form of CRYBB2 exon 5 has 100% sequence homology to the corresponding region of the pseudogene.

Bottom Line: We found significant evidence of linkage to chromosome 22, under an autosomal dominant inheritance model, with a maximum logarithm of the odds (LOD) score of 3.91 (16.918 to 25.641 Mb).We did not find these changes in six unaffected family members, including the unaffected grandfather who contributed the affected haplotype, nor did we find them in the 100 Ashkenazi Jewish controls.This study highlights how linkage mapping can be complicated by de novo mutation events, as well as how sequence-analysis pipeline mapping of short reads from next-generation sequencing can be complicated by the existence of pseudogenes or other highly homologous sequences.

View Article: PubMed Central - PubMed

Affiliation: Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, MI.

ABSTRACT

Purpose: To identify the cause of congenital cataracts in a consanguineous family of Ashkenazi Jewish ancestry.

Methods: We performed genome-wide linkage analysis and whole-exome sequencing for the initial discovery of variants, and we confirmed the variants using gene-specific primers and Sanger sequencing.

Results: We found significant evidence of linkage to chromosome 22, under an autosomal dominant inheritance model, with a maximum logarithm of the odds (LOD) score of 3.91 (16.918 to 25.641 Mb). Exome sequencing identified three nonsynonymous changes in the CRYBB2 exon 5 coding sequence that are consistent with the sequence of the corresponding region of the pseudogene CRYBB2P1. The identification of these changes was complicated by possible mismapping of some mutated CRYBB2 sequences to CRYBB2P1. Sequencing with gene-specific primers confirmed that the changes--rs2330991, c.433 C>T (p.R145W); rs2330992, c.440A>G (p.Q147R); and rs4049504, c.449C>T (p.T150M)--present in all ten affected family members are located in CRYBB2 and are not artifacts of cross-reaction with CRYBB2P1. We did not find these changes in six unaffected family members, including the unaffected grandfather who contributed the affected haplotype, nor did we find them in the 100 Ashkenazi Jewish controls.

Conclusions: Our data are consistent with a de novo gene conversion event, transferring 270 base pairs at most from CRYBB2P1 to exon 5 of CRYBB2. This study highlights how linkage mapping can be complicated by de novo mutation events, as well as how sequence-analysis pipeline mapping of short reads from next-generation sequencing can be complicated by the existence of pseudogenes or other highly homologous sequences.

Show MeSH
Related in: MedlinePlus