Spectrum Of Germline Mutations Research Articles

Mutation Spectrum Comparison between Benign Breast Lesion Cohort, Unselected Cancer Cohort and High-Risk Breast Cancer Cohort.

Mutation study for high-risk breast and ovarian cancer (HBOC) has been extensively studied in patients of different ethnicities. Here we compared the germline mutation rate and mutation spectrum of patients (n = 4341) with benign breast diseases or breast cancers, with and without other risk factors. Three cohorts of Chinese patients were recruited. The first cohort, high-risk cohort (HR, n = 3935) included high-risk breast cancer patients fulfilling high-risk HBOC criteria and who are recruited at our genetics clinic. The second cohort, unselected cancer cohort (CC, n = 307) was from general recruitment of patients with breast cancer at breast surgery clinics. The third cohort, benign breast lesion cohort (NC, n = 99) comprised 99 patients with benign breast diseases such as fibroadenoma, fibroadenomatoid hyperplasia, and intraductal papilloma. Thirty HBOC related genes were sequenced on the above-mentioned patient cohorts. The germline mutation rates of HR, CC, and NC cohort were 11.9%, 6.5%, and 8.1%, respectively. In the CC cohort, 29.3% (90/307) of patients fulfilled the National Comprehensive Cancer Network (NCCN) high-risk genetic test criteria 2022 v.2. The mutation rate for this group of patients was 11.1%, similar to that of the HR cohort, while the mutation rate for those not fulfilling testing criteria was 4.6%, like that of the NC cohort. High penetrance genes (BRCA1/2, CDH1, PALB2, PTEN, and TP53) mutations were only found in the HR (10.6%) and CC (3.3%) cohorts but were not found in the NC cohort. ATM, BRIP1, RAD51C, and RAD51D mutations were identified in all cohorts. RAD51C and RAD51D mutations showed conflicting penetrance. An unexpectedly high mutation rate of total 2% was found in the NC cohort but it was only 0.3% and 0.5% in the HR cohort and CC cohort, respectively. Our results show a clinical need to enhance genetic testing of unselected breast cancer patients to identify the high-risk patients.

Abstract PO5-16-01: Clinicogenomic analysis reveals genomic associations of brain metastatic tropism in breast cancer

Abstract Introduction: Recent progress in imaging and therapeutics has led to improvements in the treatment of advanced breast cancer. However, the incidence of brain metastasis (BM) in breast cancer is increasing and continues to be associated with poor prognosis and significant morbidity. Herein, we describe genomic enrichments associated with brain tropism from a large institutional clinico-genomic cohort. Methods: Patients who underwent tumor and matched normal sequencing utilizing hybridization-capture based targeted exonic sequencing (MSK-IMPACT) from April 2014 to March 2023 were included in this analysis; this cohort included 6,377 samples from 5,135 patients. We analyzed genomic data to inform the full spectrum of somatic and germline mutations, copy number changes and structural variants enriched in samples in resected BM specimens (n = 179), compared to primary tumors (n = 2980), stratified by receptor status. Enrichment analysis was conducted using a Fisher exact test for each respective receptor status. Similar analyses were conducted between extracranial metastatic (ECM) sites (n = 3186) and primary tumors, to differentiate the unique genomic features driving the emergence of BM as compared to general metastatic propensity. Multiple hypothesis testing was performed using Benjamini-Hochberg. Further genomic analysis, including allele specific copy number changes and mutational signatures will be reported at the 2023 SABCS meeting. Results: Oncogenic alterations in several genes were found to be enriched in BM samples compared to primary tumor, with an odds ratio exceeding that of the corresponding ECM comparison. For example, in the HR+/HER2- subset (4329 samples from 3476 patients), pathogenic variants in the following genes were enriched in BM:Primary analysis: NF1 (OR 6.4 [2.9 – 13.7], q = 0.001, 15.5% of BM), MYC (OR 3.9 [2.0 – 7.4], q = 0.001, 24.4% of BM), AGO2 (5.2 [2.4 – 10.9], q= 0.002, 15.5% of BM), CDKN2A (OR 3.9 [1.6 – 9.4], q = 0.06, 10.3% of BM), ERBB2 (OR 3.6 [1.5 – 8.6], q = 0.06, 10.3% of BM), RB1 (OR 4.2 [1.5 – 11.4], q = 0.06, 8.6% of BM), TP53 (OR 2.0 [1.1 – 3.5], q = 0.07, 40% of BM). In contrast, ESR1 variants were enriched in BM:Primary (OR 14.0 [6.7 – 28.2], but at the same level as ECM:Primary (OR 12.3 [8.7 – 17.7]). When considering HER2+ tumors (919 samples from 739 patients), only NKX.3 was enriched in the BM:Primary comparison (OR 11.5 [3.2 – 42.3], q = 0.004, 11.6% of BM). Although no TNBC samples met significance thresholds after adjustment for multiple hypothesis testing, CDH1, NTRK1, EGFR, and TP53 emerged as putatively significant. Conclusions: In a large cohort of genomically-profiled breast cancer samples, we find recurrent involvement of genes involved in cell cycle regulation (RB1, CDKN2A, TP53); these have been found to be enriched in brain metastases from other cancer types and are implicated in resistance to common lineage-directed therapies. Our approach also uncovered several targets for which therapies are actively in development (ERBB2, MYC). Further study of genomic evolution of breast cancer in the context of brain metastasis and therapeutic resistance will uncover conserved site-specific genomic changes and will identify novel, rational therapeutic targets. Citation Format: Anton Safonov, Deborah Smith, Emanuela Ferraro, Junchao Shen, Ishaani Khatri, Rahul Kumar, Julia An, Mark Robson, Sarat Chandarlapaty, Adrienne Boire, Nikolaus Schultz, Nelson Moss, Luke Pike, Pedram Razavi. Clinicogenomic analysis reveals genomic associations of brain metastatic tropism in breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-16-01.

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice.

Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice

Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations – the frequencies of C>T, A>G, etc. – will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.

Prevalence and spectrum of cancer predisposition germline mutations in young patients with the common late-onset cancers.

Pathogenic germline variants (PGVs) can play a vital role in the oncogenesis process in carriers. Previous studies have recognized that PGVs contribute to early onset of tumorigenesis in certain cancer types, for example, colorectal cancer and breast cancer. However, the reported prevalence data of cancer-associated PGVs were highly inconsistent due to nonuniform patient cohorts, sequencing methods, and prominent difficulties in pathogenicity interpretation of variants. In addition to the above difficulties, due to the rarity of cases, the prevalence of cancer PGV carriers in young cancer patients affected by late-onset cancer types has not been comprehensively evaluated to date. A total of 131 young cancer patients (1-29 years old at diagnosis) were enrolled in this study. The patients were affected by six common late-onset cancer types, namely, lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, and head-neck cancer. Cancer PGVs were identified and analyzed. based on NGS-based targeted sequencing followed by bioinformatic screening and strict further evaluations of variant pathogenicity. Twenty-three cancer PGVs in 21 patients were identified, resulting in an overall PGV prevalence of 16.0% across the six included cancer types, which was approximately double the prevalence reported in a previous pancancer study. Nine of the 23 PGVs are novel, thus expanding the cancer PGV spectrum. Seven of the 23 (30.4%) PGVs are potential therapeutic targets of olaparib, with potential implications for clinical manipulation. Additionally, a small prevalence of somatic mutations of some classic cancer hallmark genes in young patients, in contrast to all-age patients, was revealed. This study demonstrates the high prevalence of PGVs in young cancer patients with the common late-onset cancers and the potentially significant clinical implications of cancer PGVs, the findings highlight the value of PGV screening in young patients across lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, or head-neck cancer.

Identification of a novel CNV at the APC gene in a Chinese family with familial adenomatous polyposis.

Introduction: Familial adenomatous polyposis (FAP) is the second most commonly inherited colorectal cancer (CRC) predisposition caused by germline mutations within the adenomatous polyposis coli (APC) gene. The molecular defects and clinical manifestations of two FAP families were analyzed, and individual prevention strategies suitable for mutation carriers in different families were proposed. Methods and results: The pathogenic gene mutations were identified among the two families using whole-exome sequencing and verified with Sanger sequencing or quantitative polymerase chain reaction (qPCR). One novel (GRCh37:Chr5: 112145676-112174368, del, 28,692bp) and a known (c.C847T:p.R283X) mutation in the APC gene were pathogenic mutations for FAP, according to the sequencing data and tumorigenesis pattern among the family members. The two mutations led to a premature translational stop signal, synthesizing an absent or disrupted protein product. Conclusion: Our findings expand the known germline mutation spectrum of the APC gene among the Chinese population. This reaffirms the importance of genetic testing in FAP. Genetic consultation and regular follow-ups are necessary for the individualized treatment of cancer-afflicted families with APC expression deficiency. Additional work is required to develop safe and effective chemotherapy and immunotherapy for FAP based on the mutation type.

Abstract IA16: RASopathies: the other face of RAS signaling upregulation

Abstract RAS proteins control a major intracellular signaling network that, depending on the cellular context, mediates response to external stimuli to control diverse biological functions. Within this network, signal flow through the RAF-MEK-ERK (MAPK, hereafter) pathway, modulates a wide array of cellular processes as well as early and late developmental programs. Signaling through the RAS-MAPK cascade is tightly controlled, and its enhanced activation has been known for decades to represent a major event in oncogenesis. Unexpectedly, discoveries derived from a massive disease gene hunting effort have more recently established a picture in which the upregulation of this signaling cascade underlies a group of clinically related developmental disorders collectively known as “RASopathies”, which share cardiac defects, reduced postnatal growth, variable cognitive deficits, facial dysmorphism, ectodermal and musculoskeletal anomalies, and variably increased risk for certain malignancies as major features. Based on the relatively high prevalence of some of these disorders (i.e., Noonan syndrome and neurofibromatosis type 1), the dysregulation of this signaling pathway represents one of the most common events affecting development. RASopathies are caused by mutations in genes encoding RAS proteins and structurally/functionally related GTPases, regulators of RAS function, modulators of RAS interaction with effectors or downstream signal transducers of the MAPK backbone. A subset of these genes have previously been implicated in cancer. Many of these RASopathy-causing alleles encode proteins with upregulated functional behavior, but with less activating strength compared to those contributing to oncogenesis. In these genes, a largely non-overlapping spectrum of germline and somatic mutations is generally observed. On the other hand, a few disorders result from a protein with defective function. In these, the implicated proteins negatively control signal flow, and the pathogenic event contributing to oncogenesis is generally represented by a second somatic hit involving the retained wild-type allele. The understanding of the molecular mechanisms involved in the pathogenesis of RASopathies has provided novel and relevant insights in cancer research. The identification of PTPN11 as major disease gene underlying Noonan syndrome represented the basis for the discovery that SHP2, the protein encoded by PTPN11, functions as an oncoprotein in childhood hematologic malignancies when mutated. More recently, genomic sequencing of RASopathies has allowed to identify circuits and players with previously unrecognized regulatory role on RAS function and signaling through the MAPK cascade. Here is provided an overview on the genes implicated in this group of developmental disorders, the molecular basis underlying the differential impact of germline and somatic mutations in development and cancer, the unanticipated molecular mechanisms converging toward the dysregulation of this signaling cascade, and major clinically relevant genotype-phenotype correlations. Citation Format: Marco Tartaglia. RASopathies: the other face of RAS signaling upregulation [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr IA16.

The Unique Spectrum of MUTYH Germline Mutations in Colombian Patients with Extracolonic Carcinomas.

Protein MUTYH, encoded by the gene MUTYH, is an important mismatch repair enzyme in the base-excision repair pathway of DNA repair. When genetically altered, different neoplastic conditions can arise. One of the widely known syndromes associated with MUTYH mutations is MUTYH-associated polyposis, a form of familial colorectal cancer syndrome. MUTYH may also be a driver in other familial cancer syndromes, as well as breast cancer and spontaneous cancer cases. However, some controversies about the role of these alterations in oncogenesis remain, especially when affected in a heterozygous way. Most available data on MUTYH mutations are on Caucasian patients. We analyzed a small cohort of non-Caucasian, Colombian cancer patients with MUTYH germline heterozygous mutations, clinical features suggestive of familial cancer, and extensive genetic studies with no other mutations and without MUTYH-associated polyposis. With this case series, we intended to provide important data for the understanding of MUTYH as a possible driver of familial cancer, even when only heterozygous mutations are found.

BRCA1 and BRCA2 germline mutation analysis from a cohort of 1267 patients at high risk for breast cancer in Brazil

We determined the frequency and mutational spectrum of BRCA1 and BRCA2 in a series of patients at high risk for developing breast cancer from Brazil. A total of 1267 patients were referred for BRCA genetic testing, and no obligation of fulfilling criteria of mutation probability methods for molecular screening was applied. Germline deleterious mutations in BRCA1/2 (i.e., pathogenic/likely pathogenic variants) were identified in 156 out of 1267 patients (12%). We confirm recurrent mutations in BRCA1/2, but we also report three novel mutations in BRCA2, not previously reported in any public databases or other studies. Variants of unknown significance (VUS) represent only 2% in this dataset and most of them were detected in BRCA2. The overall mutation prevalence in BRCA1/2 was higher in patients diagnosed with cancer at age > 35years old, and with family history of cancer. The present data expand our knowledge of BRCA1/2 germline mutational spectrum, and it is a valuable clinical resource for genetic counseling and cancer management programs in the country.

Limited role of generation time changes in driving the evolution of the mutation spectrum in humans.

Recent studies have suggested that the human germline mutation rate and spectrum evolve rapidly. Variation in generation time has been linked to these changes, though its contribution remains unclear. We develop a framework to characterize temporal changes in polymorphisms within and between populations, while controlling for the effects of natural selection and biased gene conversion. Application to the 1000 Genomes Project dataset reveals multiple independent changes that arose after the split of continental groups, including a previously reported, transient elevation in TCC>TTC mutations in Europeans and novel signals of divergence in C>Gand T>A mutation rates among population samples. We also find a significant difference between groups sampled in and outside of Africa in old T>C polymorphisms that predate the out-of-Africa migration. This surprising signal is driven by TpG>CpG mutations and stems in part from mis-polarized CpG transitions, which are more likely to undergo recurrent mutations. Finally, by relating the mutation spectrum of polymorphisms to parental age effects on de novo mutations, we show that plausible changes in the generation time cannot explain the patterns observed for different mutation types jointly. Thus, other factors - genetic modifiers or environmental exposures - must have had a non-negligible impact on the human mutation landscape.

Spectrum of germline mutations among Mexican patients with colorectal cancer.

78 Background: Colorectal cancer (CRC) is the third most common cancer in the world, and the second most frequent cause of death due to cancer. 5-10% of CRC cases are due to a hereditary predisposing syndrome, the most frequent being Lynch Syndrome (LS) followed by Familial Adenomatous Polyposis (FAP), characterized by loss of function of mismatch repair genes (MMR) and APC, respectively. The purpose of this study is to describe the spectrum of germline pathogenic variants among Mexican CRC patients using Next-generation sequencing (NGS). Methods: This study is original research approved by IRB; all patients signed the informed consent. 43 patients between 18-60 y/o with CRC were enrolled. NGS was performed using a panel which targeted a set of 94 genes and 284 SNPs known to play a role in cancer predisposing. Bioinformatics data analysis was carried out using Pediatric Cancer Variant Pathogenicity Information Exchange (PeCanPIE) and an in-silico analysis to classify variants according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Mean age 48.71 y/o, 62.6% men. Germline pathogenic and likely pathogenic variants (PV/LP) were identified in 69% of sample. A molecular diagnosis of LS (MLH1, MSH2, MSH6, and PMS2) was confirmed in 12 (28%), and FAP in 5 (11.6%). It is remarkably the presence of 5 PV in PRF1 (2 G149S; 3 A91V), among other unusual genes for CRC. Also 12 double heterozygotes were identified, including one with PRF1 and CHEK2 PV. Conclusions: NGS allow the discover of new pathogenic variants that would not be suspected in classic hereditary syndromes. The understanding of other genes involved in other pathways could expand our understanding in the heritability of CRC. PRF1 emerges as a new candidate gene associated with CRC, previous evidence supports the role of PRF1 in solid tumors beside hematologic malignancies.

Diverse genetic spectrum among patients who met the criteria of hereditary breast, ovarian and pancreatic cancer syndrome.

Genetic high-risk assessment combines hereditary breast, ovarian and pancreatic cancer into one syndrome. However, there is a lack of data for comparing the germline mutational spectrum of the cancer predisposing genes between these three cancers. Patients who met the criteria of the hereditary breast, ovarian and pancreatic cancer were enrolled and received multi-gene sequencing. We enrolled 730 probands: 418 developed breast cancer, 185 had ovarian cancer, and 145 had pancreatic cancer. Out of the 18 patients who had two types of cancer, 16 had breast and ovarian cancer and 2 had breast and pancreatic cancer. A total of 167 (22.9%) patients had 170 mutations. Mutation frequency in breast, ovarian and pancreatic cancer was 22.3%, 33.5% and 17.2%, respectively. The mutation rate was significantly higher in patients with double cancers than those with a single cancer (p<0.001). BRCA1 and BRCA2 were the most dominant genes associated with hereditary breast and ovarian cancer, whereas ATM was the most prevalent gene related to hereditary pancreatic cancer. Genes of hereditary colon cancer such as lynch syndrome were presented in a part of patients with pancreatic or ovarian cancer but seldom in those with breast cancer. Families with a history of both ovarian and breast cancer were associated with a higher mutation rate than those with other histories. The mutation spectrum varies across the three cancer types and family histories. Our analysis provides guidance for physicians, counsellors, and counselees on the offer and uptake of genetic counseling.

OP02 Clinical characteristics and germline mutation spectrum of RB1 in Vietnamese patients with retinoblastoma

OP02 Clinical characteristics and germline mutation spectrum of RB1 in Vietnamese patients with retinoblastoma

CNSC-37. ATYPICAL GERMLINE MUTATIONS AND PRIMARY CNS TUMORS: A SINGLE-CENTER CASE SERIES AND LITERATURE REVIEW

Abstract A growing spectrum of germline mutations and their association with primary CNS tumors has been described over the last decade. These germline mutations are implicated in regulation of DNA integrity and repair, telomere maintenance, and cell cycle regulation resulting in aberrant cellular proliferation and immune surveillance evasion. To date, there are no well-defined guidelines for primary CNS tumor surveillance for these patients. Moreover, the exact role of traditional chemotherapy, immunotherapy, and radiation is unclear. We present a single-institution case series of adult patients with primary CNS tumors with atypical germline mutations and literature review. The most common germline mutations encountered involved heterozygous mutations of one of the mismatch repair (MMR) genes (MSH2, PMS2, MLH1). All patients developed high-grade gliomas defined as astrocytoma or glioblastoma WHO grade 4 based on the WHO 2021 classification. Germline mutations involving RAD51C, POT1, IDH1/2, MutyH, NTHL1, PALB2, and CHEK2 were associated with gliomas of variable grades and molecular subtypes. Non-glial tumors, including atypical rhabdoid tumors, medulloblastomas, hemangioblastomas, and meningiomas were found in association with germline SMARCB1, ATM, BRCA1, and CHEK2 mutations respectively. Review of the existing literature and knowledge obtained from our case series suggests several important concepts: (1) there is an increased risk of both glioma and non-glial tumor types in several atypical germline mutations, (2) multiple risk genes or variants of unknown significance likely contribute to primary brain tumor formation, (3) germline MMR mutations associated with high-grade glioma may be MMR gene-specific with potential increased risk of resistance and/or disease progression in the presence of alkylating agents such as temozolomide, (4) several germline mutations may increase risk of secondary tumor development after radiation, and (5) the role of screening for atypical germline mutations and subsequent disease surveillance remain unanswered.

Abstract 1451: BRCA1 and BRCA2 germline mutational spectrum in Algerian triple negative breast cancer (TNBC) patients

Abstract Background: Breast cancer is currently the leading cause of cancer morbidity and mortality among Algerian women. To date, triple negative breast cancer (TNBC) shows substantial overlap with basal type cancer and it is associated with aggressive tumor behavior, poor prognosis and BRCA1 mutations. In the present study, we screened for the prevalence of BRCA1 and BRCA2 germline mutations in a cohort of 169 TNBC patients using PCR-Sanger sequencing and NGS with a cancer panel of 30 hereditary cancer genes or BRCA1/BRCA2 genetic test. Materials and Methods: 169 TNBC patients and their relatives were referred trough several public hospitals from six years (2013-2019). BRCA1 germline mutation was screened using PCR-Sanger sequencing in 66 TNBC patients with strong family history of breast and ovarian cancer and 103 sporadic TNBC patients including all exons where a mutation was previously found in Algerian population (exons 2, 3, 4, 10, 17 and 19). BRCA2 germline mutation was screened using PCR-Sanger sequencing in 24 TNBC patients with strong family history of breast cancer including all exons where a mutation was previously found in Algerian patients (exons 10 and 22). In addition, nine (9) TNBC patients with strong family history of breast and ovarian cancer were analyzed by NGS using BRCA1 and BRCA2 test or a cancer panel of 30 hereditary genes (Colors genomics). Results: The analysis of the genomic DNA samples of 169 TNBC patients revealed that 15 patients carried pathogenic germline variants in BRCA1 gene and three patients carried pathogenic variants in BRCA2 gene (10.65%). Eight distinct germline mutations in BRCA1 have been detected in this study: c.83_84delTG, c.181T&amp;gt;G, c.798_799delTT, c.505C&amp;gt;T, c.923_924delGC, c.2125_2126insA, c.5257A&amp;gt;G and deletion of exon 15. Interestingly, the recurrent and specific mutation c.83_84delTG has been detected in 4 unrelated TNBC patients. The pathogenic variant c.2125_2126insA has been detected in three unrelated families and also in the first relatives of 2 patients. The rare likely pathogenic variant BRCA1 c.5257A&amp;gt;G/p.Arg1753Gly has been detected in young female TNBC patient. The Del exon 15 in BRCA1 has been detected in two unrelated patients. Three distinct germline mutations in BRCA2 have been detected in three TNBC patients: c.1813dupA, c.7654dupA and c.8485C&amp;gt;T. Interestingly, these three mutations are reported for the first time in Algerian population. The c.1813dupA and c.8485C&amp;gt;T pathogenic variants have been detected in two young female TNBC patients with a family history of male breast cancer. Conclusions: In the current study, we detected recurrent germline mutations in BRCA1 gene in early onset TNBC patients. BRCA2 pathogenic variants have also been detected in young female TNBC patients. TNBC immunophenotype should be considered as an additional criterion for genetic counselling and testing of BRCA genes in Algerian women with early onset breast cancer. Citation Format: Farid Cherbal, Chiraz Mehemmai, Hadjer Gaceb, Hassen Mahfouf, Kada Boualga. BRCA1 and BRCA2 germline mutational spectrum in Algerian triple negative breast cancer (TNBC) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1451.

NGS analysis of germline mutation profile of patients with hepatocellular carcinoma in China.

10585 Background: Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer-related death worldwide with very poor prognosis. Many studies have focused on oncogene characteristics, however, the germline landscape of Chinese HCC patients has not been fully clarified. The purpose of this study is to assess the inherited genetic factors regarding germline mutations in Chinese HCC patients. Methods: Genetic mutations were reviewed in 1670 Chinese HCC patients who underwent hybridization capture based next-generation sequencing (NGS). The pathogenicity of germline mutations was categorized based on American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Of 1670 patients with HCC, 110 (6.7%) patients were identified to carry 111 pathogenic variants(P) or likely pathogenic variants(LP) in 112-cancer predisposition gene panel, and there was no age difference between P/LP group and non-P/LP group (average age: 57 vs 56, p = 0.64). The most frequently germline mutated genes were BRCA1/2 (11.7%), followed by ATM(4.5%), BLM(4.5%), ERCC2(4.5%), ERCC3(4.5%) and BRIP1(3.6%), ERCC4(3.6%), FANCD2(3.6%), MUTYH(3.6%), RAD50(3.6%). Of all the 111 germline mutations, 47% (n = 52) lay in the Homologous Recombination Repair (HRR) pathways. Both in P/LP group and non-P/LP group, the most frequently somatic mutated genes were TP53, TERT and MUC16. 7/110(6.4%)of patients in P/LP group were high TMB(≥10 mutations/megabase) and 131/1560(8.5%) in non-P/LP group. There was no statistical difference in TMB between P/LP and non-P/LP group. Conclusions: Taken together, we have presented the spectrum of pathogenic germline mutations in Chinese HCC patients. P/LP germline variants in cancer predisposition genes were detected in 6.7% of those patients, and predisposition genes associated with HCC risk needs further investigation. Inherited genetics should not be overlooked in HCC as there are important implications for precision treatment, future risk of cancers, and familial cancer risk.

Territorial manifestation features of multiple primary malignant neoplasms in carriers of germline mutations in the BRCA 1 gene in Republic of Bashkortostan.

e22523 Background: Recent advances in the diagnostic and therapeutic fields of oncology have increased the life expectancy of cancer patients, and therefore carriers of germline mutations, who are at high risk of developing a malignant neoplasm, also have a higher risk of developing a second synchronous or metachronous malignant tumor. The aim of this work is to study the features of the development of primary multiple malignant neoplasms in patients with germline mutations in the repair genes. Methods: Among all treated in the Republican Clinical Oncological Dispensary patients germline mutations in the repair genes were detected in 225 persons. Mutations were determined by polymerase chain reaction (PCR). The material of the study was a sample of venous blood taken from a patient on an empty stomach. A diagnostic panel was used to detect the most common mutations in Russia in the BRCA1 (5382insC, 4153delA, 300T &gt; G, 185delAG, 2080delA, 3819delGTAAA) and BRCA2 (6174delT) genes. In the absence of a mutation, the study was carried out by the next generation sequencing (NGS) method. Results: After a molecular genetic study from 2014 to 2021, we determined the spectrum of germline mutations in residents of the Republic of Bashkortostan: BRCA 1 - c.5266dupC, c.3143delG, c.5161C &gt; T, c.5382 insC, c.3819delGTAAA, c. 300T &gt; G, c.5136G &gt; A, 185delAG, 4153delA, 2080delA; BRCA 2 - c.6621_6622del, p.39-1_39delGA, c.961_962insAA. Among carriers of germinal mutations, primary multiple cancer was registered in 14.6% (33/225) of patients with mutations in the BRCA 1 genes. The following mutations were identified in patients with primary multiple malignant neoplasms: c.5382 insC and c.3819delGTAAA in the BRCA gene 1. The first primary breast cancer was registered in 10.6% (24/225) of patients, ovarian cancer in 1.8% (4/225), gastric cancer in 0.4% (1/225), primary multiple synchronous breast and ovarian cancer in 1.8% (4/225). In carriers of germinal mutations, manifestations of the first primary cancer were observed at the age of 29 to 60 years. The manifestation of the second primary cancer was registered in 2-18 years after the manifestation of the first primary cancer. Twenty-two patients subsequently developed a second primary breast cancer and 11 patients developed ovarian cancer. Also, 6 patients had a manifestation of the third primary cancer of the breast, ovaries or stomach in 8-26 years after the manifestation of the second primary cancer. Conclusions: Primary multiple cancer in carriers of germline mutations in the Republic of Bashkortostan was observed in 14.6% (33/225) of patients with mutations in the BRCA 1 genes. The period of manifestation of a secondary malignant tumor ranged from 2 to 18 years. This study plays an important role in the process of optimizing screening for multiple primary malignant neoplasms for carriers of germline mutations.

The mutational landscape of medullary thyroid carcinoma using whole-exome sequencing in China.

6054 Background: Medullary thyroid carcinoma (MTC) is a rare malignancy, and its molecular pathogenesis is far from being understood. Therefore, a relatively comprehensive and accurate genomic profiling is needed for the future molecular diagnosis, treatment and early prevention of MTC patients. Methods: In this study, we investigated both the somatic and germline mutational spectrum of MTC, whole-exome sequencing (WES) was performed on tumor samples and matched noncancerous tissues from 30 MTC patients. Genetic alterations were defined and analyzed using MutSigCV and novel germline mutations were identified using MutationTaster and cross-referenced in PubMed. Results: In somatic mutational spectrum we found the top three significantly mutated genes (SMGs) in our MTC samples were RET, FAM186A and PRG4 genes (33%, 33% and 27%, respectively). For the germline mutations, FAT4 was detected as the most common mutated genes, following by RET and FAT1. Besides, we identified 30 novel germline mutations such as IGF1R, PDK1, NOTCH1, RPTOR, MPL, SETD2 and ARID2. Those mutated genes have been previously associated with neurofibromatosis, Lynch syndrome and other diseases respectively and now predicted potential functional pathogenicity in the patients with MTC. Conclusions: The study elucidated a relatively more comprehensive genomic landscape of MTC. In addition to the RET gene, which has been studied extensively, other SMGs may also be of interest including novel germline mutations. These findings may indicate the potential basis of molecular diagnosis, early prevention and targeted therapeutic options for patients with MTC in the future.

Mutational signatures are markers of drug sensitivity of cancer cells

Genomic analyses have revealed mutational footprints associated with DNA maintenance gone awry, or with mutagen exposures. Because cancer therapeutics often target DNA synthesis or repair, we asked if mutational signatures make useful markers of drug sensitivity. We detect mutational signatures in cancer cell line exomes (where matched healthy tissues are not available) by adjusting for the confounding germline mutation spectra across ancestries. We identify robust associations between various mutational signatures and drug activity across cancer cell lines; these are as numerous as associations with established genetic markers such as driver gene alterations. Signatures of prior exposures to DNA damaging agents – including chemotherapy – tend to associate with drug resistance, while signatures of deficiencies in DNA repair tend to predict sensitivity towards particular therapeutics. Replication analyses across independent drug and CRISPR genetic screening data sets reveal hundreds of robust associations, which are provided as a resource for drug repurposing guided by mutational signature markers.

A natural mutator allele shapes mutation spectrum variation in mice.

Although germline mutation rates and spectra can vary within and between species, commongenetic modifiers of themutation rate have not been identifiedin nature1. Here we searched for loci that influence germline mutagenesis using a uniquely powerful resource: a panel of recombinant inbred mouse lines known as theBXD, descended from the laboratory strains C57BL/6J (B haplotype) and DBA/2J (D haplotype). Each BXD lineage has been maintained by brother-sister mating in the near absence of natural selection, accumulating de novo mutations for up to 50 years on a known genetic background that is a unique linear mosaic of B and D haplotypes2. We show that mice inheriting D haplotypes at a quantitative trait locus on chromosome 4 accumulate C>A germline mutations at a 50% higher rate than those inheriting B haplotypes, primarily owing to the activity of a C>A-dominated mutational signature known as SBS18. The B and D quantitative trait locus haplotypes encode different alleles of Mutyh, a DNA repair gene that underlies the heritable cancer predisposition syndromethat causes colorectal tumors with a high SBS18 mutation load3,4. Both B and D Mutyh alleles are present in wild populations of Mus musculus domesticus, providing evidence that common genetic variation modulates germline mutagenesis in a model mammalian species.