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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

Family 581 haplotypes from SNP chip data (black lettering) and Sanger sequencing using gene-specific primers (red lettering). The affected haplotype is boxed. The symbol definitions are the same for Figure 1. The inferred haplotype is shown for V:3 (not genotyped). More than 100 markers were analyzed to generate these haplotypes. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.
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f4: Family 581 haplotypes from SNP chip data (black lettering) and Sanger sequencing using gene-specific primers (red lettering). The affected haplotype is boxed. The symbol definitions are the same for Figure 1. The inferred haplotype is shown for V:3 (not genotyped). More than 100 markers were analyzed to generate these haplotypes. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.

Mentions: Haplotype analysis (Figure 4, black lettering) identified an affected haplotype present on one copy of chromosome 22 in all of the affected individuals. Haplotype analysis supports an autosomal dominant mode of inheritance. Some affected individuals in generation VII received one of the maternal chromosomes from VI:11, while some received the other copy from her. The fact that V:3 is unaffected, that her ancestors and siblings are unaffected, and that her children are affected whether they received her maternal copy of chromosome 22 or her paternal copy all support an autosomal dominant mode of inheritance of a defect located on a chromosome that did not originate in the maternal branch of the family. Tracing transmission of the affected haplotype suggests that it originated with V:4, the unaffected paternal grandfather, whose haplotype matches one that is present in all affected individuals and none of the other unaffected individuals.


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)

Family 581 haplotypes from SNP chip data (black lettering) and Sanger sequencing using gene-specific primers (red lettering). The affected haplotype is boxed. The symbol definitions are the same for Figure 1. The inferred haplotype is shown for V:3 (not genotyped). More than 100 markers were analyzed to generate these haplotypes. 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

f4: Family 581 haplotypes from SNP chip data (black lettering) and Sanger sequencing using gene-specific primers (red lettering). The affected haplotype is boxed. The symbol definitions are the same for Figure 1. The inferred haplotype is shown for V:3 (not genotyped). More than 100 markers were analyzed to generate these haplotypes. The chromosome 22 positions are reported using hg19/GRCh37 coordinates.
Mentions: Haplotype analysis (Figure 4, black lettering) identified an affected haplotype present on one copy of chromosome 22 in all of the affected individuals. Haplotype analysis supports an autosomal dominant mode of inheritance. Some affected individuals in generation VII received one of the maternal chromosomes from VI:11, while some received the other copy from her. The fact that V:3 is unaffected, that her ancestors and siblings are unaffected, and that her children are affected whether they received her maternal copy of chromosome 22 or her paternal copy all support an autosomal dominant mode of inheritance of a defect located on a chromosome that did not originate in the maternal branch of the family. Tracing transmission of the affected haplotype suggests that it originated with V:4, the unaffected paternal grandfather, whose haplotype matches one that is present in all affected individuals and none of the other unaffected individuals.

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