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7. Influence of clusterin genetic variants on IOP elevation in pseudoexfoliation syndrome and pseudoexfoliative glaucoma in Turkish population

Author

Demirdöğen, B.C., Demirkaya-Budak, S., Demirdöğen, B.C., and Demirkaya-Budak, S.

Abstract

Purpose: Pseudoexfoliation syndrome (PEX) is distinguished by the deposition of fibrillary material within the aqueous humor and, in most cases, causes pseudoexfoliative glaucoma (PEG). The pathophysiologies of PEX and PEG are not completely explained. Therefore, this study aimed to assess the potential relationship between single nucleotide polymorphisms (SNPs) in the 3ʹ untranslated region or introns of the clusterin gene (CLU) and the susceptibility to developing PEG or PEX. Methods: Two hundred and forty patients with PEX, 239 patients with PEG, and 240 control subjects were included. Genotyping was carried out using real-time PCR (rs2279590 C/T and rs1532278 C/T) or PCR followed by restriction endonuclease digestion (rs11136000 C/T and rs3087554 T/C). Results: The minor alleles or genotypes of CLU SNPs were not significantly associated with PEX or PEG. IOP values of patients with PEX carrying the homozygote polymorphic TT genotype were significantly elevated compared with PEX cases with the CT or CC genotypes for rs2279590, rs11136000 and rs1532278 (P =.009, P =.007, P =.010, respectively). Conclusion: We present the first evidence that three SNPs in CLU gene (rs2279590, rs11136000 and rs1532278) might induce a rise in IOP in patients with PEX, conferring susceptibility to develop PEG. © 2023, The Author(s)., This study was supported by the Scientific and Technological Research Council of Turkey (TÜBİTAK, 115S360)., Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, TÜBİTAK: 115S360

Published
2023

28. Population-specific genome graphs improve high-throughput sequencing data analysis: A case study on the Pan-African genome

Author

Amit Jain, Kabakci-Zorlu D, Gungor Budak, Semenyuk, Arslan E, Davis-Dusenbery B, Kalay O, Deniz Turgut, Narci K, Tetikol Hs, Richard J. C. Brown, Demirkaya-Budak S, and Alexey Dolgoborodov

Subjects
Theoretical computer science, Computer science, media_common.quotation_subject, Human genome, Ambiguity, Construct (python library), Resolution (logic), Genome, Pipeline (software), DNA sequencing, Information overload, media_common
Abstract

Graph-based genome reference representations have seen significant development, motivated by the inadequacy of the current human genome reference to represent the diverse genetic information from different human populations and its inability to maintain the same level of accuracy for non-European ancestries. While there have been many efforts to develop computationally efficient graph-based toolkits for NGS read alignment and variant calling, methods to curate genomic variants and subsequently construct genome graphs remains an understudied problem that inevitably determines the effectiveness of the overall bioinformatics pipeline. In this study, we discuss obstacles encountered during graph construction and propose methods for sample selection based on population diversity, graph augmentation with structural variants and resolution of graph reference ambiguity caused by information overload. Moreover, we present the case for iteratively augmenting tailored genome graphs for targeted populations and demonstrate this approach on the whole-genome samples of African ancestry. Our results show that population-specific graphs, as more representative alternatives to linear or generic graph references, can achieve significantly lower read mapping errors and enhanced variant calling sensitivity, in addition to providing the improvements of joint variant calling without the need of computationally intensive post-processing steps.

Published
2021
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