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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 pedigree. The filled symbols indicate the individuals affected with congenital cataracts; the half-filled symbols indicate the individuals affected with senile cataracts. The circles indicate females and the squares indicate males. The numbers inside of the diamonds indicate the number of children in that sibship. The individuals genotyped for this study are marked with an asterisk. For simulations and analyses, we only considered the genotyped individuals and one untyped founder (individual V:3) who was unavailable for genotyping. While it is reasonable to presume that the older members of the pedigree have passed away, we do not have clear information regarding which members of the earlier generations are still alive; therefore, the symbols have not been modified to indicate deceased status. The consanguinity indicated by these earlier generations has been included in the figure to help indicate where the concept of autosomal recessive inheritance originated.
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f1: Family 581 pedigree. The filled symbols indicate the individuals affected with congenital cataracts; the half-filled symbols indicate the individuals affected with senile cataracts. The circles indicate females and the squares indicate males. The numbers inside of the diamonds indicate the number of children in that sibship. The individuals genotyped for this study are marked with an asterisk. For simulations and analyses, we only considered the genotyped individuals and one untyped founder (individual V:3) who was unavailable for genotyping. While it is reasonable to presume that the older members of the pedigree have passed away, we do not have clear information regarding which members of the earlier generations are still alive; therefore, the symbols have not been modified to indicate deceased status. The consanguinity indicated by these earlier generations has been included in the figure to help indicate where the concept of autosomal recessive inheritance originated.

Mentions: We recruited 16 individuals from three generations of family 581 (Figure 1) for this study after obtaining informed consent according to a protocol approved by the Institutional Review Board of the University of Michigan and in accordance with the tenets of the Declaration of Helsinki. Participants underwent ocular examinations at the New York Eye and Ear Infirmary. We extracted genomic DNA from peripheral blood using the Gentra Puregene Blood Kit (QIAgen, Valencia, CA). The Ashkenazi Jewish control DNAs consisted of 90 samples from Tel Aviv University and 10 samples from the Coriell Institute (Camden, NJ). As shown in Figure 1, the family is consanguineous. The family history indicates that V:4 came from a different European country than the rest of the family, suggesting that V:4 is not closely related to his wife. Assuming complete penetrance and V:4 being unaffected, simulation via FastSLINK [14,15] indicated that this family had powers of 88.4% and 88.1% to detect a logarithm of the odds (LOD) score greater than 3 under dominant and recessive inheritance models, respectively (based on 10,000 replications).


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 pedigree. The filled symbols indicate the individuals affected with congenital cataracts; the half-filled symbols indicate the individuals affected with senile cataracts. The circles indicate females and the squares indicate males. The numbers inside of the diamonds indicate the number of children in that sibship. The individuals genotyped for this study are marked with an asterisk. For simulations and analyses, we only considered the genotyped individuals and one untyped founder (individual V:3) who was unavailable for genotyping. While it is reasonable to presume that the older members of the pedigree have passed away, we do not have clear information regarding which members of the earlier generations are still alive; therefore, the symbols have not been modified to indicate deceased status. The consanguinity indicated by these earlier generations has been included in the figure to help indicate where the concept of autosomal recessive inheritance originated.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f1: Family 581 pedigree. The filled symbols indicate the individuals affected with congenital cataracts; the half-filled symbols indicate the individuals affected with senile cataracts. The circles indicate females and the squares indicate males. The numbers inside of the diamonds indicate the number of children in that sibship. The individuals genotyped for this study are marked with an asterisk. For simulations and analyses, we only considered the genotyped individuals and one untyped founder (individual V:3) who was unavailable for genotyping. While it is reasonable to presume that the older members of the pedigree have passed away, we do not have clear information regarding which members of the earlier generations are still alive; therefore, the symbols have not been modified to indicate deceased status. The consanguinity indicated by these earlier generations has been included in the figure to help indicate where the concept of autosomal recessive inheritance originated.
Mentions: We recruited 16 individuals from three generations of family 581 (Figure 1) for this study after obtaining informed consent according to a protocol approved by the Institutional Review Board of the University of Michigan and in accordance with the tenets of the Declaration of Helsinki. Participants underwent ocular examinations at the New York Eye and Ear Infirmary. We extracted genomic DNA from peripheral blood using the Gentra Puregene Blood Kit (QIAgen, Valencia, CA). The Ashkenazi Jewish control DNAs consisted of 90 samples from Tel Aviv University and 10 samples from the Coriell Institute (Camden, NJ). As shown in Figure 1, the family is consanguineous. The family history indicates that V:4 came from a different European country than the rest of the family, suggesting that V:4 is not closely related to his wife. Assuming complete penetrance and V:4 being unaffected, simulation via FastSLINK [14,15] indicated that this family had powers of 88.4% and 88.1% to detect a logarithm of the odds (LOD) score greater than 3 under dominant and recessive inheritance models, respectively (based on 10,000 replications).

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