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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

Multiple sequence alignments of βB2-crystallins. The protein sequences were aligned from the same region of the βB2-crystallins from 15 different species using MacVector. The numbering across the top is based on the human sequence. The light-blue boxes show 100% sequence identity in all species, the darker blue boxes show the consensus sequence, and the yellow boxes show mismatches. The amino acids that are altered in this family are boxed in thick black. Two of the amino acids that were altered in our congenital cataract family are completely conserved among the species studied, and one is highly conserved.
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f7: Multiple sequence alignments of βB2-crystallins. The protein sequences were aligned from the same region of the βB2-crystallins from 15 different species using MacVector. The numbering across the top is based on the human sequence. The light-blue boxes show 100% sequence identity in all species, the darker blue boxes show the consensus sequence, and the yellow boxes show mismatches. The amino acids that are altered in this family are boxed in thick black. Two of the amino acids that were altered in our congenital cataract family are completely conserved among the species studied, and one is highly conserved.

Mentions: The three nonsynonymous changes in exon 5 alter residues that are highly conserved across species and reside in a highly conserved region of βB2-crystallin (Figure 7). At two of the three positions (R145 and T150), the amino acid is completely conserved among 15 species; in our comparison, only one species (the Western clawed frog, Xenopus [Silurana] tropicalis) differs from the consensus at position 147.


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)

Multiple sequence alignments of βB2-crystallins. The protein sequences were aligned from the same region of the βB2-crystallins from 15 different species using MacVector. The numbering across the top is based on the human sequence. The light-blue boxes show 100% sequence identity in all species, the darker blue boxes show the consensus sequence, and the yellow boxes show mismatches. The amino acids that are altered in this family are boxed in thick black. Two of the amino acids that were altered in our congenital cataract family are completely conserved among the species studied, and one is highly conserved.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f7: Multiple sequence alignments of βB2-crystallins. The protein sequences were aligned from the same region of the βB2-crystallins from 15 different species using MacVector. The numbering across the top is based on the human sequence. The light-blue boxes show 100% sequence identity in all species, the darker blue boxes show the consensus sequence, and the yellow boxes show mismatches. The amino acids that are altered in this family are boxed in thick black. Two of the amino acids that were altered in our congenital cataract family are completely conserved among the species studied, and one is highly conserved.
Mentions: The three nonsynonymous changes in exon 5 alter residues that are highly conserved across species and reside in a highly conserved region of βB2-crystallin (Figure 7). At two of the three positions (R145 and T150), the amino acid is completely conserved among 15 species; in our comparison, only one species (the Western clawed frog, Xenopus [Silurana] tropicalis) differs from the consensus at position 147.

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