Contribution of MLH1, MSH2, and MSH6 large genomic rearrangements to Pakistani colorectal cancer patients

SummaryBackgroundLynch syndrome is a rare familial cancer syndrome caused by pathogenic variants in the mismatch repair genes MLH1, MSH2, MSH6, or PMS2, that cause predisposition to various cancers, predominantly colorectal and endometrial cancer. Data are emerging that pathogenic variants in mismatch repair genes increase the risk of early-onset aggressive prostate cancer. The IMPACT study is prospectively assessing prostate-specific antigen (PSA) screening in men with germline mismatch repair pathogenic variants. Here, we report the usefulness of PSA screening, prostate cancer incidence, and tumour characteristics after the first screening round in men with and without these germline pathogenic variants.MethodsThe IMPACT study is an international, prospective study. Men aged 40–69 years without a previous prostate cancer diagnosis and with a known germline pathogenic variant in the MLH1, MSH2, or MSH6 gene, and age-matched male controls who tested negative for a familial pathogenic variant in these genes were recruited from 34 genetic and urology clinics in eight countries, and underwent a baseline PSA screening. Men who had a PSA level higher than 3·0 ng/mL were offered a transrectal, ultrasound-guided, prostate biopsy and a histopathological analysis was done. All participants are undergoing a minimum of 5 years' annual screening. The primary endpoint was to determine the incidence, stage, and pathology of screening-detected prostate cancer in carriers of pathogenic variants compared with non-carrier controls. We used Fisher's exact test to compare the number of cases, cancer incidence, and positive predictive values of the PSA cutoff and biopsy between carriers and non-carriers and the differences between disease types (ie, cancer vs no cancer, clinically significant cancer vs no cancer). We assessed screening outcomes and tumour characteristics by pathogenic variant status. Here we present results from the first round of PSA screening in the IMPACT study. This study is registered with ClinicalTrials.gov, NCT00261456, and is now closed to accrual.FindingsBetween Sept 28, 2012, and March 1, 2020, 828 men were recruited (644 carriers of mismatch repair pathogenic variants [204 carriers of MLH1, 305 carriers of MSH2, and 135 carriers of MSH6] and 184 non-carrier controls [65 non-carriers of MLH1, 76 non-carriers of MSH2, and 43 non-carriers of MSH6]), and in order to boost the sample size for the non-carrier control groups, we randomly selected 134 non-carriers from the BRCA1 and BRCA2 cohort of the IMPACT study, who were included in all three non-carrier cohorts. Men were predominantly of European ancestry (899 [93%] of 953 with available data), with a mean age of 52·8 years (SD 8·3). Within the first screening round, 56 (6%) men had a PSA concentration of more than 3·0 ng/mL and 35 (4%) biopsies were done. The overall incidence of prostate cancer was 1·9% (18 of 962; 95% CI 1·1–2·9). The incidence among MSH2 carriers was 4·3% (13 of 305; 95% CI 2·3–7·2), MSH2 non-carrier controls was 0·5% (one of 210; 0·0–2·6), MSH6 carriers was 3·0% (four of 135; 0·8–7·4), and none were detected among the MLH1 carriers, MLH1 non-carrier controls, and MSH6 non-carrier controls. Prostate cancer incidence, using a PSA threshold of higher than 3·0 ng/mL, was higher in MSH2 carriers than in MSH2 non-carrier controls (4·3% vs 0·5%; p=0·011) and MSH6 carriers than MSH6 non-carrier controls (3·0% vs 0%; p=0·034). The overall positive predictive value of biopsy using a PSA threshold of 3·0 ng/mL was 51·4% (95% CI 34·0–68·6), and the overall positive predictive value of a PSA threshold of 3·0 ng/mL was 32·1% (20·3–46·0).InterpretationAfter the first screening round, carriers of MSH2 and MSH6 pathogenic variants had a higher incidence of prostate cancer compared with age-matched non-carrier controls. These findings support the use of targeted PSA screening in these men to identify those with clinically significant prostate cancer. Further annual screening rounds will need to confirm these findings.FundingCancer Research UK, The Ronald and Rita McAulay Foundation, the National Institute for Health Research support to Biomedical Research Centres (The Institute of Cancer Research and Royal Marsden NHS Foundation Trust; Oxford; Manchester and the Cambridge Clinical Research Centre), Mr and Mrs Jack Baker, the Cancer Council of Tasmania, Cancer Australia, Prostate Cancer Foundation of Australia, Cancer Council of Victoria, Cancer Council of South Australia, the Victorian Cancer Agency, Cancer Australia, Prostate Cancer Foundation of Australia, Asociación Española Contra el Cáncer (AECC), the Instituto de Salud Carlos III, Fondo Europeo de Desarrollo Regional (FEDER), the Institut Català de la Salut, Autonomous Government of Catalonia, Fundação para a Ciência e a Tecnologia, National Institutes of Health National Cancer Institute, Swedish Cancer Society, General Hospital in Malmö Foundation for Combating Cancer.

Lynch syndrome is caused by variants in DNA mismatch repair (MMR) genes and associated with an increased risk of colorectal cancer (CRC). In patients with Lynch syndrome, CRCs can develop via different pathways. We studied associations between Lynch syndrome-associated variants in MMR genes and risks of adenoma and CRC and somatic mutations in APC and CTNNB1 in tumors in an international cohort of patients. We combined clinical and molecular data from 3 studies. We obtained clinical data from 2747 patients with Lynch syndrome associated with variants in MLH1, MSH2, or MSH6 from Germany, the Netherlands, and Finland who received at least 2 surveillance colonoscopies and were followed for a median time of 7.8 years for development of adenomas or CRC. We performed DNA sequence analyses of 48 colorectal tumors (from 16 patients with mutations in MLH1, 29 patients with mutations in MSH2, and 3 with mutations in MSH6) for somatic mutations in APC and CTNNB1. Risk of advanced adenoma in 10 years was 17.8% in patients with pathogenic variants in MSH2 vs 7.7% in MLH1 (P < .001). Higher proportions of patients with pathogenic variants in MLH1 or MSH2 developed CRC in 10years (11.3% and 11.4%) than patients with pathogenic variants in MSH6 (4.7%) (P= .001 and P= .003 for MLH1 and MSH2 vs MSH6, respectively). Somatic mutations in APC were found in 75% of tumors from patients with pathogenic variants in MSH2 vs 11% in MLH1 (P= .015). Somatic mutations in CTNNB1 were found in 50% of tumors from patients with pathogenic variants in MLH1 vs 7% in MSH2 (P= .002). Noneof the 3 tumors with pathogenic variants in MSH6 had a mutation in CTNNB1, but all had mutations in APC. In an analysis of clinical and DNA sequence data from patients with Lynch syndrome from 3 countries, we associated pathogenic variants in MMR genes with risk of adenoma and CRC, and somatic mutations in APC and CTNNB1 in colorectal tumors. If these findings are confirmed, surveillance guidelines might be adjusted based on MMR gene variants.

BackgroundDepending on the population studied, large genomic rearrangements (LGRs) of the mismatch repair (MMR) genes constitute various proportions of the germline mutations that predispose to hereditary non-polyposis colorectal cancer (HNPCC). It has been reported that loss of heterozygosity (LOH) at the LGR region occurs through a gene conversion mechanism in tumors from MLH1/MSH2 deletion carriers; however, the converted tracts were delineated only by extragenic microsatellite markers. We sought to determine the frequency of LGRs in Slovak HNPCC patients and to study LOH in tumors from LGR carriers at the LGR region, as well as at other heterozygous markers within the gene to more precisely define conversion tracts.MethodsThe main MMR genes responsible for HNPCC, MLH1, MSH2, MSH6, and PMS2, were analyzed by MLPA (multiplex ligation-dependent probe amplification) in a total of 37 unrelated HNPCC-suspected patients whose MLH1/MSH2 genes gave negative results in previous sequencing experiments. An LOH study was performed on six tumors from LGR carriers by combining MLPA to assess LOH at LGR regions and sequencing to examine LOH at 28 SNP markers from the MLH1 and MSH2 genes.ResultsWe found six rearrangements in the MSH2 gene (five deletions and dup5-6), and one aberration in the MLH1 gene (del5-6). The MSH2 deletions were of three types (del1, del1-3, del1-7). We detected LOH at the LGR region in the single MLH1 case, which was determined in a previous study to be LOH-negative in the intragenic D3S1611 marker. Three tumors displayed LOH of at least one SNP marker, including two cases that were LOH-negative at the LGR region.ConclusionLGRs accounted for 25% of germline MMR mutations identified in 28 Slovakian HNPCC families. A high frequency of LGRs among the MSH2 mutations provides a rationale for a MLPA screening of the Slovakian HNPCC families prior scanning by DNA sequencing. LOH at part of the informative loci confined to the MLH1 or MSH2 gene (heterozygous LGR region, SNP, or microsatellite) is a novel finding and can be regarded as a partial LOH. The conversion begins within the gene, and the details of conversion tracts are discussed for each case.

Colorectal cancer is the second leading cause of cancer-related deaths in women and men in Algeria. Lynch syndrome (LS) is an autosomal dominant disease caused by heterozygous germline pathogenic variants in mismatch repair genes (MMR) and frequently predisposes to colorectal cancer. However, data about MMR germline pathogenic variants in Algerian patients are limited. This first nationwide study aims to describe clinicopathologic features and germline variants in MMR genes in Algerian families with suspected LS. Sixty-four (64) families with suspected LS were studied. Index cases with LS who fulfilled Amsterdam criteria were screened by PCR-direct sequencing for germline variants in MMR genes: MLH1 (exons 1, 9, 10, 13, 16), MSH2 (exons 5, 6, 7, 12), MSH6 (exons 4 and 8) and PMS2 (exons 6 and 10). We selected these specific risk exons genes since they have a higher probability of harboring pathogenic variants. In addition, two unrelated LS patients were screened by next-generation sequencing using a cancer panel of 30 hereditary cancer genes. Six germline pathogenic variants and one germline likely pathogenic variant were identified in 19 (29.68%) families (4 MLH1, 2 MSH2 and 1 MSH6). Of index cases and relatives who underwent genetic testing (n=76), 30 (39.47%) had MMR pathogenic gene variants, one (0.13%) had MMR gene likely pathogenic variant and three had MMR variant of uncertain significance, respectively. Two novel germline pathogenic variants in MLH1 (2) and one germline likely pathogenic variant in MSH6 (1) never published in individuals with LS have been detected in the present study. The recurrent MLH1 germline pathogenic variant c.1546C>T has been found in nine LS families, six of them related with two large kindreds, from four North central provinces of Algeria. In addition, the common MSH2 germline pathogenic variant c.942+3A>T has been detected in five unrelated patients with a strong LS family history. The accumulative knowledge about clinicopathological and genetic characteristics of LS in Algerian patients will impact clinical management in the areas of both prevention and treatment.

Colorectal cancer has been reported as the third leading cause of cancer related death in the world. About 5-10% of colorectal cancers are due to an inherited predisposition. This thesis focuses on investigating the prevalence of large genomic rearrangements and other types of germline mutations in novel cancer susceptibility genes in major hereditary colorectal cancer syndromes, hereditary nonpolyposis colorectal cancer (HNPCC) and familial adenomatous polyposis (FAP). Furthermore, the second somatic mutations were characterized in the tumors from DNA mismatch repair (HNPC) and APC gene mutation carriers (FAP) to address the mechanism(s) of tumorigenesis in these syndromes. All these investigations aim to understand tumor initiation and progression in hereditary colorectal cancer syndromes in order to enable early and reliable presymptomatic diagnosis of a person at increased risk and offer optimal medical management to prevent cancer. HNPCC is an autosomal dominantly inherited cancer predisposition syndrome caused by germline mutations in DNA mismatch repair (MMR) genes. Prescreening methods are routinely applied to detect MMR gene sequence alterations, but inevitably miss large genomic rearrangements. Here, novel PCR-based methods to study gene dosage were introduced in 35 MLH/MSH2 HNPCC patients in whom no mutation could be identified by conventional screening methods. These methods are QMPA (quantitative multiplex PCR amplification) and MLPA (multiplex ligation dependent probe amplification). Three patients were found to carry large deletions by QMPA and MLPA. In 1 patient, however, QMPA yielded a false positive result. Both methods, QMPA and MLPA appear to be of comparable sensitivity albeit with different specificity. Since the QMPA technique is difficult to set up and to standardize the PCR conditions, the MLPA assay is better suited to routinely search for large genomic rearrangements. The investigations subsequently continued to detect the frequency and nature of LOH as second, somatic event in tumors from MLH/MSH2 germline deletion carriers. MLPA technique was applied to analyze 18 cancer specimens from independent sets of Swiss and Finnish MLH1/MSH2 deletion carriers. Results revealed that somatic deletions identical to the ones in the germline occur frequently (55%) in CRCs and that this type of loss of the wild type allele is also present in extracolonic HNPCC associated tumors. Chromosome specific marker analysis implies that loss of the wild type allele predominantly occurs through locus restricted recombination events, i.e. gene conversion, rather than mitotic recombination or deletion of the respective gene locus. The same investigation was carried on a 31 years old colorectal cancer patient who carries de novo mutation (c.666dupA) in the MLH1 gene. The tumor analysis of this patient showed a similar somatic mutation mechanism to the large genomic deletion carriers. Prior to our analysis of the somatic in the attenuated form of familial adenomatous polyposis (AFAP), earlier investigations had shown that in classical FAP the two hits in the APC (Adenomatosis polyposis coli) gene are not occurring randomly but are in fact interdependent. AFAP is clinically characterized by fewer than 100 adenomatous polyps in the colorectum and presents with a milder phenotype compared to classical FAP. APC mutations in AFAP patients are typically located in the very 5’ and 3’ gene regions as well as in the alternatively spliced region of exon 9. In a collaborative effort we investigated the somatic alterations in 235 tumors of 35 AFAP patients. Adenomas of AFAP patients were often found to actually exhibit ‘three hits’ at the APC gene that mostly result in loss of the allele carrying the germline APC mutation. We assume that this actually leads to an optimization of the beta-catenin level, hence positively regulating the Wnt signal. Recently, bi-allelic germline mutations in the base excision repair gene MutY homologue (MYH) have been associated with an autosomal recessively inherited predisposition to multiple colorectal adenomas. They are also referred to as MYH-associated polyposis (MAP). Here, we assessed the prevalence of MYH germline alteration in 79 unrelated polyposis patients in whom no APC mutation could be detected. The aims of the study were i) to assess the MYH mutation carrier frequency among Swiss APC mutation negative patients and (ii) to identify phenotypic differences between MYH mutation carriers and APC / MYH mutation negative polyposis patients. dHPLC and direct genomic DNA sequencing were applied to screen for mutation. Overall, 7 biallelic and 9 monoallelic MYH germline mutation carriers were identified. 1 out of 10 classical polyposis and 6 out of 35 attenuated polyposis patients carried biallelic MYH alterations, 2 of which represent novel gene variants (p.R 171q and p.R 231H). On the basis of our finding and earlier reports, MYH mutation screening should be considered if all of the following criteria are fulfilled: (1) presence of classical or attenuated polyposis coli, 2) absence of a pathogenic APC mutation, and 3) a family history compatible with an autosomal recessive mode of inheritance.

Endometrial cancer has been associated with pathogenic variants in mismatch repair (MMR) genes, especially in the context of the hereditary Lynch Syndrome. More recently, pathogenic variants in genes of homology‐directed repair (HDR) have also been suggested to contribute to a subset of endometrial cancers. In the present hospital‐based study, we investigated the relative distribution of pathogenic MMR or HDR gene variants in a series of 342 endometrial cancer patients from the Oncology Clinic in Almaty, Kazakhstan. In comparison, we also sequenced 178 breast cancer patients from the same population with the same gene panel. Identified variants were classified according to ClinVar, ESM1b, and AlphaMissense prediction tools. We found 10 endometrial cancer patients (2.9%) carrying pathogenic or likely pathogenic variants in MMR genes (7 MSH6, 1 MSH2, 2 MUTYH), while 14 endometrial cancer patients (4.1%) carried pathogenic variants in HDR genes (4 BRCA2, 3 BRCA1, 3 FANCM, 2 SLX4, 1 BARD1, 1 BRIP1). In the breast cancer series, we found 8 carriers (4.5%) of pathogenic or likely pathogenic variants in MMR genes (2 MSH2, 2 MSH6, 4 MUTYH) while 12 patients (6.7%) harbored pathogenic or likely pathogenic HDR gene variants (5 BRCA1, 3 BRCA2, 1 BRIP1, 1 ERRC4, 1 FANCM, 1 SLX4). One patient who developed breast cancer first and endometrial cancer later carried a novel frameshift variant in MSH6. Our results indicate that MMR and HDR gene variants with predicted pathogenicity occur at substantial frequencies in both breast and endometrial cancer patients from the Kazakh population.

Lynch Syndrome: A Single Hereditary Cancer Syndrome or Multiple Syndromes Defined by Different Mismatch Repair Genes?

Simple SummaryLynch syndrome is the most common form of hereditary colorectal cancer associate to variants in Mismatch Repair (MMR) genes. Unfortunately, a large amount of variants identified in these genes remain of uncertain significance. Therefore, many individuals with a clinical suspicion of LS receive a diagnosis of Lynch-like syndrome. This review summarizes the main aspects of Lynch syndrome and recent advances in the molecular diagnosis and, in particular the main factors that determine the loss of expression of MMR genes.Hereditary non-polyposis colorectal cancer is also known as Lynch syndrome. Lynch syndrome is associated with pathogenetic variants in one of the mismatch repair (MMR) genes. In addition to colorectal cancer, the inefficiency of the MMR system leads to a greater predisposition to cancer of the endometrium and other cancers of the abdominal sphere. Molecular diagnosis is performed to identify pathogenetic variants in MMR genes. However, for many patients with clinically suspected Lynch syndrome, it is not possible to identify a pathogenic variant in MMR genes. Molecular diagnosis is essential for referring patients to specific surveillance to prevent the development of tumors related to Lynch syndrome. This review summarizes the main aspects of Lynch syndrome and recent advances in the field and, in particular, emphasizes the factors that can lead to the loss of expression of MMR genes.

Germline mutations in BRCA1 and BRCA2 (BRCA1/2) account for the majority of hereditary breast and/or ovarian cancers. Pakistan has one of the highest rates of breast cancer incidence in Asia, where BRCA1/2 small-range mutations account for 17% of early-onset and familial breast/ovarian cancer patients. We report the first study from Pakistan evaluating the prevalence of BRCA1/2 large genomic rearrangements (LGRs) in breast and/or ovarian cancer patients who do not harbor small-range BRCA1/2 mutations. Both BRCA1/2 genes were comprehensively screened for LGRs using multiplex ligation-dependent probe amplification in 120 BRCA1/2 small-range mutations negative early-onset or familial breast/ovarian cancer patients from Pakistan (Group 1). The breakpoints were characterized by long-range PCR- and DNA-sequencing analyses. An additional cohort of 445 BRCA1/2 negative high-risk patients (Group 2) was analyzed for the presence of LGRs identified in Group 1. Three different BRCA1 LGRs were identified in Group 1 (4/120; 3.3%), two of these were novel. Exon 1-2 deletion was observed in two unrelated patients: an early-onset breast cancer patient and another bilateral breast cancer patient from a hereditary breast cancer (HBC) family. Novel exon 20-21 deletion was detected in a 29-year-old breast cancer patient from a HBC family. Another novel exon 21-24 deletion was identified in a breast-ovarian cancer patient from a hereditary breast and ovarian cancer family. The breakpoints of all deletions were characterized. Screening of the 445 patients in Group 2 for the three LGRs revealed ten additional patients harboring exon 1-2 deletion or exon 21-24 deletion (10/445; 2.2%). No BRCA2 LGRs were identified. LGRs in BRCA1 are found with a considerable frequency in Pakistani breast/ovarian cancer cases. Our findings suggest that BRCA1 exons 1-2 deletion and exons 21-24 deletion should be included in the recurrent BRCA1/2 mutations panel for genetic testing of high-risk Pakistani breast/ovarian cancer patients.

1520 Background: Lynch syndrome (LS), caused by germline pathogenic variants in mismatch repair (MMR) genes, results in increased risk of colorectal, endometrial, and other cancers. LS has a prevalence of ~1 in 440 in European ancestry populations; prevalence data in other populations are limited. We identified and characterized carriers of pathogenic MMR gene variants in the multi-ethnic Bio Me Biobank in New York City. Methods: Exome sequence data from ~31,000 Bio Me participants were evaluated for known (per ClinVar) and predicted (loss-of-function) pathogenic variants in MMR genes. Population groups were defined by genetic ancestry. Participant questionnaires and electronic health records (EHRs) of carriers were reviewed for personal or family history of malignancy. Results: We identified 48 carriers of 33 distinct pathogenic variants in PMS2 (48%), MLH1 (27%), MSH6 (15%), and MSH2 (10%), for an estimated prevalence of ~1/640 in the Bio Me Biobank. Prevalence was higher among individuals of Non-Jewish European (N = 14; 1/400) and African (N = 14; 1/490) ancestries, compared to Puerto Rican (N = 8; 1/640), Ashkenazi Jewish (N = 6; 1/690), and other/mixed (N = 6) ancestries. Carriers had a median age of 56 (range 27 to 77) years and were 50% female. Overall rate of malignancy among carriers was 38%, with the lowest rate in PMS2 (26%) and the highest rate in MSH6 (57%) variant carriers. We found a high prevalence of endometrial cancer (21% of female carriers) and a lower prevalence of colorectal cancer (4% of all carriers). Only 2 carriers (4%) had a diagnosis of LS in their EHRs, and only 1 carrier met Amsterdam diagnostic criteria for LS. Conclusions: These data show that ~0.15% of participants in a multi-ethnic biobank are carriers of pathogenic MMR gene variants and suggest that the prevalence is higher in European and lower in non-European ancestry populations. Notably, most carriers do not have a clinical diagnosis of LS and do not meet diagnostic criteria for LS. Carriers demonstrate variable rates of cancer, which may contribute to under-diagnosis of LS. Genomic screening for pathogenic MMR variants may lead to earlier diagnosis of LS and improved outcomes.

Background: Lynch syndrome (LS) is a cancer-susceptibility syndrome associated with autosomal dominant predisposition to a spectrum of cancers, primarily of the colorectum and endometrium, which exhibit impaired DNA mismatch repair (MMR) activity. LS is caused by a hereditary (germline) pathogenic (PV) or likely pathogenic variant (LPV) in one of the mismatch repair (MMR) genes-MLH1, MSH2, MSH6, PMS2, or EPCAM. Although point mutations are the most common genetic changes in MMR genes, >20% are large genomic rearrangements. We hypothesized that a two-tier diagnostic strategy for Lynch syndrome (LS) using next generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) can increase diagnostic yield of patients with Lynch syndrome. Methods: This study included 60 patients suspected of LS. After genetic counseling, they were referred to genetic testing. Genomic DNA was extracted from peripheral blood and sequenced using NGS multigene panel testing covering 113 cancer susceptibility genes, including MMR genes. Regarding limitations of NGS analysis, which cannot reliably detect genomic alterations larger than 50 base pairs in length, the MLPA method was used for NGS negative DNA samples in order to identify larger deletions and duplications, commonly referred to as copy number variations (CNVs). Results: Different PVs were detected by NGS in 10 patients and CNVs were detected by MLPA in 7 more patients: 3xMLH1 del ex9-15, 2xMSH2 del ex1 and upstream, 1xMSH2 del ex9, and 1xMSH2 del ex1. We did not detect LPVs or variants of uncertain significance (VUS). In our cohort, the addition of MLPA provided an incremental yield of seven pathogenic CNVs, representing an 11.6% absolute increase in diagnostic sensitivity (from 16.7% to 28.3%) over the NGS-alone workflow, with CNVs accounting for 41% of all pathogenic findings. Conclusions: Our results show that MLPA is a very useful method in molecular diagnostics of LS and its implementation in routine genetic testing in combination with NGS using multigene panel testing would benefit both patients and health care providers.

Early studies of genetic predisposition due to the BRCA1 and BRCA2 genes have focused largely on sequence alterations, but it has now emerged that 4-28% of inherited mutations in the BRCA genes may be due to large genomic rearrangements of these genes. However, to date, there have been relatively few studies of large genomic rearrangements in Asian populations. We have conducted a full sequencing and large genomic rearrangement analysis (using Multiplex Ligation-dependent Probe Amplification, MLPA) of 324 breast cancer patients who were selected from a multi-ethnic hospital-based cohort on the basis of age of onset of breast cancer and/or family history. Three unrelated individuals were found to have large genomic rearrangements: 2 in BRCA1 and 1 in BRCA2, which accounts for 2/24 (8%) of the total mutations detected in BRCA1 and 1/23 (4%) of the mutations in BRCA2 detected in this cohort. Notably, the family history of the individuals with these mutations is largely unremarkable suggesting that family history alone is a poor predictor of mutation status in Asian families. In conclusion, this study in a multi-ethnic (Malay, Chinese, Indian) cohort suggests that large genomic rearrangements are present at a low frequency but should nonetheless be included in the routine testing for BRCA1 and BRCA2.

2008P - Large genomic rearrangements in BRCA1 and BRCA2 genes in the Portuguese population

Novel BRCA1 and BRCA2 genomic rearrangements in Southern Chinese breast/ovarian cancer patients

Lynch syndrome (LS) increases the risk of various cancers, including colorectal cancer, endometrial cancer and gastric cancer (GC). The incidence of LS among microsatellite instability-high (MSI-H) GC and their association in South Korea remains underexplored. This study investigates LS-associated pathogenic germline variants in MSI-H GC patients using whole-exome sequencing (WES) on normal tissues. This retrospective study included patients who underwent gastrectomy for GC at Soonchunhyang University Bucheon and Cheonan Hospitals from January 2011 to October 2023. Among 1,537 patients screened for MSI status, 127 (8.3%) were identified as MSI-H. WES was performed on normal tissues from 123 patients. Pathogenic/likely pathogenic (P/LP) variants in mismatch repair (MMR) genes were identified using in silico models and protein loss assessments in corresponding tumor tissues. Of the 127 MSI-H GC cases, characteristics aligned with typical MSI-H GC. The average age was 70.02 years, with 98 (77.2%) located in the lower body and 81 (63.8%) of the intestinal type. All five MSI markers were positive in 46.5% of cases, whereas four markers were positive in 27.6%. Of the MSI-H GCs, 10 LS candidates were identified. Three patients had known P/LP variants [MLH1 (c.1758dup), MSH6 (c.3261dup), MSH2 (c.1241T>C)]. Seven patients had variants of unknown significance (VUS) in MMR genes. Six (4.9%) patients were identified as having LS or possible LS, including one patient with the MLH1 (c.1153C>T) variant previously classified as VUS but now considered LS-associated. This large-scale screening for LS in MSI-H GC patients using retrospective samples confirmed the lower incidence of LS than those of colorectal or endometrial cancer and GC patients in Western countries, emphasizing the need for clinical consideration in managing MSI-H GC patients.