Limits...
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.

Show MeSH

Related in: MedlinePlus

Multipoint logarithm of the odds (LOD) score plots for A: the entire genome and B: chromosome 22 under the autosomal recessive model with the phenotype of V:4 set to missing. On the genome-wide plot (A), the region corresponding to the maximum LOD score is marked with a red arrow. The blue triangles on the chromosome 22 plot (B) mark the positions of the crystallin genes. Note that in B, CRYBB2 and CRYBB3 are outside of the genetic inclusion interval. The hatched bar in B marks the p-arm repetitive region that is not represented among the SNPs in the panel that was screened.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4225141&req=5

f2: Multipoint logarithm of the odds (LOD) score plots for A: the entire genome and B: chromosome 22 under the autosomal recessive model with the phenotype of V:4 set to missing. On the genome-wide plot (A), the region corresponding to the maximum LOD score is marked with a red arrow. The blue triangles on the chromosome 22 plot (B) mark the positions of the crystallin genes. Note that in B, CRYBB2 and CRYBB3 are outside of the genetic inclusion interval. The hatched bar in B marks the p-arm repetitive region that is not represented among the SNPs in the panel that was screened.

Mentions: Given that the father VI:12 and his children are affected with congenital cataracts despite there being no other family history, and given that the parents VI:11 and VI:12 are inside a consanguinity loop, we evaluated an autosomal recessive model of inheritance and found significant evidence of linkage on chromosome 22 from 16.918 to 22.437 Mb (LOD = 3.61, Figure 2), and no other regions in the genome reached significance. Figure 2B shows the genetic inclusion interval and the locations of the chromosome 22 crystallin genes (CRYBB3, CRYBB2, CRYBB1, and CRYBA4, as well as the pseudogene CRYBB2P1) that are all located outside of the autosomal recessive genetic inclusion interval. Given that more than 100 genes are located inside that interval, whole-exome sequencing was a more inexpensive approach to screening candidate genes than targeted sequencing.


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)

Multipoint logarithm of the odds (LOD) score plots for A: the entire genome and B: chromosome 22 under the autosomal recessive model with the phenotype of V:4 set to missing. On the genome-wide plot (A), the region corresponding to the maximum LOD score is marked with a red arrow. The blue triangles on the chromosome 22 plot (B) mark the positions of the crystallin genes. Note that in B, CRYBB2 and CRYBB3 are outside of the genetic inclusion interval. The hatched bar in B marks the p-arm repetitive region that is not represented among the SNPs in the panel that was screened.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f2: Multipoint logarithm of the odds (LOD) score plots for A: the entire genome and B: chromosome 22 under the autosomal recessive model with the phenotype of V:4 set to missing. On the genome-wide plot (A), the region corresponding to the maximum LOD score is marked with a red arrow. The blue triangles on the chromosome 22 plot (B) mark the positions of the crystallin genes. Note that in B, CRYBB2 and CRYBB3 are outside of the genetic inclusion interval. The hatched bar in B marks the p-arm repetitive region that is not represented among the SNPs in the panel that was screened.
Mentions: Given that the father VI:12 and his children are affected with congenital cataracts despite there being no other family history, and given that the parents VI:11 and VI:12 are inside a consanguinity loop, we evaluated an autosomal recessive model of inheritance and found significant evidence of linkage on chromosome 22 from 16.918 to 22.437 Mb (LOD = 3.61, Figure 2), and no other regions in the genome reached significance. Figure 2B shows the genetic inclusion interval and the locations of the chromosome 22 crystallin genes (CRYBB3, CRYBB2, CRYBB1, and CRYBA4, as well as the pseudogene CRYBB2P1) that are all located outside of the autosomal recessive genetic inclusion interval. Given that more than 100 genes are located inside that interval, whole-exome sequencing was a more inexpensive approach to screening candidate genes than targeted sequencing.

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