ABSTRACT
PURPOSE: To understand racial disparities in germline cancer genetic testing and the role of prior knowledge, attitudes, and sources of information. METHODS: A cross-sectional analysis of the Health Information National Trends Survey 5 (HINTS 5) was conducted between February 24th and June 15th, 2020. The study aimed to investigate knowledge and receipt of genetic testing, attitudes toward the importance of genetic testing in preventing, detecting, and treating cancer, and information sources of genetic testing in the United States of America. RESULTS: Non-Hispanic Black (NHB) and Hispanic race/ethnicity were associated with lower odds of being informed about genetic testing, whereas those of NHB race were more likely to endorse the importance of genetic testing in cancer prevention and treatment. Regarding sources of information about genetic testing: Non-Hispanic Asians were less likely to be informed about genetic testing from television (Mean Predicted Probability (MPP) 0.38 95%CI; 0.21-0.55, (Adjusted Risk Difference) ARD vs. Non-Hispanic White (NHW); -0.228, p = 0.01), NHB were less likely to report being informed about genetic testing from social media (MPP 0.27 95%CI; 0.20-0.34, ARD vs. NHW; -0.139, p < 0.01). CONCLUSIONS: NHB and Hispanic groups face unequal access to information about genetic testing. There are significant race-based differences in information sources. These differences could be used to promote equitable access to cancer genetic testing.
Subject(s)
Access to Information , Genetic Testing , Health Knowledge, Attitudes, Practice , Healthcare Disparities , Neoplasms , Humans , Black or African American , Cross-Sectional Studies , Germ Cells , Neoplasms/diagnosis , Neoplasms/genetics , Race Factors , United States , Hispanic or LatinoABSTRACT
PURPOSE: Herein, we report the frequency and distribution of germline pathogenic variants (PVs) among females with breast cancer (BC) and at least one other non-BC who underwent multi-gene panel testing (MGPT). Among females with PVs diagnosed first with BC or ovarian cancer (OC), we sought to enumerate the frequency of subsequent PV-associated cancers. METHODS: Females with BC and cancer of ≥ 1 other site (multiple primary cancers, MPC) who underwent MGPT through Ambry Genetics from March 2012 to December 2016 were included if they had testing of at least 21 genes of interest (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53). Phenotypic data were abstracted from test requisition forms and clinical notes. RESULTS: Of 6,617 evaluable patients, most were White (70.8%) and median age at first cancer, second cancer, and MGPT was 49 (interquartile range [IQR]: 18), 59 (IQR: 16), and 63 (IQR: 16) years, respectively. PVs were found among 14.1% (932/6617) of the overall cohort and in 16.4% (440/2687) of females who were diagnosed first with BC. Among those, 55.2% (243/440) had an actionable PV associated with a subsequent cancer diagnosis including 150 OCs. Of the 2443 females with breast and ovarian cancer, few (n = 97, 9.5%) were diagnosed first with OC, limiting our analysis. CONCLUSIONS: Females with MPC, including BC, have a high frequency of germline PVs (14.1%). These data delineate the opportunities for intercepting subsequent cancers associated with genetic risk among females diagnosed first with BC.
Subject(s)
Breast Neoplasms , Ovarian Neoplasms , Humans , Female , Breast Neoplasms/epidemiology , Breast Neoplasms/genetics , Genetic Predisposition to Disease , Genes, BRCA2 , Ovarian Neoplasms/genetics , Protein Serine-Threonine Kinases/genetics , Germ-Line MutationABSTRACT
Germline pathogenic TERT variants are associated with short telomeres and an increased risk of developing myelodysplastic syndrome (MDS) among patients with a telomere biology disorder. We identified TERT rare variants in 41 of 1514 MDS patients (2.7%) without a clinical diagnosis of a telomere biology disorder who underwent allogeneic transplantation. Patients with a TERT rare variant had shorter telomere length (P < .001) and younger age at MDS diagnosis (52 vs 59 years, P = .03) than patients without a TERT rare variant. In multivariable models, TERT rare variants were associated with inferior overall survival (P = .034) driven by an increased incidence of nonrelapse mortality (NRM; P = .015). Death from a noninfectious pulmonary cause was more frequent among patients with a TERT rare variant. Most variants were missense substitutions and classified as variants of unknown significance. Therefore, we cloned all rare missense variants and quantified their impact on telomere elongation in a cell-based assay. We found that 90% of TERT rare variants had severe or intermediate impairment in their capacity to elongate telomeres. Using a homology model of human TERT bound to the shelterin protein TPP1, we inferred that TERT rare variants disrupt domain-specific functions, including catalysis, protein-RNA interactions, and recruitment to telomeres. Our results indicate that the contribution of TERT rare variants to MDS pathogenesis and NRM risk is underrecognized. Routine screening for TERT rare variants in MDS patients regardless of age or clinical suspicion may identify clinically inapparent telomere biology disorders and improve transplant outcomes through risk-adapted approaches.
Subject(s)
Genetic Variation , Myelodysplastic Syndromes , Telomerase/genetics , Adult , Disease-Free Survival , Female , Humans , Male , Myelodysplastic Syndromes/enzymology , Myelodysplastic Syndromes/genetics , Myelodysplastic Syndromes/mortality , Survival RateABSTRACT
BACKGROUND: Multiple primary cancers (MPCs) are a hallmark of cancer predisposition syndromes. Here the frequency of germline pathogenic variants (PVs) among patients with MPCs is reported. METHODS: Patients with MPCs who underwent multigene panel testing from March 2012 to December 2016 were studied. Eligible patients had an analysis of 21 genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53. The frequencies of PVs by sex, number of cancers, and age at diagnosis were compared with 2-sided χ2 tests or Fisher exact tests when the number was <10. RESULTS: Among the 9714 patients analyzed, most were female (91.1%) and White (71.0%); the median age at testing was 63 years, and the median ages at first and second cancer diagnoses were 49 and 58 years, respectively. Overall, 1320 (13.6%) had PVs. The prevalence of PVs increased with the number of primary cancers (PCs): 13.1% with 2 PCs, 15.9% with 3 PCs, and 18.0% with ≥4 PCs (P = .00056). Differences in the prevalence of PVs by age at diagnosis were significant: 14.7% with 2 PCs at an age < 50 years, 15.8% with 1 PC at an age < 50 years, and 12.0% with all PCs at an age ≥ 50 years (P = 2.07E-05). PVs by the age at second cancer diagnosis were also significant: 14.7% at an age < 50 years, 13.9% at an age of 50 to 69 years, and 11.4% at an age ≥ 70 years (P for trend = .005). CONCLUSIONS: Among patients with MPCs, there is a high frequency of germline PVs, with a higher frequency found among patients with a higher number of PCs. These findings suggest that genetic testing should be considered even among patients who are older at the diagnosis of an additional primary malignancy.
Subject(s)
Breast Neoplasms , Neoplasms, Multiple Primary , Aged , Female , Genes, BRCA2 , Genetic Predisposition to Disease , Germ-Line Mutation , Humans , Male , Middle Aged , Neoplasms, Multiple Primary/epidemiology , Neoplasms, Multiple Primary/genetics , PrevalenceABSTRACT
BACKGROUND AND AIMS: CDH1 germline variants have been linked to heritability in diffuse gastric (DGC) and lobular breast cancer (LBC). Studies have not yet assessed whether CDH1 is a cancer-susceptibility gene in other cancers. Herein, we mapped the landscape of pathogenic and likely pathogenic (P/LP) germline variants in CDH1 across various cancers and ethnicities. METHODS: We evaluated CDH1 germline P/LP variants in 212,944 patients at one CLIA-certified laboratory (Invitae) and described their frequency in 7 cancer types. We screened for CDH1 variant enrichment in each cancer relative to a cancer-free population from The Genome Aggregation Database version 3 (gnomADv3). RESULTS: CDH1 P/LP variants were identified in 141 patients, most commonly in patients with DGC (27/408, 6.6%) followed by colorectal signet-ring cell cancer (CSRCC; 3/79, 3.8%), gastric cancer (56/2756, 2%), and LBC (22/6809, 0.3%). CDH1 P/LP variants were enriched in specific ethnic populations with breast cancer, gastric cancer, CRC, LBC, DGC, and CSRCC compared to matched ethnicities from gnomADv3. CONCLUSION: We report for the first time the prevalence of P/LP CDH1 variants across several cancers and show significant enrichment in CDH1 P/LP variants for patients with CSRCC, DGC, and LBC across various ethnicities. Future prospective studies are warranted to validate these findings.
Subject(s)
Antigens, CD/genetics , Breast Neoplasms/genetics , Cadherins/genetics , Carcinoma, Lobular/genetics , Carcinoma, Signet Ring Cell/genetics , Colorectal Neoplasms/genetics , Germ-Line Mutation , Stomach Neoplasms/genetics , Adult , Aged , Breast Neoplasms/ethnology , Carcinoma, Lobular/ethnology , Carcinoma, Signet Ring Cell/ethnology , Colorectal Neoplasms/ethnology , Female , Genetic Predisposition to Disease , High-Throughput Nucleotide Sequencing , Humans , Male , Middle Aged , Mutation Rate , Prevalence , Sequence Analysis, DNA , Stomach Neoplasms/ethnology , Young AdultABSTRACT
BACKGROUND: Cancer family history is a vital part of cancer genetic counseling (GC) and genetic testing (GT), but increasing indications for germline cancer GT necessitate less labor-intensive models of collection. We evaluated the impact of GC on patient pedigrees generated by an electronic cancer family history questionnaire (eCFHQ). METHODS: An Institutional Review Board-approved review of pedigrees collected through an eCFHQ was conducted. Paired pre-GC and post-GC pedigrees (n=1,113 each group) were analyzed independently by cancer genetic counselors for changes in patient-reported clinical history and to determine whether the pedigrees met NCCN GT criteria. Discrepancy in meeting NCCN GT criteria between pre-GC and post-GC pedigrees was the outcome variable of logistic regressions, with patient and family history characteristics as covariates. RESULTS: Overall, 780 (70%) patients had cancer (affected), 869 (78%) were female, and the median age was 57 years (interquartile range, 45-66 years; range, 21-91 years). Of the 1,113 pairs of pre-GC and post-GC pedigrees analyzed, 85 (8%) were blank, 933 (84%) were not discrepant, and 95 (9%) were discrepant in meeting any NCCN GT criteria. Of the discrepant pedigrees, n=79 (83%) became eligible for testing by at least one of the NCCN GT criteria after GC. Patients with discrepant pedigrees were more likely to report no or unknown history of GT (odds ratio [OR], 4.54; 95% CI, 1.66-18.70; P=.01, and OR, 18.47; 95% CI, 5.04-88.73; P<.0001, respectively) and belonged to racially and/or ethnically underrepresented groups (OR, 1.91; 95% CI, 1.08-3.25; P=.02). CONCLUSIONS: For most patients (84%), a standalone eCFHQ was sufficient to determine whether NCCN GT criteria were met. More research is needed on the performance of the eCFHQ in diverse patient populations.
Subject(s)
Genetic Counseling , Neoplasms , Electronics , Female , Genetic Testing , Humans , Male , Middle Aged , Neoplasms/diagnosis , Neoplasms/genetics , Patient Reported Outcome MeasuresABSTRACT
OBJECTIVE: Germline genetic testing is crucial to the care of ovarian cancer patients, and as part of the guideline-based care for ovarian cancer patient's adherence to this recommendation has been low. We sought to determine whether embedding a genetic counselor (GC) within a medical and gynecologic oncology clinic would increase testing rates and improve the timeliness of testing. METHODS: Prospective cohort study of 358 ovarian cancer patients seen by medical and gynecologic oncologists between 2013 and 2015. Rates of referrals, completion of counseling, and genetic testing and timeliness of counseling were abstracted before and after a GC was embedded in the clinic in 2014. An additional year of data (2015) was collected to evaluate sustainability of the intervention. RESULTS: Between 2013 and 2015, 88-92% of women were referred for genetic testing, but in 2013 only 66% completed counseling and 61% were tested. After a GC was embedded in the clinic in 2014, more than 80% of referred women completed counseling and germline genetic testing. Time to genetic counseling also decreased from a median of 107 to 40 days, irrespective of age and cancer family history (p < 0.01). CONCLUSIONS: Embedding a GC into the workflow for ovarian cancer patients is an effective way of improving access to genetic counseling, testing rates, and the timeliness of testing.
Subject(s)
Genetic Counseling/organization & administration , Genetic Testing/statistics & numerical data , Ovarian Neoplasms/diagnosis , Patient Compliance/statistics & numerical data , Adult , Aged , Aged, 80 and over , Counselors/organization & administration , Counselors/statistics & numerical data , Female , Genetic Counseling/statistics & numerical data , Genetic Predisposition to Disease , Genetic Testing/standards , Humans , Medical History Taking , Medical Oncology/organization & administration , Medical Oncology/standards , Middle Aged , Ovarian Neoplasms/genetics , Practice Guidelines as Topic , Prospective Studies , Referral and Consultation/organization & administration , Referral and Consultation/statistics & numerical data , Time Factors , Young AdultABSTRACT
PURPOSE: To date, there has not been a large, systematic evaluation of the prevalence of germline risk variants in urothelial carcinoma (UC). METHODS: We evaluated the frequency of germline pathogenic and likely pathogenic variants in 1038 patients with high-risk UC who underwent targeted clinical germline testing. Case-control enrichment analysis was performed to screen for pathogenic variant enrichment in 17 DNA repair genes in 1038 UC patients relative to cancer-free individuals. RESULTS: Among 1038 patients with UC, the cumulative frequency of patients with pathogenic variants was 24%; 18.6% of patients harbored ≥1 actionable germline variant with preventive or therapeutic utility. MSH2 (34/969, 3.5%) and BRCA1/2 (38/867, 4.4%) germline variants had the highest frequency. Germline variants in DNA damage repair genes accounted for 78% of pathogenic germline variants. Compared to the cancer-free cohort, UC patients had significant variant enrichment in MSH2 (odds ratio [OR]: 15.4, 95% confidence interval [CI]: 7.1-32.7, p < 0.0001), MLH1 (OR: 15.9, 95% CI: 4.4-67.7, p < 0.0001), BRCA2 (OR: 5.7, 95% CI: 3.2-9.6, p < 0.0001), and ATM (OR: 3.8, 95% CI: 1.8-8.3, p = 0.02). CONCLUSION: In this study, 24% of UC patients harbored pathogenic germline variants and 18.6% had clinically actionable variants. MLH1 and MSH2 were validated as UC risk genes while ATM and BRCA2 were highlighted as potential UC predisposition genes. This work emphasizes the utility of germline testing in selected high-risk UC cohorts.
Subject(s)
Carcinoma , Germ-Line Mutation , Genetic Predisposition to Disease , Germ Cells , Humans , PrevalenceABSTRACT
BACKGROUND: Inflammatory breast cancer (IBC) is an uncommon and aggressive subtype of breast cancer associated with early disease recurrence and short survival. The prevalence of germline variants in cancer predisposition genes has not been systematically evaluated in women with IBC. METHODS: Among 301 women enrolled in the clinical IBC registry at a single institution between 2010 and 2017, 168 had documented genetic testing. A second cohort of 200 IBC cases who had panel-based germline testing performed through a commercial testing laboratory from 2012 to 2017 was added to the analyses. Personal and family cancer histories and genetic testing results were evaluated when they were available for both cohorts. RESULTS: Among 501 IBC cases, 368 had documented genetic testing. Germline mutations (56 total) were identified in 53 cases (14.4%). BRCA1 or BRCA2 mutations were found in 7.3% of the subjects, 6.3% had a mutation in other breast cancer genes (PALB2, CHEK2, ATM, and BARD1), and 1.6% had mutations in genes not associated with breast cancer. The prevalence of mutations was 24% (22 of 92) among women with triple-negative IBC, 13% (13 of 99) among women with estrogen receptor- and/or progesterone receptor-positive, human epidermal growth factor receptor 2 (HER2)-negative disease, and 9.3% (10 of 108) among women with HER2-positive IBC. CONCLUSIONS: The prevalence and diversity of germline genetic mutations among patients with IBC suggest that further studies should be performed to assess the role of inherited mutations in IBC carcinogenesis in comparison with non-IBC breast cancer. Since IBC has a high metastatic potential associated with poor prognostic outcomes, proposed future studies may also inform targeted treatment options.
Subject(s)
Biomarkers, Tumor/genetics , Genetic Predisposition to Disease , Germ-Line Mutation , Inflammatory Breast Neoplasms/epidemiology , Inflammatory Breast Neoplasms/genetics , Adult , BRCA1 Protein/genetics , Checkpoint Kinase 2/genetics , Fanconi Anemia Complementation Group N Protein/genetics , Female , Follow-Up Studies , Humans , Massachusetts/epidemiology , Middle Aged , Prevalence , Prognosis , Retrospective Studies , Survival RateABSTRACT
PURPOSE: Panel testing has led to the identification of TP53 pathogenic/likely pathogenic (P/LP) variant carriers (TP53+) who exhibit a broad range of phenotypes. We sought to evaluate and compare genotype-phenotype associations among TP53+ panel-ascertained subjects. METHODS: Between 2012 and 2017, 317 TP53+ subjects (279 females and 38 males) identified through panel testing at one testing laboratory were found to have evaluable clinical histories and molecular results. Subject cancer histories were obtained from test requisition forms. P/LP variants were categorized by type and were examined in relation to phenotype. RESULTS: Loss-of-function (LOF) variants were associated with the earliest age at first cancer, with a median age of 30.5 years (P = 0.014); increased frequency of a sarcoma diagnosis (P = 0.016); and more often meeting classic LFS testing and Chompret 2015 criteria (P = 0.004 and 0.002 respectively), as compared with dominant-negative missense, other missense, or miscellaneous (splice or in-frame deletion) P/LP variant categories. CONCLUSION: Loss-of-function variants were more often associated with characteristic LFS cancer histories than other variant categories in TP53+ carriers ascertained through multigene panel testing. These findings require validation in other TP53+ cohorts. Genetic counseling for panel-ascertained TP53+ individuals should reflect the dynamic expansion of the Li-Fraumeni syndrome phenotype.
Subject(s)
Li-Fraumeni Syndrome/genetics , Tumor Suppressor Protein p53/genetics , Adult , Cohort Studies , Female , Genetic Association Studies , Genetic Predisposition to Disease , Genetic Testing/methods , Germ-Line Mutation/genetics , Heterozygote , Humans , Li-Fraumeni Syndrome/diagnosis , Loss of Function Mutation/genetics , Male , Middle Aged , Tumor Suppressor Protein p53/metabolismABSTRACT
BACKGROUND: Although rare cancers account for 27% of cancer diagnoses in the US, there is insufficient research on survivorship issues in these patients. An important issue cancer survivors face is an elevated risk of being diagnosed with new primary cancers. The primary aim of this analysis was to assess whether a history of rare cancer increases the risk of subsequent cancer compared to survivors of common cancers. METHODS: This was a prospective cohort study of 16,630 adults with personal and/or family history of cancer who were recruited from cancer clinics at 14 geographically dispersed US academic centers of the NIH-sponsored Cancer Genetics Network (CGN). Participants' self-reported cancer histories were collected at registration to the CGN and updated annually during follow-up. At enrollment, 14% of participants reported a prior rare cancer. Elevated risk was assessed via the cause-specific hazard ratio on the time to a subsequent cancer diagnosis. RESULTS: After a median follow-up of 7.9 years, relative to the participants who were unaffected at enrollment, those with a prior rare cancer had a 23% higher risk of subsequent cancer (95% CI: -1 to 52%), while those with a prior common cancer had no excess risk. Patients having two or more prior cancers were at a 53% elevated risk over those with fewer than two (95% CI: 21 to 94%) and if the multiple prior cancers were rare cancers, risk was further elevated by 47% (95% CI: 1 to 114%). CONCLUSION: There is evidence suggesting that survivors of rare cancers, especially those with multiple cancer diagnoses, are at an increased risk of a subsequent cancer. There is a need to study this population more closely to better understand cancer pathogenesis.
Subject(s)
Cancer Survivors , Neoplasms, Second Primary/epidemiology , Neoplasms/epidemiology , Adult , Cohort Studies , Female , Follow-Up Studies , Humans , Incidence , Male , Medical History Taking , Middle Aged , Prospective Studies , Risk , United States/epidemiologyABSTRACT
Transgender individuals comprise a growing patient population in genetic counseling practice. The identification of a pathogenic variant in a cancer susceptibility gene may impact a transgender person's decisions regarding hormonal and/or surgical transition. Limited scientific literature exists on specific genetic counseling needs and medical management strategies for transgender individuals. In addition, most genetic counselors have had limited experience and training in conducting genetic counseling sessions with transgender patients. In this report, we describe three cases of transgender individuals who underwent genetic counseling and testing in our clinic. All were at ≥50% risk to carry a familial BRCA1 pathogenic variant. Case 1 is a 20-year-old transgender female initiating hormonal agents. Case 2 is a 19-year-old transgender male considering surgical decisions who has a BRCA1 pathogenic variant on both sides of the family. Case 3 is a 24-year-old transgender male who had previously undergone gender-affirming mastectomy (top surgery) and is taking androgen therapy. Unique aspects of genetic testing, psychosocial counseling, and medical management of transgender individuals have arisen in the course of their care. In this report, we discuss our experiences and practices of case preparation, case management, appropriate genetic testing, and medical management such as screening, surgical decisions, and coordination of care. There is a need for more research in this area and more transgender-specific training for genetic counselors.
Subject(s)
Genes, BRCA1 , Genetic Counseling/psychology , Genetic Predisposition to Disease , Transgender Persons/psychology , Adult , Breast Neoplasms/genetics , Female , Humans , Male , Mastectomy , Young AdultABSTRACT
PURPOSE: Implementing cancer precision medicine in the clinic requires assessing the therapeutic relevance of genomic alterations. A main challenge is the systematic interpretation of whole-exome sequencing (WES) data for clinical care. METHODS: One hundred sixty-five adults with metastatic colorectal and lung adenocarcinomas were prospectively enrolled in the CanSeq study. WES was performed on DNA extracted from formalin-fixed paraffin-embedded tumor biopsy samples and matched blood samples. Somatic and germ-line alterations were ranked according to therapeutic or clinical relevance. Results were interpreted using an integrated somatic and germ-line framework and returned in accordance with patient preferences. RESULTS: At the time of this analysis, WES had been performed and results returned to the clinical team for 165 participants. Of 768 curated somatic alterations, only 31% were associated with clinical evidence and 69% with preclinical or inferential evidence. Of 806 curated germ-line variants, 5% were clinically relevant and 56% were classified as variants of unknown significance. The variant review and decision-making processes were effective when the process was changed from that of a Molecular Tumor Board to a protocol-based approach. CONCLUSION: The development of novel interpretive and decision-support tools that draw from scientific and clinical evidence will be crucial for the success of cancer precision medicine in WES studies.Genet Med advance online publication 26 January 2017.
Subject(s)
Exome Sequencing/methods , Exome/genetics , Precision Medicine/methods , Adenocarcinoma/genetics , Adenocarcinoma of Lung , Adult , Colorectal Neoplasms/genetics , Databases, Genetic , Genomics/methods , Germ-Line Mutation/genetics , High-Throughput Nucleotide Sequencing/methods , Humans , Lung Neoplasms/genetics , Mutation/genetics , Prospective Studies , Sequence Analysis, DNA/methodsABSTRACT
Since its description by Li and Fraumeni over 40 years ago, Li-Fraumeni syndrome (LFS) remains one of the most striking familial cancer predisposition syndromes. Children and adults are affected by a wide array of cancers that occur predominantly at younger ages. This review discusses LFS, describes its association with TP53, and examines the classic and evolving definitions of the syndrome. The potential implications of multigene assessments of individuals at increased cancer risk, which have already begun to identify those with very little personal or family cancer history carrying germline TP53 mutations, are considered. Newer options in the management of individuals with LFS are also discussed, highlighting the importance of further clinical trials for cancer detection, prevention, and management. Finally, we observe how the clinical criteria for TP53 mutation screening appear to be evolving as our understanding of the impact of germline TP53 mutations continues to expand.
Subject(s)
Genetic Predisposition to Disease , Germ-Line Mutation/genetics , Li-Fraumeni Syndrome/genetics , Tumor Suppressor Protein p53/genetics , Adult , Child , Genetic Counseling , Humans , Li-Fraumeni Syndrome/diagnosis , Li-Fraumeni Syndrome/pathology , Risk FactorsABSTRACT
Next-generation sequencing technology affords an unprecedented opportunity to analyze multiple breast cancer susceptibility genes simultaneously. With the incarnation of gene panels that combine testing for moderate- and high-penetrance genes, this technology has given birth to a paradigm shift in clinical genetic test offerings. A transformation in genetic counseling for cancer susceptibility will necessarily follow, with a shift from the traditional approach of single-gene testing to considerations of testing by multi-gene panels. At the same time, however, the opportunity to identify rare lesions underlying hereditary susceptibility has introduced new challenges. Available cancer risk estimates for genes included in panel tests may not be supported by evidence, and there is increased risk of identifying variants of uncertain significance (VUS). Management of individuals with rare pathogenic mutations may be unclear. We provide a summary of available evidence for breast cancer risks conferred by pathogenic mutations in genes commonly included in breast cancer susceptibility panels, as well as a review of limitations and counseling points.
Subject(s)
Breast Neoplasms/genetics , Counseling/methods , Genetic Predisposition to Disease , Genetic Testing/methods , Neoplasm Proteins/genetics , DNA Mutational Analysis , Female , Genetic Variation , Humans , Middle Aged , PedigreeABSTRACT
OBJECTIVE: Turkish genome is underrepresented in large genomic databases. This study aims to evaluate the effect of allele frequency in the Turkish population in determining the clinical utility of germline findings in breast cancer, including invasive lobular carcinoma (ILC), mixed invasive ductal and lobular carcinoma (IDC-L), and ductal carcinoma (DC). METHODS: Two clinic-based cohorts from the Umraniye Research and Training Hospital (URTH) were used in this study: a cohort consisting of 132 women with breast cancer and a non-cancer cohort consisting of 492 participants. The evaluation of the germline landscape was performed by analysis of 27 cancer genes. The frequency and type of variants in the breast cancer cohort were compared to those in the non-cancer cohort to investigate the effect of population genetics. The variant allele frequencies in Turkish Variome and gnomAD were statistically evaluated. RESULTS: The genetic analysis identified 121 variants in the breast cancer cohort (actionable = 32, VUS = 89) and 223 variants in the non-cancer cohort (actionable = 25, VUS = 188). The occurrence of 21 variants in both suggested a possible genetic population effect. Evaluation of allele frequency of 121 variants from the breast cancer cohort showed 22% had a significantly higher value in Turkish Variome compared to gnomAD (p < 0.0001, 95% CI) with a mean difference of 60 times (ranging from 1.37-354.4). After adjusting for variant allele frequency using the ancestry-appropriate database, 6.7% (5/75) of VUS was reclassified to likely benign. CONCLUSION: To our knowledge, this is the first study of population genetic effects in breast cancer subtypes in Turkish women. Our findings underscore the need for a large genomic database representing Turkish population-specific variants. It further highlights the significance of the ancestry-appropriate population database for accurate variant assessment in clinical settings.
Subject(s)
Breast Neoplasms , Carcinoma, Ductal, Breast , Carcinoma, Lobular , Humans , Female , Breast Neoplasms/epidemiology , Breast Neoplasms/genetics , Genomics , OncogenesABSTRACT
Women with germline pathogenic variants (PV) in the fumarate hydratase (FH) gene develop cutaneous and uterine leiomyomata and have an increased risk of developing aggressive renal cell carcinomas. Many of these women are unaware of their cancer predisposition until an atypical uterine leiomyoma is diagnosed during a myomectomy or hysterectomy, making a streamlined genetic counseling process after a pathology-based atypical uterine leiomyoma diagnosis critical. However, the prevalence of germline pathogenic/likely PVs in FH among atypical uterine leiomyomata cases is unknown. To better understand FH germline PV prevalence and current patterns of genetic counseling and germline genetic testing, we undertook a retrospective review of atypical uterine leiomyomata cases at a single large center. We compared clinical characteristics between the FH PV, FH wild-type (WT), and unknown genetic testing cohorts. Of the 144 cases with atypical uterine leiomyomata with evaluable clinical data, only 49 (34%) had documented genetic test results, and 12 (8.3%) had a germline FH PV. There were 48 IHC-defined FH-deficient cases, of which 41 (85%) had FH testing and nine had a germline FH PV, representing 22% of the tested cohort and 18.8% of the FH-deficient cohort. Germline FH PVs were present in 8.3% of evaluable patients, representing 24.5% of the cohort that completed genetic testing. These data highlight the disconnect between pathology and genetic counseling, and help to refine risk estimates that can be used when counseling patients with atypical uterine leiomyomata. PREVENTION RELEVANCE: Women diagnosed with fumarate hydratase (FH)-deficient uterine leiomyomata are at increased risk of renal cancer. This work suggests a more standardized pathology-genetic counseling referral pathway for these patients, and that research on underlying causes of FH-deficient uterine leiomyomata in the absence of germline FH pathogenic/likely pathogenic variants is needed.