Whole-exome sequencing identifies novel variants that co-segregates with autosomal recessive retinal degeneration in a Pakistani pedigree

Pooja Biswas, Muhammad Asif Naeem, Muhammad Hassaan Ali, Muhammad Zaman Assir, Shaheen N. Khan, Sheikh Riazuddin, J. Fielding Hejtmancik, Sheikh Amer Riazuddin, Radha Ayyagari

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Purpose : To identify the molecular basis of inherited retinal degeneration (IRD) in a familial case of Pakistani origin using whole-exome sequencing. Methods : A thorough ophthalmic examination was completed, and genomic DNA was extracted using standard protocols. Whole exome(s) were captured with Agilent V5 + UTRs probes and sequenced on Illumina HiSeq genome analyzer. The exomeSuite software was used to filter variants, and the candidate causal variants were prioritized, examining their allele frequency and PolyPhen2, SIFT, and MutationTaster predictions. Sanger dideoxy sequencing was performed to confirm the segregation with disease phenotype and absence in ethnicity-matched control chromosomes. Results : Ophthalmic examination confirmed retinal degeneration in all affected individuals that segregated as an autosomal recessive trait in the family. Whole-exome sequencing identified two homozygous missense variants: c.1304G > A; p.Arg435Gln in ZNF408 (NM_024741) and c.902G > A; p.Gly301Asp in C1QTNF4 (NM_031909). Both variants segregated with the retinal phenotype in the PKRD320 and were absent in ethnically matched control chromosomes. Conclusion : Whole-exome sequencing coupled with bioinformatics analysis identified potential novel variants that might be responsible for IRD.

Original languageEnglish (US)
Title of host publicationAdvances in Experimental Medicine and Biology
PublisherSpringer New York LLC
Pages219-228
Number of pages10
DOIs
StatePublished - Jan 1 2018

Publication series

NameAdvances in Experimental Medicine and Biology
Volume1074
ISSN (Print)0065-2598
ISSN (Electronic)2214-8019

Fingerprint

Exome
Retinal Degeneration
Pedigree
Chromosomes
Untranslated Regions
Bioelectric potentials
Bioinformatics
Genes
Phenotype
DNA
Computational Biology
Gene Frequency
Software
Genome

Keywords

  • C1QTNF4
  • Novel variants
  • Retinal degeneration
  • Whole-exome sequencing
  • ZNF408

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Biswas, P., Naeem, M. A., Ali, M. H., Assir, M. Z., Khan, S. N., Riazuddin, S., ... Ayyagari, R. (2018). Whole-exome sequencing identifies novel variants that co-segregates with autosomal recessive retinal degeneration in a Pakistani pedigree. In Advances in Experimental Medicine and Biology (pp. 219-228). (Advances in Experimental Medicine and Biology; Vol. 1074). Springer New York LLC. https://doi.org/10.1007/978-3-319-75402-4_27

Whole-exome sequencing identifies novel variants that co-segregates with autosomal recessive retinal degeneration in a Pakistani pedigree. / Biswas, Pooja; Naeem, Muhammad Asif; Ali, Muhammad Hassaan; Assir, Muhammad Zaman; Khan, Shaheen N.; Riazuddin, Sheikh; Hejtmancik, J. Fielding; Riazuddin, Sheikh Amer; Ayyagari, Radha.

Advances in Experimental Medicine and Biology. Springer New York LLC, 2018. p. 219-228 (Advances in Experimental Medicine and Biology; Vol. 1074).

Research output: Chapter in Book/Report/Conference proceedingChapter

Biswas, P, Naeem, MA, Ali, MH, Assir, MZ, Khan, SN, Riazuddin, S, Hejtmancik, JF, Riazuddin, SA & Ayyagari, R 2018, Whole-exome sequencing identifies novel variants that co-segregates with autosomal recessive retinal degeneration in a Pakistani pedigree. in Advances in Experimental Medicine and Biology. Advances in Experimental Medicine and Biology, vol. 1074, Springer New York LLC, pp. 219-228. https://doi.org/10.1007/978-3-319-75402-4_27
Biswas P, Naeem MA, Ali MH, Assir MZ, Khan SN, Riazuddin S et al. Whole-exome sequencing identifies novel variants that co-segregates with autosomal recessive retinal degeneration in a Pakistani pedigree. In Advances in Experimental Medicine and Biology. Springer New York LLC. 2018. p. 219-228. (Advances in Experimental Medicine and Biology). https://doi.org/10.1007/978-3-319-75402-4_27
Biswas, Pooja ; Naeem, Muhammad Asif ; Ali, Muhammad Hassaan ; Assir, Muhammad Zaman ; Khan, Shaheen N. ; Riazuddin, Sheikh ; Hejtmancik, J. Fielding ; Riazuddin, Sheikh Amer ; Ayyagari, Radha. / Whole-exome sequencing identifies novel variants that co-segregates with autosomal recessive retinal degeneration in a Pakistani pedigree. Advances in Experimental Medicine and Biology. Springer New York LLC, 2018. pp. 219-228 (Advances in Experimental Medicine and Biology).
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