Germline Mutation Landscape and Associated Clinical Characteristics in Chinese Patients With Renal Cell Carcinoma.

Germline Contributions to Clonal Hematopoiesis in Solid Cancer Patients

Germline Variants Associated with Cancer Predisposition and Bone Marrow Failure Are Common in KMT2A-r Infant Acute Lymphoblastic Leukemia Patients

Renal medullary carcinomas: histopathologic phenotype associated with diverse genotypes

Clonal Hematopoiesis in Telomere Biology Disorders Associates with the Underlying Germline Defect and Somatic Mutations in POT1, PPM1D, and TERT promoter

P3-09-05: Clinical outcome of patients with advanced triple negative breast cancer with germline and somatic variants in homologous recombination gene

Background: Genetic susceptibility to renal cell carcinoma (RCC) remains poorly understood and limited to specific hereditary cancer syndromes. Whereas few studies have investigated rare germline variants in specific populations, the majority of them have not taken into account differences between histological subtypes of RCC. Objective: To identify common risk-genes for RCC within the Canadian population, investigate their association to clinical annotations and outcomes, and compare gene-burden among RCC patients from various countries. Methods: We conducted targeted DNA sequencing of 19 RCC-related and 27 cancer predisposition genes for 960 RCC patients (759 with clear cell and 201 with non-clear cell RCC) from Canada. We identified genes enriched in rare germline pathogenic variants (PVs) in RCC compared to a cancer-free control population (gnomAD, n=118148). Gene associations to RCC subtypes and clinical annotations were examined using Firth’s logistic regression models and Fisher’s exact tests, respectively. In addition, we compared prevalence of PVs in Canadian patients to those in previous studies from Japan (n=1632), the UK (n=1336) and the USA (n=254). Furthermore, we evaluated the performance of current criteria for RCC genetic screening for including patients with PVs in Canada, the US, and the UK. Results: We identified 39 germline PVs in 56 RCC patients from the Canadian cohort. Compared to cancer-free controls, PVs in MITF (OR: 212.3, 95% CI: 4.0-6.8, p= 1.44 × 10−9), CHEK2 (OR: 4.8, 95% CI: 1.0-2.1, p=3.94 × 10−5), and ATM (OR: 4.5, 95% CI: 0.7-2.2, p=0.016) genes were significantly enriched in patients with clear cell RCC, whereas PVs in FH (OR: 215.1, 95% CI: 4.2-6.4, p=6.14 × 10−9) were enriched in patients with non-clear cell RCC. We observed an association between PVs in DNA repair genes BRCA1, BRCA2 and ATM with the presence of metastasis in ccRCC (p=0.004) and RCC overall (p=0.003). Comparisons of gene-burden to other populations showed an enrichment for TP53 in RCC patients from Japan, while RCC patients from Canada showed an enrichment for CHEK2 and ATM. RCC patients from the US showed an enrichment for germline PVs in FH in comparison to Canadians. Notably, our analysis reveals that current criteria for referral to genetic screening for hereditary renal cancer fail to include the majority (73%) of patients harboring rare germline PVs in risk genes for RCC, both in Canada and globally. Conclusions: MITF, CHEK2, ATM, and FH were identified as risk-genes for RCC within the Canadian population, while germline mutations in BRCA1/2 and ATM are associated with risk of metastasis. Globally, clinical guidelines for genetic screening in RCC fail to identify up to 80% of patients with rare germline PVs. Citation Format: Kate I. Glennon, Mikiko Endo, Yoshiaki Usui, Yusuke Iwasaki, Rodney H. Breau, Anil Kapoor, Simon Tanguay, Yukihide Momozawa, Yasser Riazalhosseini. Germline susceptibility to renal cell carcinoma and implications for genetic screening [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr B010.

Colorectal Cancer Genetics Screening in the Community: Are We Ready? Can We Do It?

10601 Background: The increasing integration of somatic and germline testing into oncology practice allows physicians to target oncologic therapy and identify those with cancer predisposition. We explored the impact of a somatic assay (liquid biopsy, LB) on the identification of patients appropriate for germline genetic testing. Methods: We identified a cohort of diverse cancer patients with LB to assess for targetable somatic gene variants at LAC+USC Medical Center between 2016 and 2020 (n= 467). To enrich the cohort for variants that may reflect germline findings, we focused on the 46 patients (9.9%) who had at least one variant identified with a cell-free DNA (cfDNA) fraction of 25.00% or greater. Retrospective chart review extracted demographics and medical history with variables related to cancer history and treatment. LB variants were classified based on whether germline confirmation was indicated and the results of germline tests, when done, were reviewed. Results: Table summarizes the characteristics of the 46 patients identified to have at least one variant on LB in ≤ 25% of the cfDNA. The most frequently mutated genes on LB were TP53 (n=18, 39%), KRAS (n=11, 24%), APC (n=8, 17%), BRCA2 (n=7, 15%), PIK3CA (n=6, 13.0%), and BRCA1 (n=4, 9%). Seventeen patients (40%) were referred for genetic counseling and 13 (30%) underwent germline testing of whom 10 (77%) carried pathogenic variants (PV). All germline PV were concordant with LB variants identified. Four patients with PV BRCA2 on LB and confirmed to be germline, had lung or biliary tract diagnoses, which are not part of the typical BRCA-tumor spectrum. Thirty-three patients were not referred for genetic counseling, though 24 (72%) had LB-identified variants in cancer predisposition genes and 18 (54%) merited a genetics referral. Among patients with germline mutations, three (23%) had targeted therapy and two (15%) had preventive surgery to address second primary cancer risk. Among the 467 patients with LB results, there were an additional 13 patients (not included in the enriched group) known to have a cancer predisposition gene PV. Only two (15%) had findings on LB reports that suggested germline testing would be indicated. Conclusions: While the purpose of somatic testing is to identify targeted therapy, it can provide germline insight, especially for patients not typically referred for genetic assessment. Further education and guidance is needed to assure that this aspect of somatic testing is appreciated by oncology providers and acted upon.[Table: see text]

245P - Frequency of germline mutations in women’s cancer susceptibility genes in a large cohort of Chinese breast cancer patients

551 Background: In addition to the association of SDHB genomic alterations (GA) with paraganglioma and pheochromocytoma, SDHB GA are also linked to a rare form of RCC with inactivation or homozygous deletion (complete loss) of the SDHB gene (SDHBdef-RCC) which carries a high risk for metastasis and adverse prognosis. We studied the GA landscape of SDHBdef-RCC and compared it to RCC lacking SDHB GA (SDHBwt-RCC) . Methods: 9,462 cases of clinically advanced RCC underwent hybrid capture based comprehensive genomic profiling (CGP) using the FoundationOneCDx assay to identify all classes GA. Microsatellite instability status (MSI) and tumor mutational burden (TMB) were determined from the sequencing data. PD-L1 expression was determined by IHC using the Dako TPS score (0% = negative; 1-49% = low positive and ≥50% = high positive). All cases had relapsed either loco-regionally or with metastatic disease at the time sequencing. Results: 17 (0.6%) of the sequenced advanced RCC were SDHBdef-RCC) and included 7 (41.2%) with germline short variant (SV) SDHB mutations, 6 (35.5%) with somatic SV SDHB mutations and 4 (23.5%) with homozygous SDHB deletions (complete loss of 8 of 8 exons). Their histologic RCC subtypes included 5 sarcomatoid, 5 high grade NOS, 4 oncocytic, 2 clear cell and 1 collecting duct RCC morphology; 10 RCC were sequenced using the primary kidney tumor and 7 from a metastatic site biopsy for CGP. Patients with SDHBdef-RCC were younger (mean age 45.9 yrs vs 62.5 yrs; p<.0001) and had a similar gender distribution (29.4% - 30.9% female). Biomarkers of checkpoint inhibitor efficacy including MSI-high status (0% - 0.6%), TMB level (mean 3.6 to 3.9 mutations/Mb) and any level of PD-L1 expression (40.0% vs 35.7%) were similar in both groups. Noteworthy GA summaries are shown in attached Table. Conclusions: SDHBdef-RCC is a rare form of clinically advanced RCC with predominantly oncocytic and sarcomatoid non-clear cell histology featuring either inactivating short variant SDHB germline or somatic mutations or homozygous deletion of SDHB gene. When compared with SDHDwt-RCC, SDHBdef-RCC occurs in younger patients, features non-clear cell histology, less frequent GA in tumor suppressor genes ( VHL , PBRM1 , SETD2 , BAP1 ), less frequent GA in cell cycle regulatory genes ( CDKN2A / B , T P53 ) and significant increased GA in NF2 . Further investigation of GA in this rare RCC type for clinical trial design and germline screening strategies is warranted. Limitations of this study include its retrospective nature, potential selection bias, and lack of clinically relevant data. Genomic alteration summaries of sequenced advanced RCC. SDHBmut RCC (N=17) SDHBwt RCC (N=9445) P value VHL 23.5% 43.7% NS PBRM1 0.0% 24.9% .011 SETD2 0.0% 17.0% NS BAP1 0.0% 11.3% NS CDKN2A 11.8% 25.6% NS CDKN2B 11.8% 20.1% NS MTAP 7.7% 15.0% NS TP53 5.9% 21.1% NS NF2 23.5% 6.7% .024

Germline pathogenic alleles predispose carriers to malignancies; failure to recognize the underlying cancer susceptibility and subsequent delayed diagnosis may lead to severe health impairment. It remains largely undetermined what the somatic mutation characteristics are in colorectal cancer (CRC) patients with pathogenic/likely pathogenic (P/LP) germline mutations and whether, and how, these germline mutations typically located in non-mismatch repair genes, are associated with CRC tumorigenesis. From 8,676 Chinese patients with CRC, we initially screened those who had undergone both germline and somatic mutation testing. We analyzed the relationship between germline mutations and the somatic mutational landscape in this cohort. Germline alterations were examined with a 556- or 105- gene next-generation sequencing panel, and somatic alterations were examined with a 556-gene panel. Overall, 80 CRC patients were identified as carriers of P/LP germline mutations. After excluding 6 patients lacking somatic mutation testing data, 74 patients with P/LP germline mutations and 100 patients without germline mutations were finally enrolled in this study. Twenty-one germline genes were detected in the 74 patients. Compared with patients without P/LP mutations (non-P group), those in the P/LP mutations (P group) had significantly lower age and a higher ratio of microsatellite instability. Patients harboring P/LP germline mutations in MMR genes (P-MMR) were significantly younger and more frequently exhibited high tumor mutational burden. The most frequent somatic variations were KRAS and TP53. The somatic mutational landscape revealed a significantly higher mutational frequency in the P group than in the non-P group, and in the P-MMR group than in the P-non-MMR group. The MAPK pathway was significantly enriched in the P and P-MMR groups. Our data showed lower mutation rate of MSH2 among all MMR genes than in the Western population. Population-based risk analysis indicated that the odds ratio of BRCA2 and ATM mutations exceeded 10. Our findings offer a comprehensive overview of genetic susceptibility in Chinese CRC, which may help to shape a more comprehensive understanding of genetic structure of CRC and generate accurate individualized risk management strategies for mutation carriers.

Prostate cancer (PCa) is the most common diagnosed malignancy and the second leading cause of cancer-related deaths among men in the USA. Advances in high-throughput genotyping and next generation sequencing technologies have enabled discovery of germline genetic susceptibility variants and somatic mutations acquired during tumor formation. Emerging evidence indicates that germline variations may interact with somatic events in carcinogenesis. However, the possible oncogenic interactions and cooperation between germline and somatic variation and their role in aggressive PCa remain largely unexplored. Here we investigated the possible oncogenic interactions and cooperation between genes containing germline variation from genome-wide association studies (GWAS) and genes containing somatic mutations from tumor genomes of 305 men with aggressive tumors and 52 control samples from The Cancer Genome Atlas (TCGA). Network and pathway analysis were performed to identify molecular networks and biological pathways enriched for germline and somatic mutations. The analysis revealed 90 functionally related genes containing both germline and somatic mutations. Transcriptome analysis revealed a 61-gene signature containing both germline and somatic mutations. Network analysis revealed molecular networks of functionally related genes and biological pathways including P53, STAT3, NKX3-1, KLK3, and Androgen receptor signaling pathways enriched for germline and somatic mutations. The results show that integrative analysis is a powerful approach to uncovering the possible oncogenic interactions and cooperation between germline and somatic mutations and understanding the broader biological context in which they operate in aggressive PCa.

Purpose: The most frequent cause of hereditary colorectal cancer (CRC) is Lynch syndrome, accounting for 3% of all CRC cases. The underlying germline predisposition is a mutation in any of the four mismatch repair (MMR) genes (MLH1, MSH2, MSH6, PMS2), while microsatellite instability (MSI) is a hallmark of these tumors. However, CRC cases with MSI, no MLH1 somatic hypermethylation and absence of MMR germline mutation account for up to 60% of cases of MMR-defective tumors. They have been termed Lynch-like syndrome (LLS) and treatment management decisions are complicated due to unconfirmed suspicions of hereditary cancer. The aim of the present study was to investigate whether LLS cases in patients under the age of 40 carry potentially pathogenic germline variants in new genes for CRC predisposition causing a MMR-defective tumor phenotype. Methods: We performed whole-exome sequencing (WES) in the germline and tumoral DNA of 16 early-onset LLS patients. We filtered for recessive germline variants in genes involved in DNA repair. An exhaustive functional evaluation for 2 MCM8 genetic variants detected in one patient was performed. The CRISPR/Cas9 system was used to generate MCM8ko clones in a cell model (DLD-1). Site-directed mutagenesis produced the genetic variants for ectopic expression in the MCM8ko model. Functional characterization included the comet assay, which detected DNA damage induced by oxaliplatin in the transfected cells. MCM8ko cells were evaluated for MSI after 30, 60 and 90 days of culture, and mutational signatures were assessed with SigProfiler. Results: The MCM8 variants c.351_354delAAAG (p.Lys118GlufsTer5, p.K118fs) and c.414A>G (p.Ile138Met, p.I138M) were identified in one early-onset LLS patient with biallelic somatic inactivation of MLH1. Manual evaluation of WES data showed that germline MCM8 variants were in trans. In the comet assay, both MCM8 variants revealed higher sensitivity to oxaliplatin and more DNA damage compared to the wild-type control. One of the MCM8KO clones showed MSI after 30 days of sub-culturing. After 120 days, MCM8KO clones had acquired a significant contribution of the SBS20 mutational signature, which is associated with defective MMR DNA. Conclusions: We postulate that MCM8 is a new germline CRC predisposing gene in early-onset LLS, which may be involved in both MMR and double-strand break repair. We further provide evidence that in some LLS CRC cases, especially in young patients, the biallelic somatic MMR inactivation may be caused by new CRC germline predisposing genes. Additional mutational screening is warranted for such cases. Citation Format: Mariano Golubicki, Laia Bonjoch, José G. Acuña-Ochoa, Marcos Diaz-Gay, Jennifer Muñoz, Miriam Cuatrecasas, Teresa Ocaña, Juan Robbio, Enrique L. Roca, Antoni Castells, Fracesc Balaguer, Marina Antelo, Sergi Castellvi-Bel. Germline biallelic mutations in MCM8 are associated with early-onset Lynch-like syndrome [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2366.

While the association between defect of DNA damage repair (DDR) genes and prostate cancer (PCa) risk is well-established, there has been a lack of data in East Asian population. This study reports contemporary prevalence of DDR genes mutations in Korean PCa patients. We analysed samples from 1,316 patients with PCa in Korea. Whole genome sequencing and targeted cancer panel sequencing were employed for genetic analysis. A total of 26 DDR genes were analysed based on the previous literature. Germline mutation profiling was conducted in 1,026 patients, identifying 66 mutations (6.4%) at 14 genes. Somatic mutation profiling in 550 patients revealed 105 mutations (19.1%) at 15 genes. While BRCA2 was most frequent (3.4%) among germline mutations, CDK12 was most frequent (6.5%) among somatic mutations in our study. Patients with metastatic disease showed significantly higher mutation frequency than patient with localized disease in both germline and somatic mutation (both p-value<0.05). There were statistically positive correlation between increase of grade group and higher frequency in both germline and somatic DDR gene mutations (p<0.001). The patients with higher stage showed significantly higher rate of DDR gene mutation in germline analysis (p<0.001) but not in somatic analysis (p=0.888). BRCA2 was the most prevalent in germline mutations but CDK12 was out-numbered BRCA2 in somatic mutations in the present study. The higher frequency of DDR gene mutation was associated with advanced cancer stage and higher cellular grade group.

Background To date, 5% to 6 % of all colorectal cancers (CRCs) are associated with germline pathogenic variants in cancer predisposition genes that confer inherited predisposition to CRC. The use of genetic testing to identify individuals at risk for hereditary CRC syndromes can help to prevent the development of cancer and in the clinical management of the colorectal patients in the areas of both prevention and treatment. We report here the experience of our research laboratory of genetic testing for hereditary polyposis syndromes and Lynch syndrome (LS), respectively, in 126 patients. Methods Fifty four (54) severe familial adenomatous polyposis (FAP) patients and 72-suspected Lynch syndrome (LS) patients, respectively, were selected from 2851 consecutive colorectal patients at five public hospitals during 2012-2019. Family histories of cancer were obtained from interviews, pedigrees and medical records of patients. Index cases and relatives diagnosed with FAP syndrome or Lynch syndrome have been tested for germline variants in APC, MLH1, MSH2, MSH6 and PMS2 genes, respectively, using PCR-Sanger Sequencing or by NGS using a cancer panel of 30 hereditary cancer genes (Color Genomics). Results We detected 13 germline pathogenic variants in APC gene in 17 unrelated families, one germline pathogenic variant in BMPRA1 gene in juvenile polyposis syndrome (JPS) patient; seven (7) germline pathogenic variants and 2 variants of uncertain clinical significance (VUS) in MMR genes. Interestingly, 4 novel germline pathogenic variants in APC gene and 3 novel germline pathogenic variants in MMR genes, respectively, have been detected in our study. The most occurring germline pathogenic variants in APC gene were c.3927_3931del and c.4728dup that were identified in four and two index cases in 6 unrelated FAP families, respectively. In Lynch syndrome patients, the rare germline pathogenic variant MLH1 c.1546C&amp;gt;T has been found in 21 individuals from 9 LS families, 6 of them related, with two large kindreds. In addition, the recurrent germline pathogenic variant MSH2 c.942+3A&amp;gt;T has been detected in five unrelated index cases with a strong family history of LS syndrome. Moreover, the rare germline VUS PMS2 c.989-107_989-106insA has been detected in 14 unrelated LS patients and could be reclassified as likely benign. Interestingly, our NGS analysis detected the novel BMPR1A pathogenic variant c.1474-1G&amp;gt;C in young JPS patient that has been misdiagnosed as FAP. The in-silico analysis for this novel variant showed an alteration of the wild type acceptor site and an activation of a cryptic acceptor site, respectively, most probably affecting splicing. Conclusions Our current study will contribute to the molecular genetics characterization of hereditary colorectal cancer syndromes in Algerian population that is relevant for clinical management in the areas of genetic testing, early diagnosis, treatment and prevention. Citation Format: Farid Cherbal, Asma-Lamia Boumehdi, Feriel Khider, Karima Landelouci, Abdelwahab Zemam, Sarah Sabri, Adam.Walid Damache, Mohammed Oukkal, Hassen Mahfouf, Ferhat Zebboudj, Mustapha Maaoui. Genetic testing for hereditary colorectal cancer syndromes in Algerian patients: A multicenter study. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4177.