A study of normal copy number variations in Israeli population
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ORIGINAL INVESTIGATION
A study of normal copy number variations in Israeli population Idit Maya1 · Pola Smirin‑Yosef2,3 · Sarit Kahana1 · Sne Morag2 · Shiri Yacobson1 · Ifaat Agmon‑Fishman1 · Reut Matar1 · Elisheva Bitton2 · Mordechai Shohat4,5,6 · Lina Basel‑Salmon1,3,4,7 · Mali Salmon‑Divon2,8 Received: 29 July 2020 / Accepted: 19 September 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The population of Israel is ethnically diverse, and individuals from different ethnic groups share specific genetic variations. These variations, which have been passed on from common ancestors, are usually reported in public databases as rare variants. Here, we aimed to identify ethnicity-based benign copy number variants (CNVs) and generate the first Israeli CNV database. We applied a data-mining approach to the results of 10,193 chromosomal microarray tests, of which 2150 tests were from individuals of 13 common ethnic backgrounds (n ≥ 10). We found 165 CNV regions (> 50 kbp) that are unique to specific ethnic groups (uCNVRs). The frequency of more than 19% of these uCNVRs is between 1 and 20% of the common ethnic origin, while their frequency in the overall cohort is between 0.5 and 1.6%. Of these 165 uCNVRs, 98 are reported as variants of unknown significance or as not available in dbVar; we postulate that these uCNVRs should be annotated as either "likely benign" or "benign". The ethnic-specific CNVs extracted in this study will allow geneticists to distinguish between relevant pathogenic genomic aberrations and benign ethnicity-related variations, thus preventing variant misinterpretation that may lead to unnecessary pregnancy terminations. Keywords Chromosomal microarray analysis (CMA) · Copy number variations (CNV) · Data mining · Polymorphism · Ethnicity · dbVar
Idit Maya and Pola Smirin-Yosef contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00439-020-02225-4) contains supplementary material, which is available to authorized users. * Mali Salmon‑Divon [email protected] 1
Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
2
Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel, Israel
3
Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
4
Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
5
The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel‑Hashomer, Israel
6
Maccabi Health Services, Rehovot, Israel
7
Pediatric Genetics Unit, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel
8
The Adelson School of Medicine, Ariel University, Ariel, Israel
Background Israeli ethnic origins According to the Central Bureau of Statistics in Israel (https ://old.cbs.gov.il/reade r /?MIval = cw_usr_view_SHTML &ID=705), by September 2020, the inhabitants of Israel numbered 9.2 million, of which 6.82 million (74.1%) were Jews, 1.94 mi
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