In Silico Systems Biology Analysis of Variants of Uncertain Significance in Lynch Syndrome Supports the Prioritization of Functional Molecular Validation

Abstract

Lynch syndrome (LS) is a genetic condition secondary to germline alterations in the DNA mismatch repair (MMR) genes with 30% of changes being variants of uncertain significance (VUS). Our aim was to perform an in silico re-classification of VUS from a large single institutional cohort that will help prioritizing functional validation. A total of 54 VUS were detected with 33 (61%) novel variants. We integrated family history, pathology, and genetic information along with supporting evidence from 8 different in silico tools at the RNA and protein level. Our assessment allowed us to re-classify 54% (29/54) of the VUS as probably damaging, 13% (7/54) as possibly damaging and 28% (15/54) as probably neutral. There are more than 1,000 VUS reported in MMR genes and our approach facilitates the prioritization of further functional efforts to assess the pathogenicity to those classified as probably damaging.

Germline variants in DNA repair genes associated with hereditary breast and ovarian cancer syndrome: analysis of a 21 gene panel in the Brazilian population

“…3 Schematic representation of BARD1, CHK2, PALB2 and PMS2 proteins and the variants associated with increased risk to HBOC. a Linear representation of BARD1 protein depicting the RING, Ankyrin (ANK), and BRCT domain boundaries [46], and the three variants found in that gene; (b) CHK2 depicting the SQ/TQ cluster domain (SCD), forkhead-associated domain (FHA), and the kinase domain (KD) [47], showing the localization of the two variants identified in that gene; (c) PALB2 protein with its main domains depicted: coiled coil, ChAM, MRG15-binding domain I and II (MBD I and II), WD40 repeats domain, and the nuclear export signal (NES) [48], showing the variants found as significantly associated HBOC risk; and (d) PMS2 with its ATP and MLH1 binding domains, and its endonuclease domain [49], depicting the variants identified in that gene. The graphs were built using the lolliplot function of the GenVisR package, on R environment (RStudio, version 1.2.1335), and were adapted by the authors oligomerization and transcriptional activities of p53 [59,60].…”

How Should We Test for Lynch Syndrome? A Review of Current Guidelines and Future Strategies

“…However, additional assessments are needed to confirm variant classifications. In silico analyses, which predict variant pathology by integrating clinical data and predicted changes to RNA and protein sequence, can be used to prioritise VUSs for functional assessment, as demonstrated by in silico re-classification of 53.7% (29/54) of MMR VUS as probably damaging in one single centre study [ 78 ]. Such in silico analyses can then be followed up by assays of MMR function in the presence of the VUS.…”

UniqueMLH1mutations in colonic adenomas in an obligate germline Lynch syndrome carrier

“…The c.1558+1G>A variant identified affects the putative PMS2 binding domain of MLH1 and creates an altered MLH1 transcript with defects in the remainder of MLH1, therefore preventing binding to PMS2 18 19…”