Variants In CHEK2 Research Articles

EP061: Genetic risk for breast and ovarian cancer in a diverse and unselected population

eP061: Genetic risk for breast and ovarian cancer in a diverse and unselected population

EP054: Real-world clinical characteristics and management of breast cancer in patients with germline pathogenic variants in ATM, CHEK2 and PALB2

Breast cancer is the most common type of cancer in women. While breast cancer risk associated with BRCA1 and BRCA2 variants are well-defined, the characteristics associated with germline pathogenic variants (PVs) in the moderate penetrant genes, ATM, CHEK2 and PALB2, are less clear. We describe the clinical characteristics, management, and treatment outcomes associated with germline moderate penetrant PVs in a large real-world clinical cohort.

Breast Cancer Screening Strategies for Women With ATM, CHEK2, and PALB2 Pathogenic Variants

Screening mammography and magnetic resonance imaging (MRI) are recommended for women with ATM, CHEK2, and PALB2 pathogenic variants. However, there are few data to guide screening regimens for these women. To estimate the benefits and harms of breast cancer screening strategies using mammography and MRI at various start ages for women with ATM, CHEK2, and PALB2 pathogenic variants. This comparative modeling analysis used 2 established breast cancer microsimulation models from the Cancer Intervention and Surveillance Modeling Network (CISNET) to evaluate different screening strategies. Age-specific breast cancer risks were estimated using aggregated data from the Cancer Risk Estimates Related to Susceptibility (CARRIERS) Consortium for 32 247 cases and 32 544 controls in 12 population-based studies. Data on screening performance for mammography and MRI were estimated from published literature. The models simulated US women with ATM, CHEK2, or PALB2 pathogenic variants born in 1985. Screening strategies with combinations of annual mammography alone and with MRI starting at age 25, 30, 35, or 40 years until age 74 years. Estimated lifetime breast cancer mortality reduction, life-years gained, breast cancer deaths averted, total screening examinations, false-positive screenings, and benign biopsies per 1000 women screened. Results are reported as model mean values and ranges. The mean model-estimated lifetime breast cancer risk was 20.9% (18.1%-23.7%) for women with ATM pathogenic variants, 27.6% (23.4%-31.7%) for women with CHEK2 pathogenic variants, and 39.5% (35.6%-43.3%) for women with PALB2 pathogenic variants. Across pathogenic variants, annual mammography alone from 40 to 74 years was estimated to reduce breast cancer mortality by 36.4% (34.6%-38.2%) to 38.5% (37.8%-39.2%) compared with no screening. Screening with annual MRI starting at 35 years followed by annual mammography and MRI at 40 years was estimated to reduce breast cancer mortality by 54.4% (54.2%-54.7%) to 57.6% (57.2%-58.0%), with 4661 (4635-4688) to 5001 (4979-5023) false-positive screenings and 1280 (1272-1287) to 1368 (1362-1374) benign biopsies per 1000 women. Annual MRI starting at 30 years followed by mammography and MRI at 40 years was estimated to reduce mortality by 55.4% (55.3%-55.4%) to 59.5% (58.5%-60.4%), with 5075 (5057-5093) to 5415 (5393-5437) false-positive screenings and 1439 (1429-1449) to 1528 (1517-1538) benign biopsies per 1000 women. When starting MRI at 30 years, initiating annual mammography starting at 30 vs 40 years did not meaningfully reduce mean mortality rates (0.1% [0.1%-0.2%] to 0.3% [0.2%-0.3%]) but was estimated to add 649 (602-695) to 650 (603-696) false-positive screenings and 58 (41-76) to 59 (41-76) benign biopsies per 1000 women. This analysis suggests that annual MRI screening starting at 30 to 35 years followed by annual MRI and mammography at 40 years may reduce breast cancer mortality by more than 50% for women with ATM, CHEK2, and PALB2 pathogenic variants. In the setting of MRI screening, mammography prior to 40 years may offer little additional benefit.

Abstract P3-07-02: Identification of potential germline variants (GV) on tumor comprehensive genomic profiling (CGP) in patients with advanced breast cancer (BC): BRCA1/2 and beyond

Abstract Background Detection of pathogenic GVs in patients with BC has implications for both patients and their family members. Management options such as increased surveillance, chemoprevention, and surgical prophylaxis are available to GV carriers. Beyond BRCA1/2, GVs in the cancer susceptibility genes (CSGs) PALB2, ATM, and CHEK2 confer a 2-11-fold lifetime risk of BC. One opportunity CGP assays present is the potential to detect clinically-relevant GVs in addition to targetable somatic variants. While the Breast Cancer Association Consortium found that 5.2% of women with BC carried a GV in one of these five CSGs, we sought to describe the frequency of these potential GVs detected by CGP in a cohort of patients with advanced disease. Methods We reviewed an internal database of patients with advanced BC who underwent testing with a CGP panel using tissue (n= 20,109, FoundationOne® CDx) or plasma (n= 4,182, FoundationOne®Liquid CDx or FoundationOne®Liquid). Cases with a potential GV were identified by filtering base substitutions and short indels for inclusion in ClinVar as pathogenic or likely pathogenic and by variant allele frequency (VAF) based on an optimized assay-specific threshold, focusing on the select CSGs of BRCA1/2, PALB2, ATM and CHEK2. To enable follow-up of potential GVs, we implemented a new reporting “banner” to highlight select short variants in these CSGs. Predominant patient ancestry was inferred using a SNP-based classifier and Fisher’s exact test was utilized for comparison between groups. Results A total of 24,291 unique patients with primarily advanced BC had CGP results available for study, with common actionable findings including PIK3CA mutations (8,572, 35.3%), ESR1 mutations (3,289, 13.5%), and HER2 amplification (1,602, 6.6%). Focusing on the 5 CSGs, 16.4% of patients (3,986) had at least one pathogenic alteration detected in BRCA2 (1,153, 4.7%), ATM (969, 4.0%), CHEK2 (982, 4.0%) BRCA1 (849, 3.5%) or PALB2 (308, 1.3%); 1.1% of patients (263) harbored alterations in multiple CSGs. 50.7% (2,020/3,986) of patients with pathogenic alterations in these CSGs - 8.3% (2,020/24,291) of total patients with advanced BC - had an alteration meeting criterion as a potential GV. Variants in BRCA1 (511/919, 55.6%), BRCA2 (786/1,425, 55.2%), and PALB2 (201/376, 53.5%), more frequently met criteria as potential GVs than variants in CHEK2 (328/1,046, 31.4%) or ATM (265/1,100, 24.1%). In these five CSGs, 1,796/3,195 alterations detected on tissue CGP (56.2%) and 295/1,671 detected in plasma (17.7%) met criteria as a potential GVs. Ancestry analysis of 20,108 assessable BC patients tested using tissue CGP showed potential GVs in CHEK2 were more common in European vs non-European (1.7% vs 0.4%, p<0.01) and potential GVs in PALB2 were more common in African vs non-African (1.4% vs 0.7%, p<0.01) ancestries. Of 1,961 patients with BC tested over a 2-month period, 9.7% of reports (191) included a germline banner reporting a potential GV in one of these 5 CSGs and recommending consideration of referral for germline testing. Conclusion Potential pathogenic GVs in BRCA1/2, PALB2, ATM and CHEK2 were identified in 8.3% of patients with advanced BC tested utilizing CGP when filtering by VAF and ClinVar annotation. Highlighting these potential GVs with a report banner provides the opportunity for follow-up germline testing and genetic counseling for patients who otherwise may not have been referred for additional testing. These alterations were detected in both tissue and plasma CGP and in patients of varying ancestries. The potential for detection of potential GVs plus the detection of actionable driver and resistance mechanisms may add to the clinical value of CGP for patients with breast cancer. Citation Format: Marni B Tierno, Kali C Dougherty, Erica Gornstein, Dean C Pavlick, Alexa Schrock, Geoff R Oxnard. Identification of potential germline variants (GV) on tumor comprehensive genomic profiling (CGP) in patients with advanced breast cancer (BC): BRCA1/2 and beyond [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 P3-07-02.

Abstract P2-01-16: Targeted sequencing of plasma-derived vs. urinary cfDNA from patients with triple negative breast cancer

Abstract Background: In breast cancer, genetic profiling of circulating cell-free DNA (cfDNA) from blood plasma was shown to have good potential for clinical use and might help to find individual treatment options and to monitor metastatic relapse as well as intratumoral heterogeneity. Due to limited therapy options and high risk of acquired treatment resistance based on genetic alterations of the tumor, particularly, women diagnosed with the aggressive triple negative breast cancer (TNBC) subtype might benefit from serial mutation profiling during disease courses. Here, cfDNA derived from patients’ urine might offer promising opportunities for non-invasive monitoring at frequent intervals. In this pilot study, we investigated plasma-derived and matching urinary cfDNA samples obtained from 15 presurgical TNBC patients using a targeted sequencing approach to identify common breast cancer-related genetic alterations in both bodyfluids. Methods: Blood plasma and urine samples were processed within 4 hrs after collection. We successfully adapted the manufacturer’s instructions to yield increased concentrations of extracted plasma-derived and urinary cfDNA (QIAamp MinElute ccfDNA Kit, QIAGEN). After quality control of cfDNA fragments, matched samples were applied to library preparation and target enrichment with a commercially available diagnostic breast cancer specific 93-gene panel service (QIAGEN). Libraries were analyzed by paired-end sequencing on a NextSeq550 (Illumina Inc.) instrument followed by bioinformatical analysis with QIAGEN Biomedical Genomics Workbench and subsequent interpretation of variants using QCI Interpret Translational Software (QIAGEN). Results: In the cohort, 3339 somatic breast-cancer related genetic alterations (VAF ≥ 3%) were detected, whereof 1222 vs. 2117 variants were found in plasma-derived vs. urinary cfDNA, respectively. Further, 431 variants were found in cfDNA derived from both body fluids. Per sample, we found a median number of 66 variants in plasma vs. 110 variants in urinary cfDNA. Interestingly, a median number of 31 shared variants was found per matched plasma-derived and urinary cfDNA sample resulting in a 46% recovery rate of plasma-derived mutations in urinary cfDNA (and vice versa only a 16% recovery rate of urinary cfDNA variants in plasma) throughout the cohort. Interestingly, QCI analysis revealed that 48 of the mutations found in both body fluids were pathogenic, resulting in a median number of 4 pathogenic variants per sample. The recovery rate of pathogenic plasma-derived variants in urinary cfDNA was 63% and vice versa, 66% of pathogenic urinary variants could be detected in the matched plasma samples. Further, 33 of the shared mutations were likely pathogenic. Among the patients, the most frequently occurring pathogenic and likely pathogenic mutated genes were NF1, CHEK2, KMT2C and PTEN in both body fluids. Noteworthy, a pathogenic CHEK2 (T519M) variant was found in all 30 samples and two pathogenic NF1 variants (T467I + c.2325+3A>G) as well as a pathogenic PTEN variant (C136Y) were also very frequent in the cohort. Conclusion: Taken together, our results indicated that both plasma-derived and urinary cfDNA from TNBC patients could be analyzed in a sufficient manner using a targeted sequencing approach. Both body fluids appear to be valuable sources bearing complementary information regarding the genetic tumor profile, which might be relevant for disease monitoring and individual treatment decisions. Further analyses of a larger patient cohort using adequate bioinformatics algorithms are required to find associations between somatic variants in both cfDNA sources. Key words: cfDNA, breast cancer, targeted sequencing, somatic variants, mutation, urine, plasma Citation Format: Henrike Herzog, Bahriye Aktas, Ivonne Nel. Targeted sequencing of plasma-derived vs. urinary cfDNA from patients with triple negative breast cancer [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 P2-01-16.

Pathology of Tumors Associated With Pathogenic Germline Variants in 9 Breast Cancer Susceptibility Genes

Rare germline genetic variants in several genes are associated with increased breast cancer (BC) risk, but their precise contributions to different disease subtypes are unclear. This information is relevant to guidelines for gene panel testing and risk prediction. To characterize tumors associated with BC susceptibility genes in large-scale population- or hospital-based studies. The multicenter, international case-control analysis of the BRIDGES study included 42 680 patients and 46 387 control participants, comprising women aged 18 to 79 years who were sampled independently of family history from 38 studies. Studies were conducted between 1991 and 2016. Sequencing and analysis took place between 2016 and 2021. Protein-truncating variants and likely pathogenic missense variants in ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53. The intrinsic-like BC subtypes as defined by estrogen receptor, progesterone receptor, and ERBB2 (formerly known as HER2) status, and tumor grade; morphology; size; stage; lymph node involvement; subtype-specific odds ratios (ORs) for carrying protein-truncating variants and pathogenic missense variants in the 9 BC susceptibility genes. The mean (SD) ages at interview (control participants) and diagnosis (cases) were 55.1 (11.9) and 55.8 (10.6) years, respectively; all participants were of European or East Asian ethnicity. There was substantial heterogeneity in the distribution of intrinsic subtypes by gene. RAD51C, RAD51D, and BARD1 variants were associated mainly with triple-negative disease (OR, 6.19 [95% CI, 3.17-12.12]; OR, 6.19 [95% CI, 2.99-12.79]; and OR, 10.05 [95% CI, 5.27-19.19], respectively). CHEK2 variants were associated with all subtypes (with ORs ranging from 2.21-3.17) except for triple-negative disease. For ATM variants, the association was strongest for the hormone receptor (HR)+ERBB2- high-grade subtype (OR, 4.99; 95% CI, 3.68-6.76). BRCA1 was associated with increased risk of all subtypes, but the ORs varied widely, being highest for triple-negative disease (OR, 55.32; 95% CI, 40.51-75.55). BRCA2 and PALB2 variants were also associated with triple-negative disease. TP53 variants were most strongly associated with HR+ERBB2+ and HR-ERBB2+ subtypes. Tumors occurring in pathogenic variant carriers were of higher grade. For most genes and subtypes, a decline in ORs was observed with increasing age. Together, the 9 genes were associated with 27.3% of all triple-negative tumors in women 40 years or younger. The results of this case-control study suggest that variants in the 9 BC risk genes differ substantially in their associated pathology but are generally associated with triple-negative and/or high-grade disease. Knowing the age and tumor subtype distributions associated with individual BC genes can potentially aid guidelines for gene panel testing, risk prediction, and variant classification and guide targeted screening strategies.

Identification of CHEK2 Germline Mutations in BRCA1/2- and PALB2-Negative Breast and Ovarian Cancer Patients

Introduction: The CHEK2 gene is known to be an important signal transducer involved in DNA repair, apoptosis, or cell cycle arrest in response to DNA damage. The mutations in this gene have been associated with a wide range of cancers, both sporadic and hereditary. Germline CHEK2 mutations are linked to an increased risk of breast cancer. Therefore, the aim of this study was to identify the prevalence of CHEK2 variants in BRCA1/2- and PALB2-negative early-onset patients with breast cancer and/or ovarian cancer in a Turkish population for the first time. Methods: The study included 95 patients with BRCA1/2- and PALB2-negative early-onset breast cancer and/or ovarian cancer and also 60 unaffected women. All the intron/exon boundaries and coding exons of CHEK2 were subjected to mutational analysis by heteroduplex analysis and DNA sequencing. Results: A total of 16 CHEK2 variants were found in breast cancer patients within the Turkish population. CHEK2 c.1100delC mutation most frequently studied in the CHEK2 gene was not detected in our study. The prevalence of variants of uncertain significance in CHEK2 was found to be 7.3% (n = 7) in BRCA1/2 and PALB2 mutation-negative Turkish patients with early-onset breast and/or ovarian cancer. Conclusion: The present study may shed light on alternative variations that could be significant for understanding the prevalence and clinical suitability of the CHEK2 gene.

Clinical Significance of Gene Mutations and Polymorphic Variants and their Association with Prostate Cancer Risk in Polish Men.

Objectives: We tested the association of germline variants in BRCA1, BRCA2, CHEK2, CDKN2A, CYP1B1, HOXB13, MLH1, NBS1, NOD2 and PALB2 genes, as well as in 8q24 region, with prostate cancer (PC) risk and estimated their impact on disease clinical course, including overall survival time in Polish men with localized PC qualified for radical treatment.Materials and Methods: DNA of 110 patients with localized prostate cancer treated with radical prostatectomy (RP), from each age group and with different stages of the disease. DNA samples of the control group consisted of 111 men, volunteers, without PC (age-matched to study group). Sanger sequencing, AS-PCR, RFLP-PCR, and multiplex-PCR were used for variants detection.Results: The percentage of men with ≥1 germline variant was higher in PC group (52.7%) than in healthy men (37.8%) (P = .03). The presence of ≥2 variants was associated with shorter survival than the presence of one or no variant in the PC group (P = .14, trend). The HOXB13 G84E was detected in 2.9% of PC men and in no healthy men (P = .19, trend, OR = 7.21). A CHEK2 truncating mutation (1100delC or IVS2+1G>A) was detected in 2/110 (1.8%) PC patients and in no healthy men (P = .29, OR=5.14). The NBS1 I171V was detected in 2/110 (1.8%) PC patients and in no men from the control group (OR=5.14, P = .29, NS).Conclusions: We conclude that the presence of more than 2 germline variants was probably associated with shorter survival of patients with localized prostate cancer qualified for radical treatment. The HOXB13 (G84E), CHEK2 (1100delC or IVS2+1G>A) truncating variants and NBS1 (I171V) are associated with PC and hereditary form of the disease. The HOXB13 (G84E) and NOD2 (3020insC) single variants are associated with shorter and CYP1B1 (48CC, 119GG) single genotypes with longer overall survival.

Rare coding variants in DNA damage repair genes associated with timing of natural menopause.

SummaryThe age of menopause is associated with fertility and disease risk, and its genetic control is of great interest. We use whole-exome sequences from 132,370 women in the UK Biobank to test for associations between rare damaging variants and age at natural menopause. Rare damaging variants in five genes are significantly associated with menopause: CHEK2 (p = 3.3 × 10−51), DCLRE1A (p = 8.4 × 10−13), and HELB (p = 5.7 × 10−7) with later menopause and TOP3A (p = 7.6 × 10−8) and CLPB (p = 8.1 × 10−7) with earlier menopause. Two additional genes are suggestive: RAD54L (p = 2.4 × 10−6) with later menopause and HROB (p = 2.9 × 10−6) with earlier menopause. In a follow-up analysis of repeated questionnaires in women who were initially premenopausal, CHEK2, TOP3A, and RAD54L genotypes are associated with subsequent menopause. Consistent with previous genome-wide association studies (GWASs), six of the seven genes are involved in the DNA damage repair pathway. Phenome-wide scans across 398,569 men and women revealed that in addition to known associations with cancers and blood cell counts, rare variants in CHEK2 are also associated with increased risk for uterine fibroids, polycystic ovary syndrome, and prostate hypertrophy; these associations are not shared with higher-penetrance breast cancer genes. Causal mediation analysis suggests that approximately 8% of the breast cancer risk conferred by CHEK2 pathogenic variants after menopause is mediated through delayed menopause.

Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk.

Quantitative assessment of the functional consequences of CHEK2 variants of uncertain significance identifies damaging variants associated with increased cancer risk, which may aid in the clinical management of patients and carriers.

Genomic medicine year in review: 2021

Genomic medicine year in review: 2021

Medical knowledge and information needs among women with pathogenic variants in moderate-risk genes for hereditary breast cancer attending genetic counseling at an academic hospital in Germany-A qualitative approach.

With 69,000 newly diagnosed cases every year, breast cancer (BC) is the most frequent cancer disease among women in Germany. Familial clustering is seen in about 30% of newly diagnosed cases. Besides the high-risk genes BRCA1/2, there are also moderate-risk BC genes (MBCG) that are associated with a 20%-50% risk of BC, such as CHEK2, ATM, and PALB2. In Germany, carriers of pathogenic variants in MBCG receive specific information on their test results, individual risks, and preventive options during genetic counseling for the disclosure of the results in a specialized center. Little is known about the medical knowledge that women have after attending counseling. This study aims to identify the medical knowledge, further information needs, and the possible impact of a lack of information on dealing with everyday life for women with pathogenic variants in MBCG who have attended genetic counseling at an academic hospital in Germany. Problem-centered, guided, individual interviews were conducted with twelve women carrying pathogenic variants in MBCG. The interview guide was developed based on the methods of the problem-centered interview according to Witzel. The interview analysis was based on Mayring's qualitative content analysis. The women were between 29 and 59years old and carried pathogenic variants in the risk genes CHEK2 (n=8), ATM (n=1), or PALB2 (n=3). Several medical uncertainties and information needs emerged from the data, concerning (a) medical terms, (b) risk perception, (c) BC therapy for hereditary BC, (d) lifestyle advice and risk factors, and (e) family planning and risk-reducing mastectomy. Women with pathogenic variants in MBCG might develop their own conceptions regarding the onset of disease and inheritance. In order to meet the need for information and address the uncertainties that may still exist after genetic counseling, structured, evidence-based and comprehensible written information in German should be developed for this group.

Pathogenic Germline Variants in Multiple Myeloma

BACKGROUND: There is growing evidence supporting inherited predisposition to multiple myeloma (MM). Epidemiologic studies have shown that 1st-degree relatives of MM patients (pts) have a 2-4 fold increase in risk of developing MGUS or MM. Genome-wide association studies (GWAS) have identified common SNPs as well as rare high-penetrance variants that collectively explain ~16% of the estimated heritability of multiple myeloma (PMID 30213928). Pathogenic/likely-pathogenic germline variants (PGV) in hereditary cancer genes (HCG) are common in adult cancer patients (~8%, PMID 29625052), but prevalence in MM is not known. The aim of our study is to investigate the occurrence of PGV in newly-diagnosed MM (NDMM), and to describe clinical characteristics & outcomes of carriers.METHODS: We analyzed MMRF CoMMpass data (version IA16) and identified 895 NDMM pts for whom whole-exome sequencing of germline DNA was available. We used the clinical annotation pipeline from Sema4, a CLIA/CAP certified genetic testing laboratory, to identify pts with PGV according to ACMG variant classification guidelines. We compared clinical characteristics & disease phenotypes of PGV carriers vs non-carriers. We used Chi-Square and Fisher's Exact tests to assess statistical significance, which we defined as a two-sided p value < 0.05. Logistic regression models were used for multivariate analyses. Kaplan-Meier method and Cox proportional-hazards models were used for uni- and multivariate survival analysis, respectively. Bonferroni method was used to account for multiple testing.RESULTS: We identified 83 PGV in 31 distinct HCG in 79 (8.8%) of 895 NDMM pts (83% European ancestry) [Figure 1A]. Most PGV involved DNA damage repair (DDR) genes (78%), and homologous recombination (HR) genes were the most commonly mutated (34%). PGV in CHEK2 were the most common (n=10, 1.1% of all MM pts). 2 pts carried PGV in TP53 and reported extensive family history of Li-Fraumeni-associated cancers (breast, sarcoma, gastric & melanoma). 6 pts had germline mismatch repair (MMR) gene defects (1:149, considerably higher than the estimated prevalence of Lynch syndrome in Western populations). 4 pts carried PGV in BRCA2 (previously identified in a family study as a potential MM predisposition gene, PMID 11904319). MM pts with a family history of hematologic malignancy (leukemia, lymphoma or MM) in a 1st or 2nd-degree relative were significantly more likely to carry PGV (22 vs 7.6%, OR=3.3, p<0.001), an association that remained significant in MVA (OR=4.1, p<0.001). CHEK2 variants emerged as leading drivers of this correlation (OR 18.2, 95% CI 4.1-75, adjusted p<0.01), & especially protein-truncating founder variant c.1100delC. Likelihood of being diagnosed w/ MM before age 40 was significantly higher in PGV carriers (6.3 vs 1.8%, OR=3.7, p=0.025). 25% of those younger than 40 y/o carried PGV, but none of these were in DDR-HR genes, a notable difference with other age groups (0 vs 41%, p=0.02). 2/6 MMR PGV were detected in pts diagnosed before age 40. In univariate survival analysis, DDR-PGV carriers had a significant PFS1 advantage over non-carriers (median 52 vs 35 months, p=0.008), as well as a non-significant OS advantage (p=0.08). PFS1 difference remained significant in MVA after adjusting for age, ISS stage, high-risk cytogenetics, treatment type & transplant status (OR 0.65, 95% CI 0.44-0.97, p=0.03) [Figure 1B].CONCLUSIONS: PGV in HCG were common (8.8%) in this large cohort of NDMM pts of predominantly European ancestry, especially in those with a family history of hematologic malignancy (1:4, with high prevalence of CHEK2 variants & particularly protein-truncating founder variant c.1100delC), and in those diagnosed before age 40 (1:4). Routine screening in high-prevalence subgroups might be warranted, as carriers may benefit from counseling and enrollment in early cancer detection programs. We observed a clinically and statistically significant PFS1 advantage in carriers of PGV in DDR genes, possibly due to increased sensitivity to MM therapies, a well-described phenomenon in other cancer types (PMID 33158305). Prospective validation of these findings is needed to better understand prognostic & therapeutic implications of PGV in MM. [Display omitted] DisclosuresChari: Karyopharm: Consultancy; Takeda Pharmaceutical Company: Consultancy, Research Funding; Seattle Genetics: Consultancy, Research Funding; Pharmacyclics: Research Funding; Amgen: Consultancy, Research Funding; Novartis Pharmaceuticals: Consultancy, Research Funding; Bristol Myers Squibb: Consultancy, Research Funding; Janssen Pharmaceuticals: Consultancy, Research Funding; Sanofi Genzyme: Consultancy; Oncopeptides: Consultancy; Antegene: Consultancy; Glaxosmithkline: Consultancy; Secura Bio: Consultancy. Richard: Karyopharm, Janssen: Honoraria. Richter: Sanofi: Consultancy; Antengene: Consultancy; Karyopharm: Consultancy; BMS: Consultancy; Janssen: Consultancy; Celgene: Consultancy; Adaptive Biotechnologies: Speakers Bureau; Celgene: Speakers Bureau; Janssen: Speakers Bureau; X4 Pharmaceuticals: Consultancy; Oncopeptides: Consultancy; Adaptive Biotechnologies: Consultancy; Secura Bio: Consultancy; Astra Zeneca: Consultancy. Parekh: Foundation Medicine Inc: Consultancy; Amgen: Research Funding; PFIZER: Research Funding; CELGENE: Research Funding; Karyopharm Inv: Research Funding.

Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis

Multiple primary cancers, defined as three or more primary tumours, are rare, and there are few genetic studies concerning them. There is a need for increased knowledge on the heritability of multiple primary cancers and genotype-phenotype correlations. We have performed whole-genome/exome sequencing (WGS/WES) in ten individuals with three or more primary tumours, with no previous findings on standard clinical genetic investigations. In one individual with a clinical diagnosis of MEN1, a likely pathogenic cryptic splice site variant was detected in the MEN1 gene. The variant (c.654C > A) is synonymous but we showed in a cDNA analysis that it affects splicing and leads to a frameshift, with the theoretical new amino acid sequence p.(Gly219Glufs*13). In one individual with metachronous colorectal cancers, ovarian cancer, endometrial cancer and chronic lymphocytic leukaemia, we found a likely pathogenic variant in the MLH1 gene (c.27G > A), and two risk factor variants in the genes CHEK2 and HOXB13. The MLH1 variant is synonymous but has previously been shown to be associated to constitutional low-grade hypermethylation of the MLH1 promoter, and segregates with disease in families with colorectal and endometrial cancer. No pathogenic single nucleotide or structural variants were detected in the remaining eight individuals in the study. The pathogenic variants found by WGS/WES were in genes already sequenced by Sanger sequencing and WES in the clinic, without any findings. We conclude that, in individuals with an unequivocal clinical diagnosis of a specific hereditary cancer syndrome, where standard clinical testing failed to detect a causative variant, re-analysis may lead to a diagnosis.

P-063: Pathogenic germline variants in hereditary cancer genes in patients with Multiple Myeloma

<h3>Background</h3> GWAS have identified common SNPs & rare high-penetrance variants that explain ~16% of the estimated heritability of multiple myeloma (MM)(PMID 30213928). Pathogenic/likely-pathogenic germline variants (PGV) in hereditary cancer genes (HCG) are common in adult cancer pts (~8%), but prevalence in MM is not known. The aim of our study is to investigate the occurrence of PGV in newly-diagnosed MM (NDMM) and describe clinical characteristics & outcomes of carriers. <h3>Methods</h3> We analyzed MMRF CoMMpass data & identified 895 NDMM pts with whole-exome sequencing of germline DNA. We used the clinical annotation pipeline from Sema4, a CLIA/CAP certified genetic testing laboratory, to identify pts with PGV according to ACMG variant classification guidelines. We compared clinical characteristics & disease phenotypes of PGV carriers vs non-carriers. We used Chi-Square and Fisher's Exact tests to assess statistical significance. <h3>Results</h3> We identified 83 PGV in 31 distinct HCG in 79 (8.8%) of 895 NDMM pts (83% European ancestry). Most PGV involved DNA damage repair (DDR) genes (78%), & homologous recombination (HR) genes were the most commonly mutated (34%). PGV in CHEK2 were most common (n=10,1.1% of all MM pts). 2 pts carried PGV in TP53, & 6 pts had mismatch repair (MMR) gene defects (1:149). MM pts with family history (FH) of hematologic malignancy (HM) in a 1st or 2nd-degree relative were more likely to carry PGV (22 vs 7.6%,OR=3.3,p<0.001), an association that remained significant in multivariate analysis (MVA) (OR=4.1,p<0.001). CHEK2 variants were leading drivers of this correlation (OR 18,adjusted p<0.01), & especially protein-truncating founder variant c.1100delC. Likelihood of MM dx before age 40 was significantly higher in PGV carriers (6.3 vs 1.8%,OR=3.7,p=0.025). 25% of those <40y/o carried PGV, but none of these were in DDR-HR genes, a notable difference with other age groups (0 vs 41%,p=0.02). 2/6 MMR PGV were detected in pts <40y/o. In univariate analysis, DDR-PGV carriers had a significant PFS1 advantage (median 52 vs 35 months,p=0.008) & a non-significant OS advantage (p=0.08). PFS1 difference remained significant in MVA adjusting for age, ISS stage, high-risk cytogenetics, treatment type & transplant status (OR 0.65,95% CI 0.44-0.97,p=0.03). <h3>Conclusions</h3> PGV in HCG were common (8.8%) in this large cohort of NDMM pts of predominantly European ancestry, especially in those with FH of HM (1:4, with high prevalence of CHEK2 variants), and in those <40y/o (1:4). Routine screening in high-prevalence subgroups may be warranted, as carriers can benefit from counseling & enrollment in early cancer detection programs. We observed a clinically & statistically significant PFS1 advantage in PGV carriers, possibly due to increased sensitivity to MM therapies, a well-described phenomenon in other cancers (PMID 33158305). Prospective validation of these findings is needed to better understand prognostic & therapeutic implications of PGV in MM.

Germline mutations in a DNA repair pathway are associated with familial colorectal cancer.

Aiming to identify rare high-penetrance mutations in new genes for the underlying predisposition in familial colorectal cancer (CRC), we performed whole-exome sequencing in 24 familial CRCs. Mutations in genes that regulate DNA repair (RMI1, PALB2, FANCI) were identified that were related to the Fanconi anemia DNA repair pathway. In one pedigree, we found a nonsense mutation in CHEK2. CHEK2 played an essential role in cell cycle and DNA damage repair. Somatic mutation analysis in CHEK2 variant carriers showed mutations in TP53, APC, and FBXW7. Loss of heterozygosity was found in carcinoma of CHEK2 variant carrier, and IHC showed loss of Chk2 expression in cancer tissue. We identified a second variant in CHEK2 in 126 sporadic CRCs. A KO cellular model for CHEK2 (CHEK2KO) was generated by CRISPR/Cas9. Functional experiments demonstrated that CHEK2KO cells showed defective cell cycle arrest and apoptosis, as well as reduced p53 phosphorylation, upon DNA damage. We associated germline mutations in genes that regulate the DNA repair pathway with the development of CRC. We identified CHEK2 as a regulator of DNA damage response and perhaps as a gene involved in CRC germline predisposition. These findings link CRC predisposition to the DNA repair pathway, supporting the connection between genome integrity and cancer risk.

Survival of bladder or renal cancer in patients with CHEK2 mutations.

PurposeThe purpose of this study was to compare the clinical characteristics and the survival of CHEK2 mutation positive and CHEK2 mutation negative patients diagnosed with bladder or kidney cancer.Materials and methods1016 patients with bladder and 402 cases with kidney cancer and 8302 controls were genotyped for four CHEK2 variants: 1100delC, del5395, IVS2+1G>A and I157T. Predictors of survival were determined among CHEK2 pathogenic variant carriers using the Cox proportional hazards model. The median follow-up was 17.5 years. Covariates included age (≤60; >61 years), sex (female; male), clinical characteristics (stage: TNM, grade, histopathological type), smoking status (non-smoking; smoking) and cancer family history (negative; positive).ResultsWe found no impact of CHEK2 mutations on bladder or kidney cancer survival. However, we observed a possible increased survival in the subgroup of patients with stage T1 bladder cancer with CHEK2 mutations but this did not meet statistical significance (HR = 0.14; 95% CI 0.02–1.04; p = 0.055). Moreover, we observed that the missense mutations were more frequent in the low grade invasive bladder cancer patient group (OR = 7.9; 95% CI 1.50–42.1; p = 0.04) and in patients with bladder cancer with stage Ta (OR = 2.4; 95% CI 1.30–4.55; p = 0.006). The different results where missense mutations occurs less often we observed among patients with high grade invasive bladder cancer (OR = 0.12; 95% CI 0.02–0.66; p = 0.04) and those with stage T1 disease (OR = 0.2; 95% CI 0.07–0.76; p = 0.01). Our investigations revealed that any mutation in CHEK2 occurs more often among patients with stage Ta bladder cancer (OR = 2.0; 95% CI 1.19–3.47; p = 0.01) and less often in patients with stage T1 disease (OR = 0.31; 95% CI 0.12–0.78; p = 0.01). In the kidney cancer patients, truncating mutations were present more often in the group with clear cell carcinoma GII (OR = 8.0; 95% CI 0.95–67.7; p = 0.05). The 10-year survival for all CHEK2 mutation carriers with bladder cancer was 33% and for non-carriers 11% (p = 0.15). The 10-year survival for CHEK2 mutation carriers with kidney cancer 34% and for non-carriers 20% (p = 0.5).ConclusionCHEK2 mutations were not associated with any change in bladder or kidney cancer survival regardless of their age, sex, smoking status and family history. We observed a potentially protective effect of CHEK2 mutations on survival for patients with stage T1 bladder cancer. CHEK2 missense mutations were more common among patients with low grade invasive bladder cancer and in patients with stage Ta diease. The frequencies of the I157T CHEK2 pathogenic variant were less in patients with high grade invasive bladder cancer and those with stage T1 disease. Among patients with bladder cancer with stage Ta disease, the OR for any mutation in CHEK2 was 2.0 but for those with stage T1 disease, the OR was 0.3. We observed truncating CHEK2 mutations were associated with kidney cancer patients with GII clear cell carcinoma.

MP24-15 CLINICAL UTILITY OF DETECTING LOW-FREQUENCY CELL-FREE DNA VARIANTS IN CASTRATION-RESISTANT PROSTATE CANCER

You have accessJournal of UrologyProstate Cancer: Advanced (including Drug Therapy) II (MP24)1 Sep 2021MP24-15 CLINICAL UTILITY OF DETECTING LOW-FREQUENCY CELL-FREE DNA VARIANTS IN CASTRATION-RESISTANT PROSTATE CANCER Kei Mizuno, Shusuke Akamatsu, Takayuki Sumiyoshi, Takayuki Goto, Takashi Kobayashi, Akihiro Fujimoto, Takatsugu Okegawa, and Osamu Ogawa Kei MizunoKei Mizuno More articles by this author , Shusuke AkamatsuShusuke Akamatsu More articles by this author , Takayuki SumiyoshiTakayuki Sumiyoshi More articles by this author , Takayuki GotoTakayuki Goto More articles by this author , Takashi KobayashiTakashi Kobayashi More articles by this author , Akihiro FujimotoAkihiro Fujimoto More articles by this author , Takatsugu OkegawaTakatsugu Okegawa More articles by this author , and Osamu OgawaOsamu Ogawa More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002015.15AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Plasma cell-free DNA (cfDNA) testing is emerging as a tool for precision medicine in castration-resistant prostate cancer (CRPC). However, circulating cell-free tumor DNA (ctDNA) is highly diluted by cfDNA from non-cancer cells, complicating its detection and analysis. Recently, we developed a bioinformatics pipeline, called “eVIDENCE”, which analyze molecular barcoded sequencing data and can detect low-frequency variants with high sensitivity and specificity. In this study, we examined genomic landscape of ctDNA in CRPC patients and analyzed the relevance between the findings and the clinical course. We also investigated genomic profiling of lymphocyte DNA in the same cohort to detect clonal hematopoiesis of indeterminate potential (CHIP)-associated alterations. METHODS: A total of 103 CRPC patients who were eligible for abiraterone of enzalutamide were enrolled. We extracted cfDNA and lymphocyte DNA from the blood. We then performed targeted sequencing of cfDNA and germline DNA using our custom panel targeting 88 genes. The sequencing data were analyzed using eVIDNECE and detected variants with the variant allele frequency (VAF) of ≥0.1%. Somatic variants detected in both cfDNA and matched lymphocyte DNA were considered as CHIP-associated variants. We also assessed the relevance between genomic ctDNA alterations and clinicopathological features. RESULTS: We detected 542 variants across the 103 cfDNA samples, and 191 were pathogenic variants. Of the 191, 89 (46.6%) showed VAF of <1% (0.16–0.98%); the most commonly mutated genes were TP53 (11%), AR (9.9%), and KMT2C (7.3%). The median ctDNA fraction was 1.9%, and 8 samples with the ctDNA fraction of <2% had TP53 and/or ATM pathogenic variants. Defects in ATM and BRCA2 and TP53 defects were both associated with early progression independently of clinical prognostic factors (p=0.002 and 0.047, respectively). In addition, we detected “deleterious” CHIP-associated variants in ATM (n= \7), BRCA1 (n=1) and CHEK2 (n=3). CONCLUSIONS: Defects in ATM and BRCA2 and TP53 aberrations were significantly associated with poor clinical outcomes. Some pathogenic variants in ATM and TP53 genes were detected in the samples with the ctDNA fraction of <2%, indicating the clinical utility of detecting low-frequency variants in cfDNA. However, cfDNA variants contain CHIP-associated alterations, most frequently in ATM, which require attention when considering eligibility of poly(ADP-ribose) polymerase (PARP) inhibitors based on cfDNA analysis. Source of Funding: This study was supported by a research grant provided by AstraZeneca © 2021 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 206Issue Supplement 3September 2021Page: e417-e418 Advertisement Copyright & Permissions© 2021 by American Urological Association Education and Research, Inc.MetricsAuthor Information Kei Mizuno More articles by this author Shusuke Akamatsu More articles by this author Takayuki Sumiyoshi More articles by this author Takayuki Goto More articles by this author Takashi Kobayashi More articles by this author Akihiro Fujimoto More articles by this author Takatsugu Okegawa More articles by this author Osamu Ogawa More articles by this author Expand All Advertisement Loading ...

Comprehensive Breast Cancer Risk Assessment for CHEK2 and ATM Pathogenic Variant Carriers Incorporating a Polygenic Risk Score and the Tyrer-Cuzick Model.

PURPOSEBreast cancer risks for CHEK2 and ATM pathogenic variant (PV) carriers are modified by an 86-single nucleotide polymorphism polygenic risk score (PRS) and individual clinical factors. Here, we describe comprehensive risk prediction models for women of European ancestry combining PV status, PRS, and individual clinical variables.MATERIALS AND METHODSThis study included deidentified clinical records from 358,095 women of European ancestry who received testing with a multigene panel (September 2013 to November 2019). Model development included CHEK2 PV carriers (n = 4,286), ATM PV carriers (n = 2,666), and women negative for other breast cancer risk gene PVs (n = 351,143). Odds ratios (ORs) were calculated using multivariable logistic regression with adjustment for familial cancer history. Risk estimates incorporating PV status, PRS, and Tyrer-Cuzick v7.02 were calculated using a Fixed-Stratified method that accounts for correlations between risk factors. Stratification of PV carriers into risk categories on the basis of remaining lifetime risk (RLR) was assessed in independent cohorts of PV carriers.RESULTSORs for association of PV status with breast cancer were 2.01 (95% CI, 1.88 to 2.16) and 1.83 (95% CI, 1.68 to 2.00) for CHEK2 and ATM PV carriers, respectively. ORs for PRS per one standard deviation were 1.51 (95% CI, 1.37 to 1.66) and 1.45 (95% CI, 1.30 to 1.64) in CHEK2 and ATM PV carriers, respectively. Using the combined model (PRS plus Tyrer-Cuzick plus PV status), RLR was low (≤ 20%) for 24.2% of CHEK2 PV carriers, medium (20%-50%) for 63.8%, and high (> 50%) for 12.0%. Among ATM PV carriers, RLR was low for 31.5% of patients, medium for 58.5%, and high for 9.7%.CONCLUSIONIn CHEK2 and ATM PV carriers, risk assessment including PRS, Tyrer-Cuzick, and PV status has the potential for more precise direction of screening and prevention strategies.

Yield of targeted genotyping for the recurring pathogenic variants in cancer susceptibility genes in a healthy, multiethnic Israeli population.

Several recurring pathogenic variants in BRCA1/BRCA2 and other cancer susceptibility genes are encountered in ethnically diverse Jewish populations. The yield of genotyping for these recurring pathogenic variants in healthy Israeli individuals unselected for ethnicity, sex, or a family history of cancer has not been previously reported. Individuals voluntarily participating in annual medical surveillance at the Institute of Medical Screening of Sheba Medical Center were offered genotyping for predominant pathogenic variants in BRCA1/BRCA2 and recurring variants in CHEK2, MUTYH, APC, and the Lynch syndrome genes via a chip-based assay at the oncogenetic service of Sheba Medical Center from May 15, 2018, to December 15, 2020. All study participants were unrelated to one another. The study was approved by the Sheba ethics committee. Overall, 1764 individuals, including 1008 females (57%), with a mean age of 54.2 years (range, 25-86 years) were genotyped. The yield of the testing was 4% (71 of 1764), and it was higher in Ashkenazi Jews (AJs) and mixed AJ-non-AJ participants (4.75% [58 of 1222]; 1.8% for BRCA1/BRCA2 pathogenic variants) than non-AJ patients (2.2% [9 of 401]; 1% for BRCA1 pathogenic variants). When BRCA1/BRCA2 pathogenic variants were excluded, 2.44% carried low-penetrance variants, including CHEK2 c.1283C>T (n = 3), APC c.3920T>A (n = 36), and heterozygous MUTYH c.1187G>A (n = 4). A family history of cancer was not associated with a higher yield of pathogenic variant detection. The observed rates of positive genotyping in a healthy, unselected, multiethnic Israeli population warrant consideration of the inclusion of targeted genotyping of selected pathogenic variants in high-penetrance and perhaps lower penetrance cancer susceptibility genes for all Jewish individuals in Israel, regardless of their ethnicity or family history of cancer.