French-Speaking Network of Pharmacogenetics (RNPGx) Recommendations for Gene Panel Analysis Through Genotyping or Sequencing in Pharmacogenetics.

Points to consider: is there evidence to support BRCA1/2 and other inherited breast cancer genetic testing for all breast cancer patients? A statement of the American College of Medical Genetics and Genomics (ACMG)

As DNA sequencing costs decline, genetic testing options have expanded. Whole exome sequencing and whole genome sequencing (WGS) are entering clinical use, posing questions about their incremental value compared with disease-specific multigene panels that have been the cornerstone of genetic testing. Forty-one patients with hypertrophic cardiomyopathy who had undergone targeted hypertrophic cardiomyopathy genetic testing (either multigene panel or familial variant test) were recruited into the MedSeq Project, a clinical trial of WGS. Results from panel genetic testing and WGS were compared. In 20 of 41 participants, panel genetic testing identified variants classified as pathogenic, likely pathogenic, or uncertain significance. WGS identified 19 of these 20 variants, but the variant detection algorithm missed a pathogenic 18 bp duplication in myosin binding protein C (MYBPC3) because of low coverage. In 3 individuals, WGS identified variants in genes implicated in cardiomyopathy but not included in prior panel testing: a pathogenic protein tyrosine phosphatase, non-receptor type 11 (PTPN11) variant and variants of uncertain significance in integrin-linked kinase (ILK) and filamin-C (FLNC). WGS also identified 84 secondary findings (mean=2 per person, range=0-6), which mostly defined carrier status for recessive conditions. WGS detected nearly all variants identified on panel testing, provided 1 new diagnostic finding, and allowed interrogation of posited disease genes. Several variants of uncertain clinical use and numerous secondary genetic findings were also identified. Whereas panel testing and WGS provided similar diagnostic yield, WGS offers the advantage of reanalysis over time to incorporate advances in knowledge, but requires expertise in genomic interpretation to appropriately incorporate WGS into clinical care. URL: https://clinicaltrials.gov. Unique identifier: NCT01736566.

Two issues that may influence the diagnosis of depression in the medically ill are 1) the severity with which symptoms must be expressed before they are considered clinically significant and 2) how to deal with somatic symptoms that may be caused by medical illness. This study used different approaches to case identification to examine prevalence rates for major and minor depression in a group of terminally ill cancer patients. Semistructured diagnostic interviews were conducted with 130 patients receiving palliative care. Diagnoses according to the Research Diagnostic Criteria (RDC) were compared with diagnoses according to Endicott's revised criteria (which involve replacing somatic symptoms with non-somatic alternatives) when either a low-severity or a high-severity threshold for classifying RDC criterion A symptoms was used. A low-threshold (less stringent) diagnostic approach greatly increased the overall prevalence of major and minor depressive episodes with both the RDC and the Endicott criteria. With high thresholds, the RDC and the Endicott criteria were equivalent, whereas with low thresholds the Endicott substitutions identified fewer cases of major (but not minor) depression. Small differences between investigators in the applications of symptom-severity thresholds can result in large differences in prevalence rates for depression. However, the inclusions of somatic symptoms in the diagnostic criteria inflates the rates of diagnosis only when these symptoms are used in conjunction with a low-threshold approach.

Implementation and clinical utility of multigene panels for bleeding, platelet, and thrombotic disorders.

e22530 Background: Next Generation Sequencing (NGS) technologies have transformed hereditary breast and ovarian cancer (HBOC) testing process. Several multigene panels (MP) include from 10 to 100 candidate cancer susceptibility genes, but there is a debate about what genes should and should not be tested because of lack of actionability. Few studies have been reported about MP in Europe or Spanish cancer families and no studies in Andalusian population (southern Spain). Methods: We investigated a panel of 17 known genes of high/moderate-risk for HBOC in 938 clinically suspicious HBOC Andalusian families (SEOM 2015 criteria), tested from 2017 to 2019. Multigene panel including BRCA,1 BRCA2, CHEK2, PALB2, BRIP1, ATM, MLH1, MSH2, MSH6, PMS2, CDH1, NF1, PTEN, p53, STK11, RAD51C and RAD51D was performed. Results: We identified 130 patients who carried a high- or moderate-risk pathogenic variants: 61 in BRCA2 (47%), 30 in BRCA 1 (23%), 10 in CHEK2 (8%), 7 in ATM (5%), 7 in PALB2 (5%), 4 in RAD51 (3%), 4 in BRIP1 (3%), 4 in MSH6 (3%), 2 in MLH1 (1,5%) and 1 in MSH2. We detected 220 patients carry variants of uncertain significance (VUS), with a total of 248 VUS (some patients carried more than one VUS): 46 (19%) in ATM, 38 (15%) in BRCA 2, 28 (11%) in MSH6, 19 (8%) in PMS2, 17 (7%) in BRIP1, 16 (6%) in NF1, 14 (6%) in MSH2 and 12 (5%) in CDH1 and PALB2. The most frequent criteria in the entire cohort was “High-grade epithelial non-mucinous ovarian cancer”, reported in 243 cases (26%)”, whereas “Breast cancer (BC) diagnostic under 35” was the most frequent criteria between positives (48 cases (40%)). One case carried two pathogenic variants: BRCA2 and MUTYH. Conclusions: This is the first study reporting the mutational profile of MP gene testing in Andalusia. 70% of mutations were due to BRCA1 and 2 followed by far by CHEK2, ATM and PALB2. We also identified a large amount of VUS in BRCA2, ATM and MSH6. MP improve the diagnostic in andalusian HBOC patients.

SP59 Breakthrough cancer pain management: recommendations and international guidelines

Outpatient Clinics Are a New Frontier for Palliative Care

The creation of multigene panels for prognostic and predictive purposes allows a more accurate indication of adjuvant chemotherapy for patients with breast cancer. In a previous study, we reproduced a multigene panel of 21 genes based on the commercial Oncotype-DX method. We submitted 183 embedded specimens obtained from breast surgery on patients with locoregional disease (stages I to III) between 2005 and 2010 performed at the Hospitals of the Medical School of the ABC Foundation. When we analysed the correlations between the score of the multigene panel and the progression-free interval (PFI) in all patients, we did not find a statistically significant association. However, when we selected only the 71 samples that had amplification of at least eight non-housekeeping genes, we observed that those with scores above the 75th percentile had a significantly lower PFI (p=.0054). Samples processed with nonbuffered formaldehyde were associated with a worse quality of extracted RNA (p=.004) and a significantly higher multigene panel score (p=.021). We conclude that variations in the pre-analytical processing of specimens destined for multigene panel amplification can significantly affect the results, with a potential impact on clinical management.

Introduction: Liquid biopsy as a novel and non-invasive test for the surveillance of cancer is rapidly growing, by next-generation sequencing (NGS) technologies with multi-gene panels. Objective: The aim of this study was to describe the validation and implementation of a cell free tumor DNA (cfDNA) from the patients with non-small cell lung cancer (NSCLC), to sequence for 19 genes and copy number variation analyses for 5 genes via a novel NGS platform; GeneReader NGS System. Materials and Methods: We performed the complete NGS workflow with modifications, and sequenced the cfDNA extracted from 100 NSCLC patients. The multi-gene panel includes 19 lung cancer related genes (AKT1, ALK, BRAF, DDR, ERBB2, ESR1, KIT, KRAS, MAP2K1, NRAS, NTRK, PDGFRA, PIK3CA, PTEN and ROS) to sequence and additional copy number variations of 5 genes (RICTOR, EGFR, MET, FGFR1 and ERBB2) that all were selected to represent the most actionable genes for the clinical oncology and molecular diagnostics. The sequencing was performed using a novel NGS platform (GeneReader NGS System, Qiagen). Results: The validation process and the implementation of genetic testing from the cfDNA by this novel NGS system have been utilized for the clinical use. After quality assessment, the data from this NGS system was bioinformatically processed and a tertiary analysis was performed using QCI-Analyze and QCI-Interpret bioinformatics tools. The data was then reviewed on alterations and those reported in different mutation databases. The clinically relevant alterations were identified and reported due to the testing indications. Overall, actionable variants in EGFR, ALK, KRAS, PIK3CA, MET, FGFR1 and ERBB2 genes were detected and reported in 62 % of all NSCLC patients while the majority were in EGFR. Conclusions: For each of the 100 samples tested thus far, at least one variant was detected showing the high sensitivity and specificity of both the multi-gene panel and this novel NGS platform. Our evaluation yielded good results for the actionable multi-gene panel selected and provides a comprehensive NGS analysis and workflow for this new platform. Citation Format: Atil Bisgin, Ozge Sonmezler, Ibrahim Boga. Validation and implementation of next-generation sequencing in liquid biopsies by a novel NGS platform: Focus on non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3602.

1536 Background: Current standard-of-care practice for genetic cancer risk assessment (GCRA) focuses on single-gene testing for specific hereditary cancer syndromes. Next-generation sequencing (NGS) technologies recently became available for clinical applications. This study explored the perspectives and experiences of community-based clinicians regarding NGS testing for personalized GCRA. Methods: A 27-item survey was developed and administered online to 325 members of an interdisciplinary nationwide clinical cancer genetics community of practice. Results: Of 94 (29%) respondents, 25 (27%) have ordered at least one multi-gene panel and only 2 (2.1%) have ordered a whole exome or genome test from a commercial vendor for GCRA. Concerns about clinical utility, the challenge of interpreting and communicating results, lack of knowledge about and potential costs were most often cited as reasons for not pursuing NGS testing. Respondents were significantly more confident about their ability to interpret and counsel about single gene test results compared with multi-gene panels or whole exome/genome sequencing; and about multi-gene panels over whole exome/genome sequencing (p<.0001 for all comparisons). Conclusions: Findings suggest that while NGS tests are entering the realm of GCRA, multidisciplinary genomics education and clinical support resources are needed to address barriers to utilization and promote successful integration of NGS testing into community-based GCRA practice settings.

Background: Germline genetic testing for hereditary cancer predisposition syndromes can prevent cancer and save lives by identifying individuals who will benefit from enhanced surveillance, prophylactic surgery, and other risk-reduction strategies. Classically, hereditary cancer risk assessment has involved identification of individuals with clinical histories that fulfill specific criteria for a given syndrome followed by germline testing for mutations in the associated gene(s). Recent advances in next-generation sequencing technologies now allow individuals to undergo germline evaluation of numerous genes in parallel and a growing array of multigene panels are clinically available for such diagnostic testing. Methods: This presentation will discuss updates in clinical genetic testing, specifically the growing availability of next-generation sequencing multigene panel testing for hereditary cancer risk assessment. Findings: Data regarding next-generation sequencing multigene panel testing will be presented and will be contrasted with traditional, syndrome-specific hereditary colorectal cancer risk assessment strategies. Particular areas of focus in this talk will include: the detection of unexpected/off-target germline mutations by multigene panels (e.g. BRCA1/2 mutations in patients with colorectal cancer); cost-effectiveness considerations; the significance of moderate-penetrance cancer susceptibility gene mutations; germline variants of uncertain significance; and ways in which multigene panel testing results are expanding knowledge (and uncertainty) about both well- and poorly-defined colorectal cancer predisposition syndromes. Conclusions: Next-generation sequencing multigene panels are rapidly growing in popularity and availability for assessing hereditary cancer risk, including the identification of germline mutations linked to inherited colorectal cancer risk. In order for patients considering such testing to receive optimal care, it is essential that both they and their providers have a clear understanding of the benefits and potential limitations of multigene panels, including the possibility of identifying unexpected and/or indeterminate germline results. Citation Format: Matthew B. Yurgelun. Germline next-generation sequencing panels for detection of inherited colorectal cancer syndromes. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr IA07.

Background: Next-generation sequencing technology, reduced costs and public interest have fueled a surge in more expansive germline genetic testing of breast cancer patients. However, there are no population-based data on trends in use of different test types or the distribution of results. Methods: In the iCanCare study, we surveyed 7,303 women diagnosed in 2013-15 with early-stage breast cancer and reported to the Georgia and Los Angeles County SEER registries. Of 5,080 respondents (response rate 70%), 5,050 were linked to SEER clinical data and to test results from four commercial laboratories that performed nearly all germline genetic testing for breast cancer patients in the regions. We examined trends in test type (two genes, BRCA1/2 only, vs. more cancer susceptibility genes, multigene panel) and patterns of results (positive for a pathogenic mutation; variant of uncertain significance (VUS); negative) by clinical and sociodemographic subgroups. Pre-test risk of having a pathogenic mutation was categorized as higher vs. average based on patient report of age at diagnosis, family cancer history, ancestry (Ashkenazi Jewish vs. not) and breast cancer subtype (triple-negative vs. not), according to practice guidelines criteria for genetic testing. Results: The mean age was 62 years; 26%, 49% and 25% had stage 0, I, and II cancer, respectively; 78% had estrogen receptor-positive, HER2-negative disease, and 9% had triple-negative; 28% had higher pre-test risk of having a pathogenic mutation; 56% were non-Hispanic white, 18% African American, 14% Hispanic, and 10% Asian. Genetic testing use did not change over time (p=0.695), with one-quarter of patients receiving any test (either BRCA1/2 only or multigene panel) according to clinical laboratory data. However, testing included more genes over time: multigene panels comprised 19% of tests in 2013 vs. 66% in 2015 (p<0.001). Among all patients, 14% received BRCA1/2 only and 12% multigene panel testing, with no differences in test type by pre-test risk or race/ethnicity. Among all patients, 7% had a pathogenic mutation and 14% had a VUS in any gene. Patients at high pre-test risk had a lower ratio of uninformative VUS to informative pathogenic mutations (14%/10%) than average risk patients (15%/4%, p<0.001). There was a substantially higher ratio of VUS to pathogenic mutation among African Americans (22%/7%) and Asians (23%/3%) than other racial/ethnic groups (12%/8%, p<0.001). Conclusions: In a large, diverse, contemporary sample of early-stage breast cancer patients accrued from population-based registries and linked to clinical laboratory data, one-quarter had genetic testing, with multigene panels markedly replacing BRCA1/2-only tests over time. The ratio of uninformative VUS to informative pathogenic mutation results was lowest in women at high pre-test risk and highest among racial/ethnic minorities. These findings can inform genetic counseling and they emphasize the urgent need to re-classify VUS results in racial/ethnic minorities. More research is needed to determine the impact of this marked increased in multigene panel testing on patient experiences, and the impact of test results on treatment decision-making and outcomes. Citation Format: Kurian AW, Katz SJ. Trends and results of BRCA1/2 and multigene panel testing in newly diagnosed breast cancer patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-06-07.

424P - Cancer worry, genetic knowledge, and attitudes towards NGS multigene panel testing among Korean breast cancer patients

Multiple primary tumors (MPTs) are a harbinger of hereditary cancer syndromes. Affected individuals often fit genetic testing criteria for a number of hereditary cancer genes and undergo multigene panel testing. Other genomictesting options, such as whole exome (WES) and whole genome sequencing (WGS) are available, but the utility of these genomic approaches as a second-tier test for those with uninformative multigene panel testing has not been explored.Here, we report our germline sequencing results from WGS in 9 patients with MPTs who had non-informative multigene panel testing. Following germline WGS, sequence (agnostic or 735 selected genes) and copy number variant (CNV) analysis was performed according to the American College of Medical Genetics (ACMG) standards and guidelines for interpreting sequence variants and reporting CNVs.In this cohort, WGS, as a second-tier test, did not identify additional pathogenic or likely pathogenic variants in cancer predisposition genes. Although we identified aCHEK2likely pathogenic variant and a MUTYHpathogenic variant, both were previously identified in the multigene panels and were not explanatory for the presented type of tumors. CNV analysis also failed to identify any pathogenic or likely pathogenic variants in cancer predisposition genes.In summary, after multigene panel testing, WGS did not reveal any additional pathogenic variants in patients with MPTs. Our study, based on a small cohort of patients with MPT, suggests that germline gene panel testing may be sufficient to investigate these cases. Future studies with larger sample sizes may further elucidate the additional utility of WGS in MPTs.

As sequencing technology and information of the genomic causes for cancer development expand, multi-gene panel testing for hereditary cancer is increasing in clinical practice. In this chapter, we reviewed the application of multi-gene panel with pre-/post- testing considerations and summarized genetic counseling based on panel testing results in clinical field. In addition, we introduce multi-gene panel for hereditary cancer developed in Seoul National University Hospital.