Custom capture sequencing identifies genes involved in Uveal Coloboma

Authors

• VK Kalaskar
• RKP Alur
• BP Brooks

Abstract

Uveal coloboma is a congenital ocular malformation resulting from failure of the optic fissure to close during 5th week of human embryonic development and accounts for up to 10% of childhood blindness. The purpose of this study was to identify the genetic causes underlying the development of coloboma in humans. We performed custom capture sequencing on genomic DNA samples obtained from 66 unrelated families involving 217 study subjects, which included the probands with syndromic or nonsyndromic coloboma and their first-degree relatives. Exonic regions in 196 genes, identified to be important in optic fissure development from our microarray screening and literature search, were sequenced on Illumina HiSeq2000 sequencing platform at NISC. The sequence reads were aligned to human reference genome hg19 (GRCh37) and the variants were analyzed and filtered using VarSifter based multi-tiered screening. The filtered variants identified were further verified for their population frequencies using public databases such as, 1000 genomes, exome variant server and exome aggregation consortium. Finally, the variants were scored for their pathogenicity and deleteriousness using CADD (combined annotation dependent depletion) scores, Polyphen-2, SIFT and Mutation Taster programs. Sanger sequencing was performed to confirm the identified mutations in the affected individuals. The present study identified novel variants in human genes previously not reported to be involved in development of coloboma such as, ANAPC1, NOL4, PARP3, and in some of the known genes reported to be involved in syndromic form of coloboma such as, TFAP2A, CHD7 and BMP7.

Scientific Focus Area: Genetics and Genomics

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