July 2018
Volume 59, Issue 9
Open Access
ARVO Annual Meeting Abstract  |   July 2018
Targeted sequencing to identify the candidate gene in two south Indian POAG families
Author Affiliations & Notes
  • Periasamy Sundaresan
    Genetics, Aravind Med Res Foundation, Madurai, Tamilnadu, India
  • MOHD HUSSAIN SHAH
    Genetics, Aravind Med Res Foundation, Madurai, Tamilnadu, India
  • Krishnadas S R
    Glaucoma clinic, Aravind Eye Hospital, Madurai, Tamilnadu, India
  • Bharanidharan D
    Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamilnadu, India
  • Manoj Kumar, K
    Bioinformatics, Aravind Medical Research Foundation, Madurai, Tamilnadu, India
  • Mohideen Abdul Kader
    Glaucoma clinic, Aravind Eye Hospital, Tirunelveli,, Tamilnadu, India
  • Footnotes
    Commercial Relationships   Periasamy Sundaresan, None; MOHD SHAH, None; Krishnadas R, None; Bharanidharan D, None; Manoj Kumar, K, None; Mohideen Kader, None
  • Footnotes
    Support  None
Investigative Ophthalmology & Visual Science July 2018, Vol.59, 5139. doi:
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      Periasamy Sundaresan, MOHD HUSSAIN SHAH, Krishnadas S R, Bharanidharan D, Manoj Kumar, K, Mohideen Abdul Kader; Targeted sequencing to identify the candidate gene in two south Indian POAG families. Invest. Ophthalmol. Vis. Sci. 2018;59(9):5139.

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      © ARVO (1962-2015); The Authors (2016-present)

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Abstract

Purpose : Primary open angle glaucoma (POAG) is a complex disease, it may either be caused by the combined action of many genes or caused by mutations in a single gene such as Myocilin, Optinurein and TBK1. We have two large pedigrees with POAG, those pedigree does not harbor mutations in the three genes currently known to cause POAG and suggests that further studies of this pedigree have the potential to identify a new candidate gene. Therefore, the aim of study is to identify additional candidate gene for POAG using targeting sequencing.

Methods : Two families were recruited: 1) a single large four generation south Indian family from Kayalpatanam and 2) Devakottai, Tamil Nadu, India. 240 members from Kayalpatanam family and 51 from Devakottai family were participated in this study. DNA were isolated from 12 samples (7 POAG, 2 POAG suspect and 3 controls) from Kayalpatanam and 4 samples (2 POAG, one suspect and one control) from Devakottai families for Targeted exome sequencing (TES) using Miseq . The individual steps in TES and bioinformatics analysis were shown in the Figure. Briefly, the raw reads obtained was quality filtered and mapped to Hg19 reference sequence, which was further submitted to variant calling programs. The raw variant call file, including both SNVs and InDels, were subjected to several filtering steps to identify rare and low frequency causal variants.

Results : Targeted exome sequencing was performed on 85 genes, based on the previous exome data and reports of POAG-associated genes, to screen causal variants in 16 samples. After stringent filtering rare and low frequency causal variants of three genes (FNDC3B, FOXO1, DOCK6) were identified in few POAG patients of Kayalpatanam family, of which one novel causal variant was identified in DOCK6 gene. Rest of the two genes already associated with POAG in European and American ethnic population. While two novel genes (SLC24A1, ZNF155) were identified in Devakottai family. Of these, SLC24A1 are found to be associated with congenital stationary night blindness, while as ZNF155 has not been reported with any of the ocular disease so far.

Conclusions : TES approach revealed five genes from these two large south Indian families with POAG. These genes may be associated in the pathogenesis of POAG. Further, functional characterization and the inheritance pattern of variants identified are necessary to prove their involvement in the pathogenesis of POAG.

This is an abstract that was submitted for the 2018 ARVO Annual Meeting, held in Honolulu, Hawaii, April 29 - May 3, 2018.

 

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