Spectrum Of Germline Mutations Research Articles

141P Molecular landscape of hereditary breast cancer in Ukrainian women

Breast cancer (BC) is the most frequent malignancy in Ukrainian women. Among the growing number of cases, hereditary BC comprises 5-15% of cases worldwide. Inheritance of genetic alterations is approximated to underlie 5-10% of BC occurrences and is a major point of concern regarding women's health. Despite the existence of national screening for BC in Ukraine, little is known about the rate and genetic causes of hereditary BC in the Ukrainian population. The goal of the study was to assess the spectrum of germline mutations in patients with BC with respect to the molecular subtypes.

Abstract GS4-08: Comprehensive genomic profiling of patients with breast cancer identifies germline-somatic interactions mediating therapy resistance

Abstract Background: Germline genetic alterations are established mediators of breast carcinogenesis, often giving rise to specific forms of genomic instability. BRCA1/2 pathogenic variants (PVs) are emblematic of this phenomenon through their induction of homologous recombination deficiency. While specific patterns of genomic instability may sensitize cancers to therapies such as PARP inhibitors (PARPi) or platinum chemotherapy, their implications for lineage-directed therapies such as endocrine therapy (ET) or CDK4/6 inhibitors (CDK4/6i) are unknown. Herein, we systematically investigated the patterns of association of germline alterations with specific somatic alterations and explored the resulting effect on clinical outcomes. Methods: Patients who underwent germline and matched tumor tissue sequencing utilizing MSK-IMPACT from April 2014 to May 2021 and had available germline analysis results were included. The final analysis presented at SABCS will include 6000 tumors from 5,150 patients, anonymized according to established institutional IRB guidelines to allow for germline analysis on the full cohort. We analyzed genomic data to inform the full spectrum of somatic and germline mutations, ploidy, and allele-specific copy number to determine loss of heterozygosity (LOH). We performed gene- and pathway-level enrichment analyses between somatic variants and germline PVs. Univariable and multivariable Cox proportional hazards models were constructed to assess the association of therapy-specific progression-free survival (PFS) with select germline PVs and germline-somatic interactions. Results: The preliminary analysis includes 2,798 tumors from 2,242 patients with germline and somatic sequencing results. The most frequent germline PVs were: BRCA2 (n = 81), BRCA1 (n = 67), CHEK2 (n = 57), ATM (n = 32), PALB2 (n = 19). The cohort robustly confirmed previously established relationships such as mutual exclusivity of gATM and TP53 variants (OR 0.10, 95% CI 0.032 - 0.33, q = 0.005). Alterations of TP53 were seen in 83% (56/67) of gBRCA1 patients; however, this did not achieve significance when adjusted for receptor subtype (OR 3.90, 95% CI 1.34-11.38, q = 0.15). The size of the cohort allowed discovery of several novel relationships. For instance, gBRCA2 loss was associated with alterations in TGF-B pathway components (OR 3.58, 95% CI 1.70 - 7.56, q = 0.002), potentially relevant to metastatic disease progression. PIK3CA mutations were significantly less prevalent in both gBRCA2 (OR 0.52, 95% CI 0.31 - 0.87, q = 0.063) and gBRCA1 PVs (OR 0.21, 95% CI 0.085 - 0.51, q = 0.014). Our analysis uncovered a strong association between gBRCA2 and somatic RB1 pathogenic alterations (OR 3.58, 95% CI 1.70 - 7.56, q = 0.011), with most variants (80%) encountered in metastatic gBRCA2 tumors. Given the essential role of RB1 in CDK4/6i response, we investigated the effect of BRCA2 status on clinical efficacy of CDK4/6i-ET. Strikingly, gBRCA2 PVs were significantly associated with inferior PFS (HR 2.17, 95% CI 1.46-3.22, p < 0.001) on first line treatment with CDK4/6i-ET. We posited the enrichment of somatic RB1 loss as a potential mechanism of resistance to CDK4/6i. Given the proximity of RB1 to BRCA2 on chromosome 13, we hypothesized that co-LOH of BRCA2 and RB1 predisposes the cancer cells to bi-allelic loss under therapeutic pressure of CDK4/6i. Indeed, 18/26 gBRCA2 (69.2%) tumors evaluable for allele-specific copy number had evidence of RB1 LOH. Discussion: Analysis of germline-somatic interactions yielded novel associations relevant to breast cancer progression and treatment resistance. Among these, we demonstrated BRCA2 carriers to have inferior outcomes to first line CDK4/6i-ET with potential implications for optimal first line therapy and sequencing of CDK4/6i vs PARPi in this patient population. Citation Format: Anton Safonov, Chai Bandlamudi, Paulino Tallón de Lara, Emanuela Ferraro, Fatemeh Derakhshan, Marie Will, Mark Donoghue, Pier Selenica, Joshua Drago, Ezra Rosen, Carlos dos Anjos, Elaine Walsh, Elizabeth A Comen, Mehnaj Ahmed, Barbara Acevedo, Ahmet Zehir, Michael F Berger, David Solit, Larry Norton, Ronglai Shen, Zsofia Stadler, Simon Powell, Jorge S Reis-Filho, Sarat Chandarlapaty, Mark Robson, Pedram Razavi. Comprehensive genomic profiling of patients with breast cancer identifies germline-somatic interactions mediating therapy resistance [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr GS4-08.

Genetic spectrum in a Canadian cohort of apparently sporadic pheochromocytomas and paragangliomas: New data on multigene panel retesting over time.

Pheochromocytomas (PHEOs) and paragangliomas (PGLs), collectively known as PPGLs, are tumours with high heritability. The prevalence of germline mutations in apparently sporadic PPGLs varies depending on the study population. The objective of this study was to determine the spectrum of germline mutations in a cohort of patients with apparently sporadic PPGLs over time. We performed a retrospective review of patients with apparently sporadic PPGLs who underwent genetic testing at our referral centre from 2005 to 2020. We included patients with apparently sporadic PPGLs who underwent genetic testing at our referral center. Genetic analysis included sequential gene sequencing by Sanger method or next generation sequencing (NGS) with a multigene panel. The prevalence of germline mutations was 26.2% (43/164); 40.0% (30/75) in PGLs and 14.6% (13/89) in PHEOs. We identified four novel pathogenic variants (two SDHB and two SDHD). Patients carrying germline mutations were younger (38.7 vs. 49.7 years old) than patients with no identified germline mutations. From 2015 to 2020, we performed NGS with a multigene panel on 12 patients for whom the initial genetic analysis was negative. Germline mutations in previously untested genes were found in four (33.3%) of these patients (two MAX and two SDHA), representing 9.3% (4/43) of the mutation carriers. The prevalence of germline mutations in our cohort of patients with apparently sporadic PPGLs was 26.2%. Genetic re-evaluation over time using multigene sequencing by NGS assay in a subgroup of patients leads to an increase in the detection of mutations.

Germline Variants Identified in Patients with Early-onset Renal Cell Carcinoma Referred for Germline Genetic Testing

BackgroundDespite guidelines recommending genetic counseling for patients with early-onset renal cell carcinoma (RCC), studies interrogating the spectrum of germline mutations and clinical associations in patients with early-onset RCC are lacking. ObjectiveTo define the germline genetic spectrum and clinical associations for patients with early-onset RCC diagnosed at age ≤46 yr who underwent genetic testing. Design, setting, and participantsWe retrospectively identified patients with early-onset RCC who underwent germline testing at our institution from February 2003 to June 2020. Outcome measurement and statistical analysisThe frequency and spectrum of pathogenic/likely pathogenic (P/LP) variants were determined. Clinical characteristics associated with mutation status were analyzed using two-sample comparison (Fisher’s exact or χ2 test). Results and limitationsOf 232 patients with early-onset RCC, 50% had non–clear-cell histology, including unclassified RCC (12.1%), chromophobe RCC (9.7%), FH-deficient RCC (7.0%), papillary RCC (6.6%), and translocation-associated RCC (4.3%). Overall, 43.5% had metastatic disease. Germline P/LP variants were identified in 41 patients (17.7%), of which 21 (9.1%) were in an RCC-associated gene and 20 (8.6%) in a non–RCC-associated gene, including 17 (7.3%) in DNA damage repair genes such as BRCA1/2, ATM, and CHEK2. Factors associated with RCC P/LP variants include bilateral/multifocal renal tumors, non–clear-cell histology, and additional extrarenal primary malignancies. In patients with only a solitary clear-cell RCC, the prevalence of P/LP variants in RCC-associated and non–RCC-associated genes was 0% and 9.9%, respectively. ConclusionsPatients with early-onset RCC had high frequencies of germline P/LP variants in genes associated with both hereditary RCC and other cancer predispositions. Germline RCC panel testing has the highest yield when patients have clinical phenotypes suggestive of underlying RCC gene mutations. Patients with early-onset RCC should undergo comprehensive assessment of personal and family history to guide appropriate genetic testing. Patient summaryIn this study of 232 patients with early-onset kidney cancer who underwent genetic testing, we found a high prevalence of mutations in genes that increase the risk of cancer in both kidneys and other organs for patients and their at-risk family members. Our study suggests that patients with early-onset kidney cancer should undergo comprehensive genetic risk assessment.

Genome-Wide Analysis of Cadmium-Induced, Germline Mutations in a Long-Term Daphnia pulex Mutation-Accumulation Experiment.

Background:Germline mutations provide the raw material for all evolutionary processes and contribute to the occurrence of spontaneous human diseases and disorders. Yet despite the daily interaction of humans and other organisms with an increasing number of chemicals that are potentially mutagenic, precise measurements of chemically induced changes to the genome-wide rate and spectrum of germline mutation are lacking.Objectives:A large-scale Daphnia pulex mutation-accumulation experiment was propagated in the presence and absence of an environmentally relevant cadmium concentration to quantify the influence of cadmium on germline mutation rates and spectra.Results:Cadmium exposure dramatically changed the genome-wide rates and regional spectra of germline mutations. In comparison with those in control conditions, Daphnia exposed to cadmium had a higher overall mutation rates and a lower overall mutation rate. Daphnia exposed to cadmium had a higher intergenic mutation rate and a lower exonic mutation rate. The higher intergenic mutation rate under cadmium exposure was the result of an elevated intergenic rate, whereas the lower exon mutation rate in cadmium was the result of a complete loss of exonic mutations—mutations that are known to be enriched at 5-hydroxymethylcytosine. We experimentally show that cadmium exposure significantly reduced 5-hydroxymethylcytosine levels.Discussion:These results provide evidence that cadmium changes regional mutation rates and can influence regional rates by interfering with an epigenetic process in the Daphnia pulex germline. We further suggest these observed cadmium-induced changes to the Daphnia germline mutation rate may be explained by cadmium’s inhibition of zinc-containing domains. The cadmium-induced changes to germline mutation rates and spectra we report provide a comprehensive view of the mutagenic perils of cadmium and give insight into its potential impact on human population health. https://doi.org/10.1289/EHP8932

Germline mutation analyses of malignant ground glass opacity nodules in non-smoking lung adenocarcinoma patients.

BackgroundGermline mutations play an important role in the pathogenesis of lung cancer. Nonetheless, research on malignant ground glass opacity (GGO) nodules is limited.MethodsA total of 13 participants with malignant GGO nodules were recruited in this study. Peripheral blood was used for exome sequencing, and germline mutations were analyzed using InterVar. The whole exome sequencing dataset was analyzed using a filtering strategy. KOBAS 3.0 was used to analyze KEGG pathway to further identify possible deleterious mutations.ResultsThere were seven potentially deleterious germline mutations. NM_001184790:exon8: c.C1070T in PARD3, NM_001170721:exon4:c.C392T in BCAR1 and NM_001127221:exon46: c.G6587A in CACNA1A were present in three cases each; rs756875895 frameshift in MAX, NM_005732: exon13:c.2165_2166insT in RAD50 and NM_001142316:exon2:c.G203C in LMO2, were present in two cases each; one variant was present in NOTCH3.ConclusionsOur results expand the germline mutation spectrum in malignant GGO nodules. Importantly, these findings will potentially help screen the high-risk population, guide their health management, and contribute to their clinical treatment and determination of prognosis.

Abstract 2204: Spectrum of pathogenic germline mutations in Chinese head and neck cancer patients through next-generation sequencing

Abstract Background: Head and neck cancer is currently a leading cause of cancer-associated mortality worldwide. Despite the increasing evidences of variants that were associated with head and neck cancer risk, investigations of genetic factors and their roles in genetic susceptibility to head and neck cancer were limited. The purpose of this study is to assess the inherited genetic factors regarding germline mutations in Chinese head and neck cancer population. Methods: Genomic profiling of DNA was performed through a next-generation sequencing (NGS) (panel on 381/733-gene) on tissue from Chinese patients with head and neck cancer between January 06, 2017 and June 02 2020. TMB was defined as total number of somatic non-synonymous mutations in coding region. MSI was evaluated by NGS of 500 known MSI loci. PD-L1 expression was evaluated using immunohistochemistry (Dako 22C3). Results: Of 357 patients with head and neck cancer, 325 (91.04%) patients were identified to carry 457 pathogenic or likely pathogenic germline mutations in 88 cancer predisposition genes, with a frequency of 91.09% (91/101) in nasopharyngeal carcinoma, and 91.41% (234/256) in non-nasopharyngeal carcinoma of the head and neck. In head and neck cancer patients, the most frequently germline mutated genes were CYP2C19 (56.92%), followed by DPYD (37.85 %), CYP2D6 (31.69%), RAC1 (29.85%), VEGFA (29.85%), MGMT (28%), CD74 (24.31%), BCL2L11 (11.69%), and APC (6.46%). Of all the 88 germline mutated genes, 27.27% (n=24) lay in the DNA damage repair (DDR) pathways. The highest frequency of DDR germline mutations was BARD1 (6.15%), followed by BRCA2 (6.15%), PLAB2 (5.54%), FANCD2(5.23%), ATM(4.92%), FANCA (4.62%), RAD50 (4.62%), BRCA1(3.69%), MSH2 (3.38%), and MLH1 (3.08%). Of the 89 nasopharyngeal carcinoma patients with germline mutations that could be evaluated for MSI and TMB, only 1 (1.12%) patient was identified as MSI-H, and 3 (3.37%) patients had TMB≥10Muts/Mb. PD-L1 status analysis was performed in 77 nasopharyngeal carcinoma patients with germline mutated genes, and the results showed that 63 (81.81%) patients were PD-L1 positive (CPS≥1). In non-nasopharyngeal carcinoma with germline mutated genes, MSI status analysis was performed in 228 patients, and the results showed that 2 (0.87%) patient was identified as MSI-H. In addition, 108 (108/198, 27.6%) patients were PD-L1 positive (CPS≥1). Of the 229 non-nasopharyngeal carcinoma that could be evaluated for TMB, 54 (23.58%) patients had TMB≥10Muts/Mb. Conclusions: Taken together, we have presented the spectrum of pathogenic germline mutations in a Chinese head and neck cancer cohort. The findings of inherited genetic variations may provide clues for the oncology treatment strategy and cancer prevention. Citation Format: Jianming Gao, Yating Zheng, Wenzhuan Xie, Mengli Huang. Spectrum of pathogenic germline mutations in Chinese head and neck cancer patients through next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2204.

Abstract 2178: Spectrum of pathogenic germline mutations in Chinese esophageal squamous cell carcinoma patients through next-generation sequencing

Abstract Background: Esophageal Squamous Cell Carcinoma (ESCC) is one of the leading cause of cancer death in China, while the nature of genetic factors related to ESCC has not been well-studied. The purpose of this study is to assess the inherited genetic factors regarding pathogenic germline mutations in Chinese ESCC population. Methods: Tumor tissue samples from Chinese patients with ESCC were analyzed using next generation sequencing (NGS) (panel on 381/733-gene). MSI was evaluated by NGS of 500 known MSI loci. PD-L1 expression was evaluated using immunohistochemistry (Dako 22C3). TMB was defined as total number of somatic non-synonymous mutations in coding region. Results: Genomic profiling of DNA of 271 ESCC patients were analyzed using NGS, of which 251 (92.6%) harbored 354 pathogenic or very likely pathogenic germline mutations in 94 genes. In ESCC patients with germline mutations, the most frequently germline mutated genes were CYP2C19 (54.18%), followed by UGT1A1 (41.04%), RAC1 (35.06%), VEGFA (34.66%), DPYD (33.47%), CD74 (31.47%), MGMT (31.08%), CYP2D6 (29.88%), BCL2L11 (12.35%), FANCA (7.97%), ALK (7.57%), APC (7.17%), and BARD1 (5.98%). Of all the 94 germline mutated genes, 26.6% (n=25) lay in the DNA damage repair (DDR) pathways. The most frequently germline mutated DDR genes were FANCA (7.97%), followed by BARD1 (5.98%), FANCG (5.98%), BLM (5.58%), BRCA2 (5.18%), BRCA1 (4.78%), FANCD2 (4.78%), POLD1 (3.98%), ATM (3.59%), and POLE (3.58%). MSI status analysis was performed in 246 of 251 ESCC patients with germline mutated genes, and the results showed that all the patients with germline mutated genes were determined to be MSS. In addition, among 251 ESCC patients with germline mutated genes, 163 of them were tested for PD-L1. The results showed that 45 (27.6%) of the ESCC patients were PD-L1 positive (CPS≥10) and 118 (72.4%) were PD-L1 negative. Of the 247 ESCC patients with germline mutations that could be evaluated for TMB, 60 (24.29%) patients had TMB≥10Muts/Mb. Conclusions: As the first study to explore the pathogenic germline mutation profile of Chinese ESCC patients, our study provides valuable clues for the assessment and clinical management of genetic susceptibility to ESCC patients. Citation Format: Ruijun Cai, Yating Zheng, Wenzhuan Xie, Mengli Huang. Spectrum of pathogenic germline mutations in Chinese esophageal squamous cell carcinoma patients through next-generation sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2178.

Abstract PS16-08: Germline mutation landscape in Chinese breast cancer patients

Abstract Background: Genetic testing for patients with breast cancer (BCa) patients may change the routine patient care and shift the paradigm towards more personalized managing and treatment strategies. In particular, testing germline mutations in BRCA1/2 has become a part of the standard clinical practice for patients with BCa. However, our understanding of genetic epidemiology of BCa is mainly driven by data from Caucasian populations and it has been evident that gene alterations may be ethnic specific in breast cancer. Methods: Aiming to delineate the landscape of germline mutations in Chinese patients with BCa to breast cancer, we collected blood samples from in 356 BCa patients at stage I-IV in Beijing Cancer Hospital between Jan. 2013 to Dec. 2019. Peripheral blood mononuclear cells were isolated from blood samples and genomic DNA were extracted for capture-based NGS sequencing. A large comprehensive 600 gene panel (PredicineATLAS, Huidu Medical Science Techonology, Inc.) was used to detect germline mutations in the covered genes with average 300x sequencing depth. Results: A total of 356 BCa patients were included in our study, with the median age at first diagnosis of 49 years (Range: 21-87). Among all cases, 21.9% (78/356, 95% confidence interval [CI]: 17.7-26.6%) carried pathogenic or likely pathogenic mutations in 48 cancer related genes. Twenty-seven patients (7.6%, 95% CI: 5.1-10.8%) harbored BRCA1/2 mutations, followed by 5 patients carrying ATM mutations and RAD50 mutations respectively. Other commonly mutated genes include BARD1 (1.1%), FANCD2 (1.1%), CHEK2 (0.6%), FANCC (0.6%), FANCM (0.6%), PMS2 (0.6%), and TP53 (0.6%), most of which are related to DNA damage repair pathway. Moreover, BRCA1/2 carriers were more likely to appear among those with breast or ovarian cancer family history than those without (OR=3.41, 95% CI: 1.14-9.12, P=0.01). Compared with patients that aged older than 50 years at first diagnosis, those aged 30 years or younger were 6 times more likely to detect germline mutations in BRCA1/2 (95% CI: 1.18-26.1, P=0.02). In addition, mutations in BRCA1/2 were differentially associated with breast cancer subtypes. BRCA1 mutations were strongly enriched in triple-negative breast cancer (TNBC) (OR=6.7, 95% CI: 1.54-33.13, P=0.005). There is no strong significant survival difference observed between BRCA1/2 carriers and non-carriers, however, patients carrying ATM or RAD50 mutations tend to have lower disease-free survival. Conclusions: This is a comprehensive analysis of germline mutation spectrum in a large Chinese patient cohort with breast cancer. Collectively, a substantial proportion of patients with breast cancer had hereditary risk factors. Distinct distribution of pathogenic mutations in breast cancer subtypes and differential associations between mutation status and clinical features were further observed. All these findings will advance our understanding regarding the pathologies and heterogeneity of breast cancer. Citation Format: Nan Wang, Jiayang Zhang, Lu Tan, Hao Liao, Yaxin Liu, Xinyu Gui, Jiaxin Niu, Feng Xie, Yue Zhang, Yong Huang, Jianjun Yu, Huiping Li. Germline mutation landscape in Chinese breast cancer patients [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS16-08.

Germline mutational spectrum in Armenian breast cancer patients suspected of hereditary breast and ovarian cancer

Hereditary breast and ovarian cancer (HBOC) can be identified by genetic testing of cancer-causing genes. In this study, we identified a spectrum of genetic variations among 76 individuals of Armenian descent either with a family history of cancer or breast cancer before the age of 40. We screened 76 suspected HBOC patients and family members as well as four healthy controls using a targeted and hereditary comprehensive cancer panel (127 genes). We found 26 pathogenic (path) and 6 likely pathogenic (LPath)variants in 6 genes in 44 patients (58%); these variants were found in BRCA1 (17), BRCA2 (19), CHEK2 (4), PALB2 (2), and NBN (1). A few different variants were found in unrelated individuals; most notably, variant p.Trp1815Ter in the BRCA1 gene occurred in four unrelated patients. We did not find any known significant variants in five patients. Comprehensive cancer panel testing revealed pathogenic variants in cancer genes other than BRCA1 and BRCA2, suggesting that testing only BRCA1 and BRCA2 would have missed 8 out of 44 suspected HBOC patients (18%). These data also confirm that a comprehensive cancer panel testing approach could be an appropriate way to identify most of the variants associated with hereditary breast cancer.

Clinical characteristics and germline mutation spectrum of RB1 in Chinese patients with retinoblastoma: A dual-center study of 145 patients

Retinoblastoma (Rb) is the most common primary intraocular childhood malignancy and one of the main causes of blindness in children. In China, most tumors are diagnosed at an advanced stage and have relatively poor outcomes compared to developed countries. Here, we aimed to update the clinical manifestations and RB transcriptional corepressor 1 (RB1) mutation spectrum in Chinese Rb patients. Medical charts of 184 eyes in 145 Chinese Rb patients belonging to unrelated families were reviewed. Genomic DNA was isolated from peripheral blood of the patients and their parents. Mutation analysis of whole coding regions, promoter regions and flanking splice sites in the RB1 gene was performed. In addition, multiplex ligation-dependent probe amplification (MLPA) was done to detect gross aberrations. Germline RB1 mutations were observed in 37.2% (54/145) of Rb patients. RB1-mutated patients presented with earlier age of diagnosis (p = 0.019), with a significantly larger proportion of bilateral cases (p = <0.001) and secondary malignancies (p = 0.027) relative to those without RB1 mutations. For ocular clinical presentations, RB1-mutated retinoblastomas presented with a larger proportion of ectropion uveae (p = 0.017) and iris neovascularization (p = 0.001). These RB1 mutations comprised of 13 (24.1%) nonsense mutation, 13 (24.1%) splicing mutations, 11 (20.4%) frameshift deletions, 11 (20.4%) gross mutations, 3 (5.6%) missense mutations, 2 (3.7%) promoter mutations and 1 (1.9%) non-frameshift deletion. In addition, 8 novel RB1 mutations were identified. These germline RB1 mutations were not related to age at diagnosis or laterality. Here, we provide a comprehensive spectrum of RB1 germline mutations in Chinese Rb patients and describe correlations between RB1 mutations and clinical presentations. Our study also provides new evidence that will inform management and genetic counselling of Rb patients and families.

Spectrum of Germline Mutations Within Fanconi Anemia-Associated Genes Across Populations of Varying Ancestry.

Fanconi anemia (FA) is a rare genetic disorder associated with hematological disorders and solid tumor predisposition. Owing to phenotypic heterogeneity, some patients remain undetected until adulthood, usually following cancer diagnoses. The uneven prevalence of FA cases with different underlying FA gene mutations worldwide suggests variable genetic distribution across populations. Here, we aim to assess the genetic spectrum of FA-associated genes across populations of varying ancestries and explore potential genotype-phenotype associations in cancer. Carrier frequency and variant spectrum of potentially pathogenic germline variants in 17 FA genes (excluding BRCA1/FANCS, BRCA2/FANCD1, BRIP1/FANCJ, PALB2/FANCN, RAD51C/FANCO) were evaluated in 3523 Singaporeans and 7 populations encompassing Asian, European, African, and admixed ancestries from the Genome Aggregation Database. Germline and somatic variants of 17 FA genes in 7 cancer cohorts from The Cancer Genome Atlas were assessed to explore genotype-phenotype associations. Germline variants in FANCA were consistently more frequent in all populations. Similar trends in carrier frequency and variant spectrum were detected in Singaporeans and East Asians, both distinct from other ancestry groups, particularly in the lack of recurrent variants. Our exploration of The Cancer Genome Atlas dataset suggested higher germline and somatic mutation burden between FANCA and FANCC with head and neck and lung squamous cell carcinomas as well as FANCI and SLX4/FANCP with uterine cancer, but the analysis was insufficiently powered to detect any statistical significance. Our findings highlight the diverse genetic spectrum of FA-associated genes across populations of varying ancestries, emphasizing the need to include all known FA-related genes for accurate molecular diagnosis of FA.

Germline and Somatic Mutations in Archived Breast Cancer Specimens of Different Subtypes

Molecular profiling of tumors may provide promising options for personalized treatment. We have examined the spectrum of germline and somatic mutations in 23 breast cancers (ВС) of various molecular subtypes, including tumors 1) with expression of estrogen, progesterone and/or epidermal growth factor receptor HER2/neu, and 2) with a triple negative phenotype. Genomic DNA specimens were isolated from archived tumor and normal tissue samples and subjected to targeted sequencing of the coding regions of 25 cancer-associated genes with a mean coverage of x 1000. In the triple negative subtype of ВС, the pathogenic germline mutations BRCA1 c.66_67delAG (185delAG) and BRCA1 c.3226_3227AG (3347delAG) were detected, while the germline mutation BRCA2 658_659del (886delGT) was found in patients with positive receptor staining. Mutations in BRCAl/2 were overrepresented by frequency (80%), pointing at common loss of heterozygosity affecting the normal allele. Somatic mutations in the TP53 gene were found in 7/10 (70%) patients with the triple negative subtype of ВС and in 3/13 (23%) in the group with positive receptor staining. Additionally, in both groups of patients, somatic mutations of the PTEN, MSH2, MSH6, and MUTYH genes were detected.

Pathogenic Germline Mutations of DNA Repair Pathway Components in Early-Onset Sporadic Colorectal Polyp and Cancer Patients.

Simple SummaryColorectal cancer (CRC) screening by immuno-fecal occult blood tests (iFOBTs) begins at age 50 in average-risk persons. However, the incidence of early-onset CRC has risen; of the cases, at least half are sporadic CRC without a family history. The authors of this study found a high percentage of de novo germline mutation in young sporadic CRC patients, as well as in sporadic colorectal polyp and control groups. All the mutated genes contribute to various DNA-repair pathways, hinting that a loss of genomic integrity play a crucial role in the development of CRC. The early identification of cancer-susceptible individuals by multigene panels in younger individuals who may be missed under current iFOBT screening could contribute to preventing CRC.Given recent increases in the proportion of early-onset colorectal cancer (CRC), researchers are urgently working to establish a multi-gene screening test for both inherited and sporadic cancer-susceptible individuals. However, the incidence and spectrum of germline mutations in young sporadic CRC patients in East Asian countries and, especially, in sporadic polyp carriers and normal individuals are unknown. Peripheral blood samples were collected from 43 colonoscopy-proved normal controls and from 50 polyp patients and 49 CRC patients with no self-reported family history of cancer. All participants were under 50 years old. Next-generation sequencing with a panel of 30 CRC-associated susceptibility genes was employed to detect pathogenic germline mutations. The germline mutation carrier rates were 2.3%, 4.0%, and 12.2% in the normal, polyp, and cancer groups, respectively. A total of seven different mutations in six DNA repair pathway-related genes (MLH1, BRCA1, BRCA2, CHEK2, BLM, and NTHL1) were detected in nine participants. One frameshift mutation in BRCA2 and one frameshift mutation in the CHEK2 gene were found in a normal control and two colorectal polyp patients, respectively. One young sporadic CRC patient carried two heterozygous mutations, one in MLH1 and one in BRCA1. Three mutations (MLH1 p.Arg265Cys, MLH1 p.Tyr343Ter and CHEK2 p.Ile158TyrfsTer10) were each found in two independent patients and were considered “founder” mutations. This is the first report to demonstrate high percentage of germline mutations in young sporadic colorectal polyp, CRC, and general populations. A multi-gene screening test is warranted for the proactive identification of cancer-predisposed individuals.

Prevalence of germline TP53 variants among early-onset breast cancer patients from Polish population

BackgroundThe objective of this study was to determine spectrum and prevalence of germline mutations in TP53 gene among Polish women with early-onset breast cancer (BC), which has not been determined until now.MethodsA cohort of 100 females with BC diagnosed ≤ 30 years of age and with a positive family history of cancer was used as a discovery cohort. 1880 women with BC ≤ 45 years old and a control group of 2000 healthy women were genotyped as a replication phase of this study.ResultsFour heterozygous pathogenic missense mutations were detected in a group of 100 patients with early-onset breast cancer. On the basis of software prediction and available literature data, all these variants were defined as pathogenic. None of these TP53 variants were detected among 1880 breast cancer patients and 2000 healthy controls. No large mutations were found among early-onset cases using MLPA reaction.ConclusionGermline pathogenic TP53 variants were found in 4% early-onset Polish BC patients. No founder mutations were identified in Polish population. To improve the treatment and surveillance screening, the search for germline TP53 pathogenic variants is recommended for all female BC cases diagnosed ≤ 30 years old.

Abstract 3533: Germline POLE and POLD1 proofreading domain mutations in endometrial carcinoma from Middle Eastern region

Abstract Endometrial carcinoma (EC) accounts for 5.8% of all cancers in Saudi females. Although most ECs are sporadic, 2%-5% tend to be familial, being associated with Lynch syndrome and Cowden syndrome. In this study, we attempted to uncover the frequency, spectrum and phenotype of germline mutations in the proofreading domain of POLE and POLD1 genes in a large cohort of ECs from Middle Eastern region. We performed Capture sequencing and Sanger sequencing to screen for proofreading domains of POLE and POLD1 genes in 432 EC cases, followed by evaluation of protein expression using immunohistochemistry. Variant interpretation was performed using PolyPhen-2, MutationAssessor, SIFT, CADD and Mutation Taster. In our cohort, four mutations (0.93%) were identified in 432 EC cases, two each in POLE and POLD1 proofreading domains. Furthermore, low expression of POLE and POLD1 was noted in 41.1% (170/1414) and 59.9% (251/419) of cases, respectively. Both the cases harboring POLE mutation showed high nuclear expression of POLE protein, whereas, of the two POLD1 mutant cases, one case showed high expression and another case showed low expression of POLD1 protein. Our study shows that germline mutations in POLE and POLD1 proofreading region are a rare cause of EC in Middle Eastern population. However, it is still feasible to screen multiple cancer related genes in EC patients from Middle Eastern region using multigene panels including POLE and POLD1. Keywords: POLE; POLD1; Endometrial carcinoma; Proof-reading domain mutations; Germline. Citation Format: Abdul K. Siraj, Sandeep K. Parvathareddy, Rong Bu, Kaleem Iqbal, Sarah Siraj, Tariq Masoodi, Laila Ghazwani, Yan Kong, Maria A. Sabido, Wafaa Albalawy, Ingrid F. Victoria, Mary J. Galvez, Khawla S. Al-Kuraya. Germline POLE and POLD1 proofreading domain mutations in endometrial carcinoma from Middle Eastern region [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 3533.

Abstract 3540: Germline mutation landscape of DNA damage repair genes in Oriental pancreatic cancer

Abstract BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is recognized as the most lethal solid malignancies with very few therapeutic options. Until very recently, FDA approved the first molecularly targeted therapy with the PARP inhibitor Olaparib for pancreatic cancer patients with germline mutations on BRCA1/2, two types of homologous recombination (HR)/DNA damage repair (DDR) genes. In addition, the sensitivity of platinum-based chemotherapy and anti-PD-1 antibodies have been connected with DDR spectrum. However, the genetic landscape of PDAC is mainly based on data from Caucasian population. In this study, we sought to explore the germline mutation spectrum of DDRs in oriental PDAC for clinical practice. METHODS Germline DNA extracted from 256 Asian peri ampullary cancer patients (201 PDAC, 20 adenosquamous carcinoma, and 35 vater periampullary carcinoma) underwent whole exome sequencing. The mean depth of sequencing was 67 X. 229 DDR genes were focused for variant callings using the GATK and its pathogenicity according to the guidelines from ACMG. Pathogenic or likely pathogenic(P/LP) were further analyzed. RESULTS Pathogenic variants were identified in 26 of 256 patients (10.2%),and one patient had mutations in two genes. The 27 pathogenic mutations occurred in 16 different genes,including ERCC2 (n=4), OGG1 (n=4), PALB2 (n=3), FAN1 (n=3), RAD54L (n=2), WRN (n=1), POLH (n=1), MUTYH (n=1), MSH6 (n=1), MLH3 (n=1), LIG1 (n=1), ERCC6 (n=1), CHEK2 (n=1), BRCA2 (n=1), BRCA1 (n=1), and ATM (n=1). The detailed gene profiles were mainly involved in five pathways, Homologous recombination(HR), Fanconi anemia(FA), Mismatch repair(MMR), Base excision repair(BER)and Nucleotide excision repair(NER. Of note, two mutations MSH6 c.261-1G&amp;gt;A and BRCA2 c.3912_3916del, were first reported to be associated with cancer and classified as likely pathogenic owing to their frameshift variant or splice site and low frequencies of occurrence. To determine the difference of germline DDR mutation landscape between oriental and American populations, we compared our cohort with American cohorts from Yurgelun and TCGA. The BRCA1/2 germline mutations were found at low levels in our cohort (0.8%) compared to the American cohorts (2.4~2.7%), Furthermore, the whole DDR mutations exhibited highest proportion [10.5% (27/256) from our study, compared with 7.3% (21/289) from Yurgelun, and 5.4% (10/185) from TCGA, respectively]. CONCLUSION In conclusion,our results characterized the germline mutation landscape of DDRs in the largest oriental cohort of pancreatic cancer to date, and first discovered two novel germline mutations in pancreatic cancer. Most importantly, nearly 10% of PDAC patients in this study were found to harbor germline DDR mutations, which may benefit more patients with an effective therapeutic synergy for PARP and PD-1 inhibitors in clinical practice. Citation Format: Shiwei Guo, Lisha Jiang, Xiaohan Shi, Suizhi Gao, Bo Li, Ling Lin, Jun Yu, Gang Jin. Germline mutation landscape of DNA damage repair genes in Oriental pancreatic cancer [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 3540.

Germline Genetic Findings Which May Impact Therapeutic Decisions in Families with a Presumed Predisposition for Hereditary Breast and Ovarian Cancer.

In this study, we aim to gain insight in the germline mutation spectrum of ATM, BARD1, BRIP1, ERCC4, PALB2, RAD51C and RAD51D in breast and ovarian cancer families from Spain. We have selected 180 index cases in whom a germline mutation in BRCA1 and BRCA2 was previously ruled out. The importance of disease-causing variants in these genes lies in the fact that they may have possible therapeutic implications according to clinical guidelines. All variants were assessed by combined annotation dependent depletion (CADD) for scoring their deleteriousness. In addition, we used the cancer genome interpreter to explore the implications of some variants in drug response. Finally, we compiled and evaluated the family history to assess whether carrying a pathogenic mutation was associated with age at diagnosis, tumour diversity of the pedigree and total number of cancer cases in the family. Eight unequivocal pathogenic mutations were found and another fourteen were prioritized as possible causal variants. Some of these molecular results could contribute to cancer diagnosis, treatment selection and prevention. We found a statistically significant association between tumour diversity in the family and carrying a variant with a high score predicting pathogenicity (p = 0.0003).

Abstract A03: Prevalence and spectrum of germline mutations in children with high-risk cancer

Abstract Introduction: Zero Childhood Cancer’s National Precision Medicine for Children with Cancer Study (PRISM) utilizes novel technologies to guide individualized management of children with high-risk cancer (expected overall survival less than 30%). Germline DNA is utilized to distinguish cancer-specific somatic variants from constitutional variants or polymorphisms, allowing identification of clinically relevant germline mutations. The prevalence of cancer predisposition syndromes in pediatric cancer may range from 8.5% to as high as 33%. Method PRISM combines molecular genomic analysis (WGS and RNASeq) with in vitro high-throughput drug screening and patient-derived xenograft drug efficacy testing. A Molecular Tumour Board (MTB) of Oncology and Genetics professionals convenes to determine the significance of genomic analysis as curated by bioinformaticians, molecular scientists, and clinicians. Results: Between September 2017 and June 2019, 218 children aged under 21 years have been recruited in PRISM (37% with central nervous system tumors, 47% with non-CNS solid tumors, and 16% with hematologic malignancies), and results are available for 208 after discussion at MTB meeting. Forty-two reportable germline variants were detected in 35 participants (detection rate: 16.8%), comprising 28 pathogenic and 14 likely pathogenic variants, across 22 cancer predisposition genes. The most frequently affected gene was CHEK2 (n=7), followed by SMARCB1 (n=5) and BRCA2 (n=3) and NF1 (3). In one out of three participants with germline mutations, somatic analysis revealed a double hit in the same gene altered in the germline. Distributions of participants with germline mutation per group were 16% of patients with CNS tumors (12/77), 19% of patients with non-CNS solid tumors (18/96), and 15% of patients with hematologic malignancies (5/34). Conclusion: Germline mutation detection rate in cancer predisposition genes was higher than expected, 16.8%; however, it may result from selection bias (i.e., cohort of high-risk cancers). Although genomic sequencing has expanded our understanding of pediatric cancer predisposition and presented opportunities for genetics-mediated care, identifying underlying germline mutations with potential clinical implications remains a clinical challenge for pediatric oncologists. Citation Format: Paulette Barahona, Alexandra Sherstyuk, Mark Cowley, Paul Ekert, Judy Kirk, Dong-Anh Khuong-Quang, Amit Kumar, Loretta Lau, Chelsea Mayoh, Glenn Marshall, Emily Moud, Tracey O’Brien, Mark Pinese, David Thomas, Vanessa Tyrell, David Ziegler, Michelle Haber, Katherine Tucker, Noemi Auxiliadora Fuentes-Bolanos, Meera Warby. Prevalence and spectrum of germline mutations in children with high-risk cancer [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A03.

Abstract B058: Germline mutation spectrum in hereditary cancer syndromes in a Latin American population

Abstract Introduction: Only 4% of the submissions to CLINVAR are from Latin American countries, similarly to Latino/Hispanic representation in other population genetic databases. We don’t know the spectrum of mutations affecting Colombian families with hereditary cancer syndromes; moreover, these cases are under diagnosed in our Country. We aimed to identify germline risk mutations in patients with a suspected hereditary cancer syndrome who were referred for genetic counseling at the largest cancer reference Institution in Colombia (INC-E.S.E.). Materials and methods: Descriptive cohort of patients referred to genetic counseling within the Hereditary Cancer Program at the INC-E.S.E. Germline genetic studies were performed on 147 individuals through NGS multi-gene panels and confirmed with Sanger sequencing or MLPA. Genetic results from more patients will be added to these statistics as those are being analyzed. Results: So far, results were obtained from 90 patients with a foreign company to study 83 genes, and 57 additional patients were studied at the INC-E.S.E., with a panel of 105 genes from Illumina in a MiSeq. Two bioinformatic pipelines (Illumina Variant Interpreter and SOPHIA Genetics) were used. Single Nucleotide Variants (SNVs), small insertions and deletions (INDELs), and Copy Number Variants (CNVs), were classified according to the ACMG criteria. Likely pathogenic or pathogenic mutations were identified in 22% of the patients (32/147). Of the total number of patients with an identified hereditary breast cancer syndrome (11/147, 7.48%), 6 are carriers of homologous repair genes mutation (3 in BRCA1, 1 in PALB2, 1 in CHEK2 and 1 in RAD51D); in BRCA1, one corresponds to the Colombian founder mutation A1708E and two carry the mutation BRCA1: c.1674delA (p.Gly559Valfs). The second most frequent was Lynch syndrome (8/147, 5.44%), 4 carry mutations in MLH1, 2 in PMS2, 1 in MSH6 and 1 in MSH2. It is interesting that 3/4 patients with mutations in MLH1 had the same splicing alteration (MLH1 c.790 + 1G&amp;gt; A). Other 5 patients with a hereditary cancer syndrome were identified, including one of each: Li-Fraumeni, Multiple Endocrine Neoplasia type 1, Von Hippel Lindau, Neurofibromatosis 1 and MUTYH - Associated Polyposis (carrier of the two most frequent mutations in MUTYH; c.1187G&amp;gt;A &amp; c.536A&amp;gt;G). Variants of Uncertain Significance (VUSs) were found in 47.62% and negative results in 32.65%. Conclusions: The finding of pathogenic mutations in 22% of this cohort is similar to what was previously reported for Colombia, but the percentage of VUSs is higher than other reports. Our lack of knowledge of the mutational spectrum in Colombians and our use of extensive multigene panels can explain this VUSs high rate. Citation Format: María Carolina Sanabria-Salas, Gonzalo Guevara, Ana Lucía Rivera, Antonio Huertas, Vilma Medina, Lina María Trujillo, Esperanza Peña, Carolina Wiesner. Germline mutation spectrum in hereditary cancer syndromes in a Latin American population [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr B058.