eP039: Does Lynch syndrome cause predisposition to breast cancer? Experience from a hereditary breast cancer clinic in Pakistan

Document Type



Paediatrics and Child Health; Pathology and Laboratory Medicine; Breast Surgery


Background: Lynch Syndrome (LS), also known as hereditary non-polyposis colorectal cancer syndrome, is an autosomal dominant disorder caused by the presence of germline pathogenic (P) or likely pathogenic (LP) variants in DNA mismatch repair (MMR) genes, which include MLH1, MSH2, MSH6, PMS2, and EPCAM. Presence of a disease-causing variant in any of these MMR genes increases an individual’s lifetime risk of developing colorectal cancer (CRC) (61%), endometrial (57%), ovarian (38%), renal pelvis or ureter (28%), prostate (24%), breast (19%), small bowel (11%), gastric (9%), brain (8%), hepatobiliary cancer (4%) and pancreatic cancer (2%). It is still unclear whether LS causes a predisposition to breast cancer, with current data suggesting a risk < 15%, which is close to the general population risk of 13%. Guidelines for high-risk surveillance and management of individuals with LS are thus not well-established for breast cancer, which at present is to be managed based on family history.
Identification of germline disease-causing variants in MMR genes is thus pivotal for optimizing the treatment and surveillance of patients with LS and for the identification of at-risk family members, to reduce cancer-related morbidity and mortality. This is best done using Next Generation Sequencing (NGS) multi-gene panel testing, which increases the diagnostic yield, but also increases the chances of finding variants of uncertain significance (VUS). As the Pakistani population remains under-represented, the likelihood of finding a VUS is high, making it difficult to use these results for clinical decision-making.
• To study the presence of disease-causing variants as well as VUSs in MMR genes causing LS in a series of patients diagnosed with breast cancer who underwent genetic testing using a multi-gene NGS panel
• To study the clinical characteristics of patients with LS who presented with breast cancer
• To use immunohistochemistry (IHC) on breast tumour tissue samples to clarify whether VUSs in MMR genes in breast cancer patients are associated with loss of staining.
Methods: Retrospective chart review of patients who visited the hereditary cancer (HBC) clinic and proceeded with Hereditary Breast and Gynecological Cancer multi-gene NGS panel testing (at Prevention Genetic and Invitae Genetics, USA) from May 2017 to Oct 2021, at an Academic Medical Centre, Aga Khan University Hospital, Karachi, Pakistan. IHC was performed using standard antibodies against the protein products of MLH1, MSH2, MSH6 and PMS2.
Results and Discussion: A total of 460 breast cancer patients qualified and proceeded with testing, considering their personal and/or family history of disease, based on NCCN criteria. 94 patients (20.4%) had a positive genetic test result, which included Pathogenic (P) and Likely Pathogenic (LP) variants. Of the remaining patients, 167 (36.3%) had one or more VUS[s], and 199 (43.3%) had a negative genetic test result.
Five out the total 460 patients (1.1%) or five of the 94 patients with positive results (5.3%), tested positive for LS, with an average age at diagnosis of 40 years. One patient had a personal history of colon cancer at age 38 and had then presented with breast cancer at age 43; and had a family history of colon cancer. Another patient who presented with breast cancer only, harbored a pathogenic variant in MSH6 as well as BRCA1, having a positive family history of breast and uterine cancer. In the remaining three patients, personal or family history was not indicative of any possible established link with LS, and their diagnoses would have been missed if MMR genes were not included in the multi-gene panel. Thus, multi-gene testing including MMR genes increased the diagnostic yield by 4.3% (4/94), even after excluding the patient with a personal history of colon cancer. Details of these patients are mentioned in Table 1.
Out of the total 460 patients who underwent testing, 28 (6.1%) harbored a VUS in MMR genes, namely PMS2 (n=12), MSH2 (n=7), MSH6 (n=8) and one patient had a VUS in both PMS2 and MSH2. No VUS in MLH1 was identified in breast cancer patients.
IHC was done on 18/28 (64.3%) and no loss of staining was observed on any tissue sample, possibly indicating that the variants are not disease-causing. We also observed six recurrent VUSs in unrelated patients, which included, (variant.1) v.1: MSH2 NM_000251.2 (p.L135V) (Rs193096019 MAF in South Asians=0.05%), v.2: MSH6 NM_000179.2 (p.L1356Dfs*4), (rs775836476, MAF in South Asians=0.04%), v.3: MSH6, (p.R911Q), (Rs761622304,MAF in South Asians= 0.006%), v.4: PMS2 NM_000535.5 (p.R294W) (rs563433235, MAF in South Asians= 0.03%), v.5: PMS2 (p.L454S) (absent from population database), v.6: PMS2 (p.D784N) (unreliable region coverage).It is worth noting that, v. 2, 4 and 6 have been reported in diseased individuals, while v.5 is a novel variant, absent from the gnomAD, highlighting the need for further functional studies to understanding the role of these variants in tumorigenesis.
Conclusions: In our experience with genetic testing in the HBC, a small proportion of patients were diagnosed with Lynch Syndrome, some presenting with breast cancer alone, without a personal or family history of LS associated tumors. This may justify the need to include MMR genes in multi-gene panels being offered to breast cancer patients. VUSs in these genes remain challenging, especially in underrepresented populations, and IHC may be a way to at least partially clarify their significance. More ethno-specific genomic studies, as well as better functional studies are required provide better clinical care.

Publication (Name of Journal)

Genetics in Medicine