Genetic mutation risk calculation in Lynch syndrome inheritance: Evaluating the utility of the PREMM1,2,6 model in Lyon: The first French study

Genomics and integrative clinical data machine learning scoring model to ascertain likely Lynch syndrome patients

BACKGROUND

Lynch syndrome (LS) screening methods include multistep molecular somatic tumor testing to distinguish likely-LS patients from sporadic cases, which can be costly and complex. Also, direct germline testing for LS for every diagnosed solid cancer patient is a challenge in resource limited settings. We developed a unique machine learning scoring model to ascertain likely-LS cases from a cohort of colorectal cancer (CRC) patients.

METHODS

We used CRC patients from the cBioPortal database (TCGA studies) with complete clinicopathologic and somatic genomics data. We determined the rate of pathogenic/likely pathogenic variants in five (5) LS genes (MLH1, MSH2, MSH6, PMS2, EPCAM), and the BRAF mutations using a pre-designed bioinformatic annotation pipeline. Annovar, Intervar, Variant Effect Predictor (VEP), and OncoKB software tools were used to functionally annotate and interpret somatic variants detected. The OncoKB precision oncology knowledge base was used to provide information on the effects of the identified variants. We scored the clinicopathologic and somatic genomics data automatically using a machine learning model to discriminate between likely-LS and sporadic CRC cases. The training and testing datasets comprised of 80% and 20% of the total CRC patients, respectively. Group regularisation methods in combination with 10-fold cross-validation were performed for feature selection on the training data.

RESULTS

Out of 4800 CRC patients frorm the TCGA datasets with clinicopathological and somatic genomics data, we ascertained 524 patients with complete data. The scoring model using both clinicopathological and genetic characteristics for likely-LS showed a sensitivity and specificity of 100%, and both had the maximum accuracy, area under the curve (AUC) and AUC for precision-recall (AUCPR) of 1. In a similar analysis, the training and testing models that only relied on clinical or pathological characteristics had a sensitivity of 0.88 and 0.50, specificity of 0.55 and 0.51, accuracy of 0.58 and 0.51, AUC of 0.74 and 0.61, and AUCPR of 0.21 and 0.19, respectively.

CONCLUSIONS

Simultaneous scoring of LS clinicopathological and somatic genomics data can improve prediction and ascertainment for likely-LS from all CRC cases. This approach can increase accuracy while reducing the reliance on expensive direct germline testing for all CRC patients, making LS screening more accessible and cost-effective, especially in resource-limited settings.

The Role of Colonoscopy in the Management of Individuals with Lynch Syndrome: A Narrative Review

The history of Lynch syndrome changed definitively in 2000, when a study published in Gastroenterology demonstrated a significant reduction in mortality among individuals with Lynch syndrome who undergo regular endoscopic surveillance. As a consequence of this clinical evidence, all scientific societies developed guidelines, which highlighted the role of colonoscopy in the management of Lynch syndrome, especially for individuals at high risk of colorectal cancer. Over the years, these guidelines were modified and updated. Specialized networks were developed in order to standardize endoscopic surveillance programs and evaluate all the clinical data retrieved by the results of colonoscopies performed for both the screening and the surveillance of individuals with Lynch syndrome. Recent data show that the impact of colonoscopy (with polypectomy) on the prevention of colorectal cancer in individuals with Lynch syndrome is less significant than previously thought. This narrative review summarizes the current discussion, the hypotheses elaborated and the algorithms depicted for the management of individuals with Lynch Syndrome on the basis of the recent data published in the literature.

Genetics, diagnosis and treatment of Lynch syndrome: Old lessons and current challenges

Lynch syndrome (LS) is an autosomal dominant genetic disorder associated with germline mutations in DNA mismatch repair (MMR) genes. The carriers of pathogenic mutations in these genes have an increased risk of developing a colorectal cancer and/or LS-associated cancer. The LS-associated cancer types include carcinomas of the endometrium, small intestine, stomach, pancreas and biliary tract, ovary, brain, upper urinary tract and skin. The criteria for the clinical diagnosis of LS and the procedures of the genetic testing for identification of pathogenetic mutations carriers in MMR genes have long been known. A crucial point in the mutation detection analysis is the correct definition of the pathogenecity associated with MMR genetic variants, especially in order to include the mutation carriers in the endoscopy surveillance programs more suited to them. Therefore, this may help to improve the LS-associated cancer prevention programs. In the present review, we also report the recent discoveries in molecular genetics of LS, such as the new roles of MMR protein and immune response of MMR repair deficiency in colorectal cancer. Finally, we discuss the main therapeutic approaches, including immunotherapy, which represent a valid alternative to traditional therapeutic methods and extend the life expectancy of patients that have already developed LS-associated colorectal cancer.