July 2, 2022

Whole Genome Sequencing Applied in Familial Hamartomatous Polyposis Identifies Novel Structural Variations

Revital Kariv 1,2,*,†, Dvir Dahary 3,†, Yuval Yaron 2,4, Yael Petel-Galil 1, Mira Malcov 4,‡, Guy Rosner1,2,‡

1 Department of Gastroenterology, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel

2 Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel

3 Geneyx Ltd., Tel Aviv 6805018, Israel

4 IVF Unit, Tel Aviv Sourasky Medical Center, Tel Aviv 64239, Israel

* Author to whom correspondence should be addressed.

These authors contributed equally to this work.

These authors contributed equally to this work.

Academic Editor: Christos K. Kontos

Genes 202213(8), 1408; https://doi.org/10.3390/genes13081408 (registering DOI)

Received: 2 July 2022 / Revised: 3 August 2022 / Accepted: 4 August 2022 / Published: 8 August 2022

(This article belongs to the Special Issue Advances in Genetics of Colorectal Cancer (CRC))

Hamartomatous polyposis syndromes (HPS) are serious rare cancer-predisposing conditions with an approximate prevalence of 1 in 30,000 to 1 in 200,000, presenting with multiple hamartomatous polyps (HP) and adenomas across the gastrointestinal tract, respectively. Kariv, et al. (2022, PMID: 36011318) performed a genome sequencing (GS) of 5 patients with HPS whose initial routine workup did not detect any pathogenic genetic variants. 

Geneyx Analysis was used to run the primary and secondary analysis pipelines, and call complex structural variants (SVs), copy number variants, single nucleotide variants, and short tandem repeats. The results showed the presence of a unique intragenic BMPR1A inversion, a novel intragenic inversion in the STK11 gene, two BMPR1A gene 11-exons deletions, and a short BMPR1A indel variant that resulted in a frameshift in 5 patients. 

The authors noted that GS could be used in the case of normal NGS gene panel testing results to exclude SVs. Geneyx facilitated the discovery of pathogenic variants through the comprehensive annotation of VCF files and the presentation of the results in an interactive user interface for variant interpretation. 

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