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At AACC, Researcher Discusses Variants of Unknown Significance Found Through NGS Panel Test

ATLANTA (GenomeWeb) – When researchers from Progenetica-Hermes Pardini Institute in Brazil screened a dozen patients using a next-generation sequencing-based gene panel test they developed, they uncovered a number of variants of unknown significance (VUS), one of the investigators said at the American Association for Clinical Chemistry annual meeting here yesterday.

Giovana Torrezan and her Progenetica colleagues screened a dozen women lacking BRCA1 or BRCA2 mutations for other breast cancer-linked mutations to find that eight of them harbored VUS.

But, she added, when the significance of these variants was later re-examined, some had been reclassified as benign and others as potentially damaging.

"This is a changing field," Torrezan noted.

Breast cancer is the most common cancer afflicting women, and some 5 percent to 10 percent of tumors are hereditary. While BRCA1 and BRCA2 mutations account for nearly half of hereditary breast cancer cases, variants in other genes have also been linked to disease risk, posing what Torrezan said is a diagnostic challenge.

In addition to developing a BRCA1 and BRCA2 gene panel test, Torrezan and her colleagues also created one called Breast Cancer Panel 2 (BCP2) that examines variants in 15 genes, including ATM, CHEK2, PTEN, RAD50, and TP53.

Beginning in January 2014, they used the BCP2 panel to screen 12 women who lacked BRCA1 or BRCA2 mutations.

Using peripheral blood samples from each patient, the researchers extracted DNA samples for sequencing on the Thermo Fisher Ion PGM, followed by Sanger sequencing-based validation.

They then developed a report based on the results they obtained and a literature search of what those results might mean.

Torrezan said that the report could have one of three findings: a positive finding in that it uncovered a known pathogenic variant, a finding of a VUS, or a negative finding in that they didn't find either a known pathogenic variant or a VUS.

She noted, though, that a negative result wasn't necessarily conclusive as that woman might harbor a mutation in a gene they didn't examine.

In this study, the researchers were unable to find a clinical mutation in four patients, while in the eight other patients, they uncovered variants of unknown clinical significance in one or more genes. Four patients, she said, had VUS in the ATM gene and three patients had them in the PALB2 gene.

Many of these VUS, she said, were novel missense mutations or missense mutations with low minor allele frequencies.

But the status of some of the VUS have already changed, Torrezan said. As she prepared her presentation, she said that she re-performed database searches on these variants, and the VUS in PALB2 and CHEK2 have now been reclassified as benign and damaging, respectively.

This, Torrezan said, underscores the need for in silico analysis tools to keep databases up to date as well as familial segregation and functional studies of different variants so as to know their significance.

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