Ambry Genetics Research Articles

Hereditary Transthyretin Amyloidosis in Patients Referred to a Genetic Testing Program.

Diagnosis of hereditary amyloid transthyretin (hATTR) amyloidosis with cardiomyopathy is frequently delayed, in large part because of symptom overlap with other cardiovascular diseases and limited provider knowledge of this disease. The sponsored and provider referred hATTR Compass Genetic Testing Program (Ionis, Carlsbad, CA; Ambry Genetics, Aliso Viejo, CA) provided no-cost genetic testing to adults with a family history or clinical suspicion of hATTR amyloidosis. This study aims to characterize patients with hATTR amyloidosis and increase awareness of genetic testing for hATTR. Patients were referred to the hATTR genetic testing program, and a cross-sectional post hoc analysis was performed. A pathogenic TTR variant was identified in 1503 (6.6%) of 22 886 patients referred for genetic testing between June 2018 and March 2022. Patients were identified in all US states, 3 US territories, and Canada. Median age at testing was 63 years, and 44% were female. The p.V142I TTR variant was the most common (n=1263, 84.0%). Only 32% of patients with a pathogenic TTR variant reported a known family history; a lower percentage of Black individuals reported a known family history compared with other racial and ethnic groups. Black patients accounted for 23.7% of all patients referred and 81.9% of patients with the p.V142I variant. This sponsored genetic testing program identified a large number of patients with a pathogenic TTR variant, notably, in geographic regions not previously reported, and demographic groups that are historically underrepresented in the literature.

12345 Staying Ahead of Cowden’s Syndrome in Differentiated Thyroid Cancer

Abstract Disclosure: M.S. Gordon: None. M.B. Gordon: None. Cowden’s syndrome or multiple hamartoma syndrome, is an uncommon autosomal dominant genodermatosis and is a member of the spectrum of disorders involving mutations in the phosphatase and tensin homolog gene (PTEN). It is associated with differentiated thyroid cancer (DTC), ¾ papillary, including follicular variant (FVPTC), 1/4 follicular (FTC), and other malignancies, including breast (most common), colorectal, renal cell, endometrial and skin cancers. We report a case of Cowden’s syndrome in which the patient presented with FVPTC but had no other apparent indication of a genetic abnormality until she was found to have a melanoma and was noted to have macrocephaly. The patient presented at age 26 with a thyroid nodule of 2.7 cm in maximal dimension. FNA was benign. By age 31 the lesion had grown to 3.3 cm and a repeat FNA showed a follicular neoplasm. She underwent left lobectomy and isthmusectomy revealing a 3.0 cm FVPTC with focal Hurthle cell features. There was capsular irregularity, and subsequently she underwent completion thyroidectomy showing a right sided 8mm FVPTC. She then received 30 mCi I 131. There were no apparent pathologic mucocutaneous lesions, intellectual deficits, and no family history of Cowden’s syndrome. At age 39 she was found to have a Stage IA malignant melanoma of the periumbilical skin which was resected. With two malignancies diagnosed at a relatively young age, she was evaluated for genetic syndromes and it was simultaneously noted that she had macrocephaly with head circumference of 66 cm. (>99 percentile). An analysis of 69 genes by Ambry genetics revealed a pathogenic variant in the PTEN gene (c.388 C>T (p.R130*). PTEN R130* results in a premature truncation of the PTEN protein at amino acid 130 of 403 within the phosphatase tensin-type domain resulting in loss of function. Macrocephaly (2% population frequency) is seen in 80% of patients with PTEN mutations. Twenty percent of patients with thyroid carcinoma and macrocephaly have a PTEN mutation and lifetime risk of melanoma in DTC is 25%. BRAF and RAS mutations may cooperate with PTEN loss and explain the increased co-occurrence of malignancies with BRAF and RAS mutations such as melanoma, FTC, and PTC in Cowden’s syndrome. In conclusion, we suggest that head circumference should be measured in all patients with DTC to screen for PTEN abnormalities. Patients with DTC also should have a thorough skin examination. Presentation: 6/2/2024

Outcomes of a universal germline screening program in a community urology practice.

The role of germline genetic testing in urologic oncology has expanded in recent years. However, implementation of genetic testing in community practices remains a challenge, often due to limited access to qualified genetics trained providers. In this study, we report outcomes of a universal germline screening program in a community urology practice. Between November 2021 and September 2022, all patients referred for urology clinic visits at Frederick Health (Frederick, MD, USA) were provided an online genetics screening questionnaire prior to the visit. Responses were compared against National Comprehensive Cancer Network (NCCN) criteria for germline testing. Those who met criteria were provided educational materials at the end of the questionnaire, and then counseled by a trained urologic oncologist (HC) in the clinic or referred to a genetic counselor prior to testing. Testing was performed with a 36-gene pan-cancer panel (CancerNext) or a 14-gene targeted prostate cancer panel (ProstateNext), with or without additional RNA analysis (RNAinsight) (Ambry Genetics, CA, USA). Demographic and clinical parameters, as well as genetic testing results, were retrospectively collected under IRB approval. In the study period, 765 patients were seen over 1370 clinic visits. Of these, 505 patients (66.0%) completed the screening questionnaire. The majority were completed via email (54.5%) with the remainder (45.5%) via text message. Of the patients who completed screening, 125/505 (24.7%) met NCCN criteria for germline testing. 58/125 patients (46.4%) who met criteria underwent germline testing, of whom 5/58 (8.6%) had distinct pathogenic mutations identified. These included actionable mutations in BRCA1, BRCA2, and CHEK2, as well as an additional pathogenic mutation in NBN. Variants of unknown significance were identified in 8/58 patients (13.8%) in 11 total genes. Challenges to implementation of this program included meeting institutional requirements for genetic testing consent, facilitating specimen collection in clinic, and integration of results into the electronic health record. Genetic risk assessment for high-risk individuals is feasible as part of a universal screening program in a community urology practice. Approximately 8% of tested patients were found to have pathogenic germline mutations, which is consistent with contemporary tertiary referral cohorts.

Clinical features of prostate cancer by polygenic risk score.

Genome-wide association studies have identified more than 290 single nucleotide variants (SNVs) associated with prostate cancer. These SNVs can be combined to generate a Polygenic Risk Score (PRS), which estimates an individual's risk to develop prostate cancer. Identifying individuals at higher risk for prostate cancer using PRS could allow for personalized screening recommendations, improve current screening tools, and potentially result in improved survival rates, but more research is needed before incorporating them into clinical use. Our study aimed to investigate associations between PRS and clinical factors in affected individuals, including age of diagnosis, metastases, histology, International Society of Urological Pathology (ISUP) Grade Group (GG) and family history of prostate cancer, while taking into account germline genetic testing in known prostate cancer related genes. To evaluate the relationship between these clinical factors and PRS, a quantitative retrospective chart review of 250 individuals of European ancestry diagnosed with prostate cancer who received genetic counseling services at The Ohio State University's Genitourinary Cancer Genetics Clinic and a 72-SNV PRS through Ambry Genetics, was performed. We found significant associations between higher PRS and younger age of diagnosis (p = 0.002), lower frequency of metastases (p = 0.006), and having a first-degree relative diagnosed with prostate cancer (p = 0.024). We did not observe significant associations between PRS and ISUP GG, histology or a having a second-degree relative with prostate cancer. These findings provide insights into features associated with higher PRS, but larger multi-ancestral studies using PRS that are informative across populations are needed to understand its clinical utility.

Somatic mutations in tumor-adjacent normal breast tissue in young women with high risk family history.

576 Background: It’s incompletely understood why some women without germline breast cancer predisposing mutations develop early onset breast cancer. Breast cancer in young women is often more aggressive, with high histologic grade, worse prognosis, and higher risk of recurrence. We hypothesize that these women have somatic mutations in the normal breast tissue that contribute to breast cancer tumorigenesis. Methods: Whole exome sequencing (WES) data was analyzed from normal tissue adjacent to breast tumor and compared to matched peripheral blood (n=28). All patients were <50yo, had high risk family history as per NCCN guidelines, and had negative Ambry Genetics panel testing. FFPE sections were reviewed by two pathologists to identify normal breast tissue furthest away from tumor. WES was performed on Illumina HS4000 using 100-base pair paired-end reads. Samples were mapped to the human reference genome (vGRCh38). PCR duplicates were marked (Picard), and indel regions were adjusted (GATK). High-quality germline variants (HaplotypeCaller), somatic mutations (Mutect), and indels (IndelGenotyper) were called. Low-quality variants were filtered out. The classification and number of mutations per gene per sample were extracted and analyzed. Results: Majority of patients were white (86%), median age 45, with invasive ductal carcinoma (86%), ER+/PR+/HER2- (100%). Median somatic variants per sample were 97 (range: 45-285), all single nucleotide variants, mostly missense mutations, C>T conversions were seen in 45% of mutations. This suggests cytidine deaminase (APOBEC) involvement. All samples had alterations in at least one of the top ten affected genes which include transcription factors in zinc finger family (listed below). Zinc finger proteins play a key role in tumorigenesis, cancer progression and metastasis in a variety of cancers. Upregulation of zinc finger proteins has been associated with worse prognosis in breast cancer. Conclusions: We describe novel somatic mutations in zinc finger proteins in normal breast tissue adjacent to tumor that may contribute to early onset breast cancer in patients with high risk family history. [Table: see text]

Breast cancer risk associated with missense variants in BRCA2.

10501 Background: Greater than 90% of missense variants in BRCA2 are classified as variants of uncertain significance (VUS). In addition, among the few known missense pathogenic variants (PVs) in BRCA2, breast cancer risk has been reported to be lower compared to pathogenic truncating variants (PTVs) (Li et al., 2022) . Herein, we aim to reclassify several missense variants in BRCA2 and investigate the associated breast cancer risk. Methods: A total of 450 BRCA2 missense variants in the C-terminal DNA binding domain (DBD) were evaluated for functional effect utilizing a previously validated homology-directed DNA double-strand repair (HDR) assay. The results of the functional evaluation along with clinical, structural, and in-silico data were applied to the rules-based ACMG/AMP criteria for variant classification to identify pathogenic/likely pathogenic (P/LP) variants and benign/likely benign (B/LB) variants. A pooled case-control analysis was performed comparing the frequency of reclassified P/LP missense variants among 82,372 women with breast cancer within the Ambry Genetics database as cases and 174,167 unaffected women within gnomAD, CARRIERS, and BRIDGES datasets as controls to evaluate associated breast cancer risk. Separate case-control analysis and comparisons with BRCA2 DBD PTVs, exon 11 PTVs, and known missense PV standards in ENIGMA were also performed. Results: From the 450 missense variants in the DBD, 137 (30.4%) were noted to be functionally deleterious and 313 (69.6%) were functionally neutral by the HDR assay. Incorporation of the functional and other data into an ACMG/AMP model led to the reclassification of 439 (97.6%) variants, with 131 as P/LP and 308 as B/LB variants. In a pooled case-control analysis, reclassified BRCA2 missense P/LP variants were associated with clinically significant increased risks of breast cancer (Odds Ratio (OR):5.6, 95%CI:3.9–8.0), whereas B/LB missense variants were not (OR:1.1, 95%CI:1.1–1.2). Similarly elevated risks of breast cancer were observed for BRCA2 PTVs in the DBD (OR:6.8, 95%CI:5.1–9.0) and missense PV standards in ENIGMA (OR:7.8, 95%CI:4.1–14.7). However, PTVs in exon 11 of BRCA2 were associated with a lower risk of breast cancer (OR:4.4, 95%CI:3.8–4.9) compared to PTVs in DBD, confirming the ovarian cancer cluster region effect in BRCA2. Conclusions: The study demonstrates that the HDR functional assay in conjunction with other clinical and genomic data can be a powerful tool that can aid in the reclassification of > 95% of missense variants in BRCA2. In addition, missense PVs in DBD were noted to have a similarly elevated risk of breast cancer as PTVs. The reclassification of the BRCA2 missense VUS and identification of associated breast cancer risk in this study will significantly influence breast cancer risk assessment and management strategies among carriers of these missense variants.

Digital cancer genetic risk assessment in a gynecologic oncology clinic.

10612 Background: Population-based screening for hereditary cancer syndromes and referral of those who screen positive for genetic testing is a cost effective, evidence-based national health priority. However, under-recognition of hereditary cancer syndromes remains a critical concern, with fewer than 20% of individuals with Hereditary Breast and Ovarian Cancer Syndrome and Lynch Syndrome identified. Here, we evaluate the Ambry Genetics Comprehensive, Assessment, Risk, and Education (CARE) Program, a risk-stratification tool to assess eligibility for National Comprehensive Cancer Network (NCCN) genetic testing criteria and lifetime risk for breast cancer based on the Tyrer-Cuzick (version 8.0) risk algorithm. Methods: Between November 2022 and February 2023, new patients in a gynecologic oncology clinic were prompted by text message to complete CARE prior to their appointment. Those using CARE then completed a System Usability Scale (SUS), a validated 10-item questionnaire for the assessment of perceived usability. Results: Sixty patients presented for a new patient gynecologic oncology appointment and were prompted to complete CARE. The median patient age was 55 years (interquartile range, 40-68). The patients self-identified as Non-Hispanic White (44, 73%), Non-Hispanic Black (5, 8%), Asian (5, 8%), Hispanic (3, 5%), other (2, 3%), and unknown (1, 2%). All identified as female. Forty-three patients (72%) completed CARE. Among CARE users, 11 (26%) were identified as meeting criteria for genetic testing; of these, 9 (82%) proceeded with point-of-care same day genetic testing. Nine (21%) patients were eligible for enhanced breast cancer screening based on an estimated lifetime breast cancer risk of 20% or greater; of these, 100% were referred for high-risk breast screening. There were no patient demographics associated with completion of CARE. Forty-one patients (72%) completed the SUS survey; the median SUS score was 80 (interquartile range, 60-92.5), which corresponded to 85-89th percentile and a letter grade of A-. Conclusions: Implementation of a digital tool for cancer genetic risk assessment identified a quarter of patients to be eligible for genetic testing, among whom 82% completed same-day genetic testing. Additionally, the tool was reviewed favorably by patient users. Large randomized controlled trials of health information technology tools are needed to move closer to the goal of population-based hereditary cancer risk assessment.

MP54-12 IMPLEMENTATION AND OUTCOMES OF A UNIVERSAL GERMLINE SCREENING PROGRAM IN A COMMUNITY UROLOGY PRACTICE

You have accessJournal of UrologyCME1 Apr 2023MP54-12 IMPLEMENTATION AND OUTCOMES OF A UNIVERSAL GERMLINE SCREENING PROGRAM IN A COMMUNITY UROLOGY PRACTICE Neil Mendhiratta, Herman Hauver, Whitley Hatton, Andrew Ostrusky, Devika Sathe, Patricia Rice, Sandeep Gurram, and Heather Chalfin Neil MendhirattaNeil Mendhiratta More articles by this author , Herman HauverHerman Hauver More articles by this author , Whitley HattonWhitley Hatton More articles by this author , Andrew OstruskyAndrew Ostrusky More articles by this author , Devika SatheDevika Sathe More articles by this author , Patricia RicePatricia Rice More articles by this author , Sandeep GurramSandeep Gurram More articles by this author , and Heather ChalfinHeather Chalfin More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000003307.12AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: The role of germline genetic testing in urologic oncology has expanded in recent years. However, implementation of genetic testing in community practices remains a challenge, often due to limited access to qualified genetics trained providers. In this study, we report outcomes of a universal germline screening program in a community urology practice. METHODS: Between August 1st, 2021 and September 19th, 2022, all patients referred for urology clinic visits at Frederick Health (Frederick, MD, USA) were provided an online genetics screening questionnaire prior to the visit. Responses were compared against National Comprehensive Cancer Network (NCCN) criteria for germline testing. Those who met criteria were provided educational materials at the end of the questionnaire, and then counselled by a trained urologic oncologist (HC) in the clinic or referred to a genetic counselor prior to testing. Testing was performed with a 36-gene pan-cancer panel (CancerNext) or a 14-gene targeted prostate cancer panel (ProstateNext), with or without additional RNA analysis (RNAinsight) (Ambry Genetics, CA, USA). Demographic and clinical parameters, as well as genetic testing results, were retrospectively collected under IRB approval. RESULTS: In the study period, 846 patients were seen over 1,580 clinic visits. Of these, 540 patients (63.8%) completed the screening questionnaire. The majority were completed via email (59.7%) with the remainder (40.3%) via text message. Of the patients who completed screening, 136/540 (25.2%) met NCCN criteria for germline testing. 49/136 patients (36%) who met criteria underwent germline testing, of whom 6/49 (12.2%) had distinct pathogenic mutations identified. These included actionable mutations in BRCA1 (c.4616dupT), BRCA1 (c.4964_4982del19), BRCA2 (p.D2723H; c.8167G>C), and CHEK2 (1100delC); additional pathogenic mutations were found in LZTR1 (c.774delT;p.F258Lfs*93) and NBN (p.S706,c.2117c>G). Variants of unknown significance were identified in 8/49 patients (16.3%) in 9 total genes. Challenges to implementation of this program included meeting institutional requirements for genetic testing consent, facilitating specimen collection in clinic, and integration of results into the electronic health record. CONCLUSIONS: Genetic risk assessment for high-risk individuals is feasible as part of a universal screening program in a community urology practice. Approximately 12% of tested patients were found to have pathogenic germline mutations, which is consistent with contemporary tertiary referral cohorts. Source of Funding: None © 2023 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 209Issue Supplement 4April 2023Page: e758 Advertisement Copyright & Permissions© 2023 by American Urological Association Education and Research, Inc.MetricsAuthor Information Neil Mendhiratta More articles by this author Herman Hauver More articles by this author Whitley Hatton More articles by this author Andrew Ostrusky More articles by this author Devika Sathe More articles by this author Patricia Rice More articles by this author Sandeep Gurram More articles by this author Heather Chalfin More articles by this author Expand All Advertisement PDF downloadLoading ...

Pathogenic variants among females with breast cancer and a non-breast cancer reveal opportunities for cancer interception

PurposeHerein, 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.MethodsFemales 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.ResultsOf 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.ConclusionsFemales 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.

Abstract A003: Risks of ductal carcinoma in situ of the breast associated with pathogenic variants in cancer predisposition genes

Abstract Introduction: The relationship between germline pathogenic variants (PVs) in cancer predisposition genes and ductal carcinoma in situ (DCIS) is not well established. The objective of this study is to determine the risks of DCIS and contralateral breast cancer among women with DCIS associated with germline PVs in cancer predisposition genes. Methods: Associations between pathogenic variants in 11 cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MSH6, PALB2, RAD51C, and RAD51D) and DCIS were determined in case control analyses of a population-based cohort of 3876 women with DCIS and age-matched unaffected women, and in a clinical cohort of 9887 DCIS cases undergoing clinical genetic testing at Ambry Genetics and unaffected reference controls. The incidence of contralateral breast cancer risk in BRCA1, BRCA2, and PALB2 PV carriers with DCIS was also evaluated in a time-to-event analysis. Results: The mean age at diagnosis of DCIS was 50 years in the clinical testing cohort and 59 years in the population-based cohort. The frequency of PVs in 11 predisposition genes among DCIS cases was 6.9% in the clinical testing cohort and 4.9% in the population-based cohort. PVs in ATM, BRCA1, BRCA2, CHEK2, MSH6, PALB2, and RAD51D were associated with significantly increased risks (Odds Ratio (OR) >2) of DCIS in the clinical testing cohort whereas only PVs in BRCA1, CHEK2, PALB2, and ATM were associated with significantly increased risks of DCIS in the population-based cohort. The cumulative incidence of contralateral breast cancer among BRCA1, BRCA2, and PALB2 PV carriers with DCIS was 11% in 5-years and 20% in 15-years. Conclusions: This study provides new insights into PVs that predispose to DCIS. In addition, it establishes an increased risk of contralateral breast cancer risk among women with DCIS who are carriers of PVs in BRCA1, BRCA2, or PALB2. These findings will guide surveillance and risk reducing strategies in germline PV carriers with DCIS. Citation Format: Huaizhi Huang, Ronan E. Couch, Holly LaDuca, Siddhartha Yadav, Eric C. Polley, Nicholas J. Boddicker, Jie Na, Rohan D. Gnanaolivu, David E. Goldgar, Tina Pesaran, Steven N. Hart, Jill S. Dolinsky, Julie R. Palmer, Lauren Teras, Alpa V. Patel, Kathryn J. Ruddy, Janet E. Olson, Celine M. Vachon, Peter Kraft, Song Yao, Amy Trentham-Dietz, Katherine L. Nathanson, Jeffrey N. Weitzel, Susan M. Domchek, Fergus J. Couch, Chunling Hu. Risks of ductal carcinoma in situ of the breast associated with pathogenic variants in cancer predisposition genes [abstract]. In: Proceedings of the AACR Special Conference on Rethinking DCIS: An Opportunity for Prevention?; 2022 Sep 8-11; Philadelphia, PA. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_1): Abstract nr A003.

Development of a Comprehensive Program for Evaluation of Hereditary Predisposition to Hematologic Malignancies

Introduction Germline pathogenic variants underlie or contribute to an estimated 20% of leukemia and up to 50% of aplastic anemia. Early diagnosis of inherited predisposition to hematologic malignancy (IPHM) and bone marrow failure is critical for treatment planning both due to the risk of subjecting patients to excessive toxicity from standard doses of chemotherapy or radiation and because affected relatives who are potential donors for stem cell transplant (SCT) should be identified. Further, identification of associated risks for other non-hematologic cancers and multisystem diseases provide opportunities for screening, monitoring, and early treatment. Family members may also be at risk for complications related to the IPHM identified in the proband and therefore are candidates for screening with counseling and surveillance. Methods We established a multicenter collaborative program between three hospitals [Huntsman Cancer Institute at University of Utah, LDS Hospital at Intermountain Healthcare, and Primary Children's Hospital (all in Salt Lake City, UT)] with specific criteria for genetic evaluation defined prospectively (Table 1). All patients identified for evaluation were assessed by a certified genetic counselor. Germline genetic testing was performed using DNA from culture fibroblast derived from skin biopsies. Laboratory selection for germline genetic testing was based on the patient's insurance coverage, admission status, personal history, family history, requested turnaround time, time to SCT, and comprehensiveness of panel. Germline genetic testing was performed at one of the following laboratories: Prevention Genetics, GeneDX Laboratories, ARUP Laboratories, Ambry Genetics, and Invitae Genetics. Chromosome breakage analysis and telomere length measurement were performed on patients with clinical suspicion of Fanconi anemia or a telomere biology disorder, respectively. Results Between October 2021 and April 2022, 61 patients were identified prospectively who met evaluation criteria for referral to genetic counseling (Table). Of these patients, 42 were males and 19 were females. Median age was 35 years (range newborn to 77 years). The most common reasons for evaluation were cytopenia (n=14), myelodysplastic syndrome (n=10), and acute myeloid leukemia (n=16). Four potential SCT donors were evaluated. Of 61 patients, 60 patients were referred directly to a genetic counselor. Of the 58 patients who kept their appointment (58/61, 95%), the median time from referral to clinic evaluation was 6 days (range, same day to 99 days,). Fifty-two patients underwent genetic testing with 47 having panel testing and 5 having gene specific testing. Twenty-nine patients underwent skin biopsy (all hematologic malignancies and one case of aplastic anemia), and 23 patients underwent testing on saliva or blood samples. Of the 52 patients who underwent germline genetic testing, eight were found to have pathogenic/likely pathogenic variants and eight were identified with suspicious variants of uncertain significance (Table 2). Identification of 16 patients with pathogenic or suspicious genetic test results led to testing of four potential HSCT donors. Conclusion The results of this study show the feasibility of developing a comprehensive, collaborative program for evaluation of IPHM. Essential to the success of such a program is a genetic counselor who is readily available for consultation and whose breath of knowledge is sufficient both to guide patient evaluation and to interpret findings that impact directly on management of patients and family members. Other important contributors to program success include active communication with pediatric and adult clinicians who treat patients with hematologic malignancies and bone marrow failure, and laboratory support for obtaining skin biopsies, culturing fibroblasts, and extracting and preserving DNA. Our program can serve as a blueprint for establishing a service line for comprehensive germline testing for IPHM at other medical centers. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

122. Prostate cancer and other clinical features by polygenic risk score

Prostate cancer is the second most common cancer in American men and the second leading cause of cancer death in the USA. Genome-wide association studies (GWAS) have identified more than 170 single nucleotide polymorphisms (SNPs) associated with prostate cancer, which can be combined to make a Polygenic Risk Score (PRS) and give an individual their risk to develop prostate cancer. To our knowledge, studies have not been done to determine if there is a relationship between PRS and features of prostate cancer in men ascertained in a clinical setting. Thus, this study aims to investigate risk factors associated with prostate cancer including: age of diagnosis, ISUP Grade Group, metastatic status, histology, and family history of prostate cancer, to determine how they correlate with PRS amongst men who do not have a germline pathogenic variant in a known prostate cancer related gene. A quantitative retrospective chart review of 175 men diagnosed with prostate cancer, who received genetic counseling services at the Ohio State University's Genitourinary Cancer Genetics Clinic, and a PRS through Ambry Genetics was generated. Men diagnosed over 60 years of age were more likely to have a low PRS (57%) than a high PRS (32%) (p-value of 0.009). This supports the hypothesis that men diagnosed with prostate cancer at younger ages will have higher PRS and vice versa. We did not find a significant relationship between PRS and ISUP GG, metastatic status, histology, or family history in a first or second-degree relative.

Mutation spectrum and rates of variants of uncertain significance among African American males undergoing prostate cancer germline testing: Need for equity in genetic testing.

10502 Background: Germline testing (GT) for prostate cancer (PCA) is central to metastatic disease management, PCA screening strategies, and hereditary cancer assessment. African American (AA) males have a higher burden of PCA, yet have lower engagement in germline testing which limits understanding of genetic contribution to PCA. Here we evaluated the germline spectrum of AA and White males with PCA undergoing clinical multigene panel testing (MGPT) to inform germline testing strategies with attention to equity. Methods: Study participants included AA men and White men with PCA who underwent a 14-gene MGPT between April 2012 - December 2020 at a clinical diagnostic laboratory (Ambry Genetics). Exclusions were men with known pathogenic variants reported in their families or who had prior genetic testing. MGPT included: ATM, BRCA1, BRCA2, CHEK2, EPCAM, HOXB13, MLH1, MSH2, MSH6, NBN, PALB2, PMS2, RAD51D, TP53. Sanger or next generation sequencing analysis was performed per standard clinical testing protocol. Variant classification was per ACMG 5-tier system. Descriptive statistics summarized results with counts and percentages for categorical variables and mean and standard deviation for continuous variables. Data were compared with Fisher’s exact, Chi-squared, two proportion z-test, or two sample t-test, as appropriate. Significance level was set a priori at 0.05. Results: The dataset included genetic and clinical data from 427 males who had undergone MGPT: White males (n = 190; 45.5%) and AA males (n = 237; 55.5%). Mean age at diagnosis was 59 + 9.3 years. Among men whose Gleason score was indicated (72%), 47% had Gleason > = 8. Majority of men indicated having a 1st/2nd degree relative with PCA (68.97%) or 1st/2nd degree relative with any cancer (99.2%). In the entire cohort, 8.2% tested positive for a pathogenic/likely pathogenic variant; AA males (n = 14, 5.91%) and White males (n = 21, 11.05%). VUS only was reported in 21.31% of the overall cohort with a significant difference noted between AA and White males (25.32% vs. 16.32%, respectively; p = 0.0238). Mutation spectrum in AA males included: BRCA2 (n = 7), PALB2 (n = 3), ATM (n = 3), and BRCA1 (n = 1). Among White males, a wider spectrum of mutations was observed: BRCA2 (n = 6), ATM (n = 5), HOXB13 (n = 5), CHEK2 (n = 2), TP53 (n = 1), and NBN (n = 2). The proportion of AA males with multiple VUS was significantly higher than for Caucasian males (5.1% vs. 0.53%, p = 0.003). Conclusions: Clinical germline testing among AA males reveals a narrow spectrum of mutations in key DNA repair genes, with important implications for precision therapy and hereditary cancer assessment. Furthermore, AA males had significantly higher rates of multiple VUS, indicating critical need for greater inclusion of diverse populations in genetic studies to discern the pathogenic spectrum contributing to PCA aggressiveness and risk.

Prevalence of DNA damage repair (DDR) alterations in patients with metastatic hormone-sensitive prostate cancer (mHSPC) receiving enzalutamide (ENZA) or placebo (PBO) plus androgen deprivation therapy (ADT): ARCHES post hoc analysis.

5074 Background: DDR alterations are associated with poorer prognosis, including shorter overall survival (OS), in patients with mHSPC. In ARCHES (NCT02677896), patients with mHSPC treated with ENZA + ADT had a reduced risk of radiographic progression or death and improved OS versus PBO + ADT. This post hoc analysis assessed the prevalence of DDR alterations and associated baseline characteristics in patients with mHSPC in ARCHES. Methods: Patients with mHSPC (n=1150) were randomized 1:1 to ENZA (160 mg/day) + ADT or PBO + ADT. Germline DDR alteration testing was performed in blood using Ambry Genetics CustomNext-Cancer panel; 16 DDR-related genes were reported in the subset of patients who consented to participate in a pharmacogenomic study (n=664; Table). Descriptive analyses of baseline demographics and disease characteristics by DDR status were performed. Results: Of 664 patient samples tested, 652 were evaluable for analysis (ENZA + ADT, n=326; PBO + ADT, n=326). Baseline characteristics of these patients were similar to the ARCHES intent-to-treat population. The prevalence of DDR+ patients was lower than expected (n=34/652, 5.2%; Table). Of DDR+ patients, 13 (38.2%) had low-volume disease, compared with 228 (36.9%) of DDR− patients. High-volume disease was present in 21 (61.8%) DDR+ and 390 (63.1%) DDR− patients. Of DDR+ patients, 6 (17.6%) had localized disease at initial diagnosis (M0), compared with 145 (23.5%) DDR− patients. De novo metastatic disease at initial diagnosis (M1) was present in 28 (82.4%) DDR+ patients and 465 (75.2%) DDR− patients. Of DDR+ patients, 29 (85.3%) were from Europe, four (11.8%) were from North America, and one (2.9%) was from the Asia-Pacific region. Conclusions: This post hoc analysis found a lower prevalence of DDR alterations in patients with mHSPC in ARCHES, compared with the 7–12% previously reported in patients with metastatic castration-resistant prostate cancer (Lozano et al. Br J Cancer 2021; Pritchard et al. N Engl J Med 2016). We did not identify differences in baseline disease characteristics based on DDR status. Clinical trial information: NCT02677896. [Table: see text]

Abstract P2-09-03: Pathogenic variants among female breast cancer patients with a subsequent cancer demonstrate preventable cancer burden

Abstract Background: Among females with breast cancer, multiple primary cancers (MPCs) are a hallmark of cancer predisposition syndromes. Herein we report the frequency of germline pathogenic/likely pathogenic variants (PVs) among females with breast cancer (BC) and primary cancer of >1 other site who underwent multi-gene panel testing (MGPT) through a single lab. Among females first diagnosed with BC who had a PV in an actionable gene, we quantified the frequency of subsequent breast and non-breast cancers. Among those who later developed a second BC, ovarian, endometrial or colon cancer, we determined the percentage of patients with MPCs who would have been identified as high-risk if all women had had MGPT after a first diagnosis of breast cancer. Methods: Females with breast cancer and MPCs who underwent germline genetic testing with Ambry Genetics from 3/2012 to 12/2016 were included in our cohort. Eligible individuals had multigene panel testing, which included 21 genes at minimum (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53). Clinical factors including age at diagnosis, age at testing and cancer type were obtained from test requisition forms and clinical notes. Patients with >1 PV were excluded from the analysis. Results: Of the 6617 patients with MPCs including BC tested for the 21 genes in the analytic cohort, most were white (70.8%), with median age at testing 63 years (IQR: 16). The median ages of first and second cancer diagnosis were 49 (IQR: 18) and 59 (IQR: 16) years, respectively. Considering the diagnostic order of BC, PV prevalence was 16.5% (444/2687) with BC as the 1st cancer diagnosis, 11.2% (296/2641) with BC as the 2nd cancer diagnosis, 15.2% (49/323) as 3rd or later diagnosis (p<0.001). Based on the PV identified through genetic testing, 411 of 2687 (15.3%) females with BC as a first diagnosis would have been identified as high-risk and 227 (8.4%) as eligible for altered surveillance or risk-reducing interventions for a cancer that they subsequently developed. Specifically, of the 318 (11.8%) females with a PV in ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, NF1, PTEN, STK11, or TP53, 73 (23%) developed a subsequent BC. Of the 241 (9.0%) females with PVs in genes including ovarian cancer susceptibility (BRCA1, BRCA2, BRIP1, PALB2, RAD51C, or RAD51D), 143 (59.3%) developed ovarian cancer, 21 of whom also developed a second breast cancer. Among the 41 (1.5%) females with Lynch syndrome, 25 (61.0%) were later diagnosed with endometrial cancer and 10 (24.4%) were diagnosed with colorectal cancers (3 had both). Conclusions: Our data show a significant prevalence of germline PV in cancer susceptibility genes in women with MPC including BC. Further, the data suggest that a strategy testing all BC patients at diagnosis to identify actionable PV could permit the appropriate use of risk-reducing and surveillance strategies to reduce the occurrence of MPC among BC survivors. Citation Format: Brittany L. Bychkovsky, Min-Tzu Lo, Amal Yussuf, Carrie Horton, Parichehr Hemyari, Holly LaDuca, Judy E. Garber, Huma Q. Rana. Pathogenic variants among female breast cancer patients with a subsequent cancer demonstrate preventable cancer burden [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 P2-09-03.

RNA Studies Demonstrate that the LDLR c.2389+4A>G Intronic Variant Causes Familial Hypercholesterolemia through an RNA Splicing Impact

Lead Author's Financial Disclosures H.Z. is an employee of Ambry Genetics. Study Funding None. Background/Synopsis Familial hypercholesterolemia (FH) is an inherited disorder characterized by high plasma levels of low-density lipoprotein cholesterol (LDL-C). Mutations in the low-density lipoprotein receptor (LDLR) gene are the most common cause of FH. However, not all alterations in LDLR are pathogenic; some represent benign genetic variation, and the clinical significance of any given variant is not always clear. Variants of uncertain significance (VUS) require additional studies to elucidate their pathogenicity. Objective/Purpose We sought to further characterize an intronic LDLR alteration originally classified as a VUS in a large family with clinical FH. Methods We performed multigene panel testing for four genes associated with FH (APOB, LDLR, LDLRAP1, and PCSK9) on the proband of a large family with a strong family history of high cholesterol and premature death; additional affected and unaffected family members were genotyped by Sanger sequencing for an identified intronic LDLR variant. The splicing impact of the LDLR variant was ascertained by RT-PCRseq performed on three affected individuals. Results Panel testing detected LDLR c.2389+4A>G in the proband. No other pathogenic variants, likely pathogenic variants, or VUSs were identified. Subsequent familial testing indicated that LDLR c.2389+4A>G cosegregates with disease. RNA studies demonstrated that this alteration causes skipping of exon 16, which is predicted to result in the in-frame deletion of 26 amino acids. This deletion removes part of the transmembrane domain and is expected to disrupt the ability of LDLR to insert into the membrane, resulting in loss of receptor function. Other pathogenic alterations impacting the same donor splice site have been shown to have a similar impact on splicing (LDLR c.2389G>T and LDLR c.2389+1G>T; Bourbon M et al. J. Med. Genet., 2009 May;46:352-7; Holla ØL et al. Mol. Genet. Metab., 2009 Apr;96:245-52). Conclusions The LDLR c.2389+4A>G intronic variant is a pathogenic mutation that results in a splice defect and cosegregates with disease. In this case, RNA and family studies resulted in a reclassification from a VUS to a pathogenic mutation and confirmed the molecular cause of the multigenerational FH. Clinical management recommendations exist for individuals with a confirmed FH diagnosis, and an accurate genetic diagnosis can improve patient outcomes through tailored treatments (Brown E et al. J. Clin. Lipidol.,2020 Jul-Aug;14:398-413). Our findings highlight the utility of familial testing and RNA studies in clarifying the classification of DNA variants. H.Z. is an employee of Ambry Genetics.

Ordering Trends and Report Outcomes for Lipid Genes on a Comprehensive Cardiovascular Genetics Menu

Lead Author's Financial Disclosures M.T. is an employee of Ambry Genetics, a Konica Minolta Company. Study Funding None. Background/Synopsis By identifying the molecular etiologies for dyslipidemias, genetic testing can improve diagnostic accuracy, guide personalized medical management recommendations, and identify at-risk family members for proactive surveillance and cascade testing. The utility of genetic testing for dyslipidemias and clinical indications for testing are well described. However, many monogenic dyslipidemias, especially familial hypercholesterolemia, are vastly underdiagnosed. Objective/Purpose To assess ordering trends and genetic testing outcomes for dyslipidemia genetic testing performed at a large clinical lab. Methods We reviewed a retrospective, unselected cohort of individuals undergoing evaluation for personal or family history of dyslipidemia at our laboratory between 2014 and 2020. We classified test orders as (1) single-site genotype analysis (SSA), (2) targeted gene sequencing, next-general sequencing (NGS) panel testing for (3) familial hypercholesterolemia, (4) familial chylomicronemia or (5) sitosterolemia, or a (6) custom NGS panel of up to 167 cardiovascular-related genes chosen by the ordering provider (Table 1). Testing outcomes categorized as positive, uncertain, carrier, or negative were tabulated by test type, gene, and proband age. Statistical analysis was performed using Fisher's exact test. Results Overall, 31.42% (n=1046) of probands received a positive finding on genetic testing. Most individuals tested (69.78%) were over the age of 36, although children were significantly more likely to receive positive results (p<0.00001). Targeted gene sequencing (51.09%) and SSA (48.95%) had the highest diagnostic rates, suggesting that previous family member diagnosis or strong clinical evidence informed the specific ordering choice. Of all custom NGS panel orders, 36.27% included at least one lipid gene, of which 31.69% also included non-lipid cardiovascular genes suggesting that the patient had non-dyslipidemia cardiovascular features such as cardiomyopathy or arrhythmia. 120 patients had biallelic alterations in LDLR, one individual had biallelic alterations in PCSK9, and one individual had pathogenic alterations in LDLR and APOB. Two other individuals had a pathogenic alteration in LDLR and were carriers for a second recessive disorder (LDLRAP1 and ABCG8). Conclusions Determining a genetic cause for dyslipidemias can provide clinicians with specific guidance for optimizing patient outcomes and follow-up surveillance of at-risk family members. Multigene panel tests may identify compounding molecular diagnostics, which can help in further tailoring treatment. As the field of precision medicine continues to grow, the importance of an accurate molecular diagnosis is increasingly more vital. M.T. is an employee of Ambry Genetics, a Konica Minolta Company.

Outcomes Following Biochemical or Clinical Progression in Patients with Multiple Myeloma

Outcomes Following Biochemical or Clinical Progression in Patients with Multiple Myeloma

Ocular Toxicity of Commercially Available Belantamab Mafodotin in Patients with Advanced Multiple Myeloma

Ocular Toxicity of Commercially Available Belantamab Mafodotin in Patients with Advanced Multiple Myeloma

Mortality Trends in Multiple Myeloma after the Introduction of Novel Therapies in the United States

Mortality Trends in Multiple Myeloma after the Introduction of Novel Therapies in the United States