Incidental germline findings during molecular profiling of tumor tissues for precision oncology: molecular survey and methodological obstacles

Alexandra Lebedeva,Margarita Sharova,Ekaterina Rozhavskaya,Ancha Baranova,Ekaterina Ignatova,Tatiana Grigoreva,Sofia Manicka,Divyasphoorthi Vardhan,Maxim Ivanov,Vladislav Mileyko,Daria Seriak,Yulia Shaykhutdinova

doi:10.1186/s12967-022-03230-z

Abstract

BackgroundA fraction of patients referred for complex molecular profiling of biopsied tumors may harbor germline variants in genes associated with the development of hereditary cancer syndromes (HCS). Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized.MethodsData from Next-Generation Sequencing (NGS) of biopsied tumor samples referred for complex molecular profiling were analyzed for germline variants in HCS-associated genes. Analysis of variant origin was performed employing bioinformatic algorithms followed by manual curation. When possible, the origin of the variant was validated by Sanger sequencing of the sample of normal tissue. The variants’ pathogenicity was assessed according to ACMG/AMP.ResultsTumors were sampled from 183 patients (Males: 75 [41.0%]; Females: 108 [59.0%]; mean [SD] age, 57.7 [13.3] years) and analysed by targeted NGS. The most common tumor types were colorectal (19%), pancreatic (13%), and lung cancer (10%). A total of 56 sequence variants in genes associated with HCS were detected in 40 patients. Of them, 17 variants found in 14 patients were predicted to be of germline origin, with 6 variants interpreted as pathogenic (PV) or likely pathogenic (LPV), and 9 as variants of uncertain significance (VUS). For the 41 out of 42 (97%) missense variants in HCS-associated genes, the results of computational prediction of variant origin were concordant with that of experimental examination. We estimate that Sanger sequencing of a sample of normal tissue would be required for ~ 1–7% of the total assessed cases with PV or LPV, when necessity to follow with genetic counselling referral in ~ 2–15% of total assessed cases (PV, LPV or VUS found in HCS genes).ConclusionIncidental findings of pathogenic germline variants are common in data from cancer patients referred for complex molecular profiling. We propose an algorithm for the management of patients with newly detected variants in genes associated with HCS.

Highlights

Next-Generation Sequencing (NGS) is gaining recognition as an in vitro companion diagnostic aid in clinical decision-making
In the context of managing oncology patients, NGS is predominantly used as a tool for predicting the efficacy of therapies that may be influenced by the presence or lack of specific somatic mutations [7]
Compared to conventional methods for DNA analysis, such as Sanger sequencing or PCR (Polymerase Chain Reaction), NGS can identify a large array of DNA regions, which are not limited to the short list of mutations that clinicians expect to find in a patient with a certain diagnosis

Summary

Introduction

NGS is gaining recognition as an in vitro companion diagnostic aid in clinical decision-making. Lebedeva et al Journal of Translational Medicine (2022) 20:29 cancer-related genetic alterations [1, 2]. A typical result of diagnostic NGS is represented by a list of identified mutations, only some of which are related to the specific disease phenotype, and others, unrelated to the specific disease, that have the potential for clinical relevance [8]. The latter type of reported variance is known as “incidental”, or secondary findings. Neither the bioinformatic analysis nor the reporting of such incidental germline findings are standardized

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Discussion

Conclusion