ISSN: 1308-5727 | E-ISSN: 1308-5735
Volume: 14 Issue: 2 Year: 2022
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Abstracting & Indexing
Turkish Society for Pediatric Endocrinology and Diabetes
Comparative Analyses of Turkish Variome and Widely Used Genomic Variation Databases for the Evaluation of Rare Sequence Variants in Turkish Individuals: Idiopathic Hypogonadotropic Hypogonadism as a Disease Model [J Clin Res Pediatr Endocrinol]
J Clin Res Pediatr Endocrinol. Ahead of Print: JCRPE-52824 | DOI: 10.4274/jcrpe.galenos.2022.2022-3-11

Comparative Analyses of Turkish Variome and Widely Used Genomic Variation Databases for the Evaluation of Rare Sequence Variants in Turkish Individuals: Idiopathic Hypogonadotropic Hypogonadism as a Disease Model

Leman Damla Kotan
Cukurova University, Faculty of Medicine, Division of Pediatric Endocrinology, Adana, Turkey

INTRODUCTION: Objective: With the increasing use of whole-exome sequencing, one of the challenges in identifying the causal allele for a Mendelian disease is the unavailability of population-specific human genetic variation reference databases. People of Turkey were not represented in GnomAD or other publicly available large databases until recently when the first comprehensive genomic variation database, Turkish Variome (TRV), was published. This study aims to evaluate whether TRV or other publicly available large genomic variation databases can reliably be used for rare disease variant evaluation from Turkish individuals.
METHODS: Methods: We identified 60 non-disease-causing non-synonymous variants (minor allele frequencies >1%) in 58 genes that are known to be associated with idiopathic hypogonadotropic hypogonadism (IHH) from a large Turkish patient cohort. We then compared the allelic frequencies of these variants with those in various public genomic variation databases, including TRV.
RESULTS: Results: Our cohort variants showed the highest correlations with those in the TRV, Iranome, and The Greater Middle East Variome, in decreasing order.
DISCUSSION AND CONCLUSION: Conclusion: These results suggest that the TRV is the appropriate database for the Turkish population for rare genomic variant evaluations. Our data also point out that variomes from geographic neighborhoods may serve as substitute references for populations devoid of their own genomic variation databases.

Keywords: Allele Frequency, Turkish Variome, variant evaluation, genomic variation databases



Corresponding Author: Leman Damla Kotan, Türkiye
Manuscript Language: English
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