PhD Scientific Days 2024

Budapest, 9-10 July 2024

Molecular Medicine III.

Whole genome sequencing completes the molecular genetic testing workflow of patients with Lynch syndrome

Author(s)

Klaudia Horti-Oravecz1,2, Anikó Bozsik1,3,4, Tímea Pócza1, Ildikó Vereczkey5, Tamás Strausz5, Erika Tóth3,5, Tatiana Sedlackova6,7, Diana Rusnakova6,7, Tomas Szemes6,7,8, István Likó4, Edit Oláh1, Henriett Butz1,3,4,9,10, Attila Patócs1,3,4,9, János Papp1,3,4, Vince Kornél Grolmusz1,3,4,9
1: Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
2: Semmelweis University, Doctoral School, Budapest
3: National Tumorbiology Laboratory, National Institute of Oncology, Budapest, Hungary
4: Hereditary Tumors Research Group, HUN-REN – Semmelweis University, Budapest, Hungary
5: Department of Surgical and Molecular Pathology, National Institute of Oncology, Budapest, Hungary
6: Comenius University Science Park, Bratislava, Slovakia
7: Geneton Ltd., Bratislava, Slovakia
8: Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
9: Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
10: Department of Oncology Biobank, National Institute of Oncology, Budapest, Hungary

Text of the abstract

Introduction
Lynch syndrome (LS) is a frequent cancer predispositon associating with germline pathogenetic variants (PVs) in MLH1, MSH2, MSH6, PMS2 and EPCAM genes. Although the wide-ranging availability of multigene panel tests (MGPTs) revolutionized the genetic testing of LS, noncoding PVs localized outside the targeted exons can only be identified by whole-gene/whole-genome approaches.
Aims
Our aim was to determine a straightforward and biomarker-driven sample prioritization procedure to select high-risk patients with negative MGPT results for whole genome sequencing (WGS).
Methods
A comprehensive molecular genetic testing workflow has been executed utilizing germline DNA-, RNA- and tumor tissue-based techniques in a prospective, pilot study for patients with clinical suspicion of LS. Samples of patients with MLH1-deficient tumors without somatic MLH1 promoter methlyation and samples exhibiting allelic imbalance on the RNA level of a germline heterozygote marker were prioritized for WGS. An additional retrospective cohort of 10 high-risk patients with negative genetic testing results has also been subjected to WGS analysis.
Results
Among the 100 enrolled patients with colorectal or endometrial cancer, MGPT detected 28 pathogenic single nucleotide or copy number variations, while an additional 3 complex PVs were further characterized. WGS analysis returned a germline deep intronic MLH1 variant (c.306+1222A>G) which creates a novel splice donor, resulting in the exonization of a 288-bp intronic sequence and confirming pathogenicity. Interestingly, all of these complex and deep intronic PVs were confirmed to be recurrent in our studied population, which highlights the clinical importance of this workflow.
Conclusion
Our biomarker-driven prioritization method can optimalize the role of WGS in the diagnostic procedure of LS.
Funding
2022-2.1.1-NL-2022-00010, TKP2021-EGA-44, NLP-17, NKFIH-FK-138377, BO/00141/21, ÚNKP-22-5-SE-25, ÚNKP-23-5-SE-16, NRDI NKFI-FK135065, ÚNKP-23-5-SE-4.

klaudiaoravecz@gmail.com
Semmelweis University, Molecular Medicine
Vince Kornél Grolmusz, M.D., Ph.D.