Identification Of Germline Mutations Research Articles

Abstract PO2-08-11: The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours

Abstract Background: Identification of germline mutations in hereditary breast cancer (HBC) genes can have profound benefits in the treatment of breast cancer (BC) and manging risk for patient and the family. In addition, sequencing of the tumours can reveal clinically relevant somatic features, such as homologous recombination deficiency (HRD) and mutational signatures, that can guide treatment which are not discernible by germline sequencing alone. We hypothesised that current standard of care where women diagnosed with BC are not routinely offered tumour sequencing is suboptimal as fails to exploit all therapeutic vulnerabilities which can be exploited in the treatment of BC. The MAGIC study is the first prospective trial in Australia of unselected invasive BCs in general oncology practice combining both germline and tumour sequencing. Methods: The MAGIC study included a total of 651 consecutive consented patients presenting with non-metastatic BC between June 2020 to March 2023. It included invasive BC, high-grade DCIS and pleomorphic LCIS. The sequencing was conducted in two phases; for phase one, 157 cases underwent whole genome sequencing (WGS) on both germline and matched BC DNA while for phase two, 494 cases underwent only germline whole exome sequencing. Germline variants were interrogated for pathogenic variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, BARD1, BRIP1, RAD51B, RAD51C, RAD51D, MLH1, MSH2, MSH6, PMS2, CDH1, PTEN, STK11, TP53 and NTHL1. Tumour homologous recombination (HR) repair deficiency was calculated using HRDetect (Nat Med 2017;23:517). For BCs showing a high HRDetect score ( >0.75) all HBC gene promoter CpG islands were assessed for hypermethylation using the Twist NGS Methylation system. Mutational signatures were calculated from somatic mutations identified from whole genome sequenced BCs using the DeconstructSig package in R (Genome Biol. 2016;17:31) and referenced against the COSMIC v2 signature catalogue. Results: Actionable germline variants in any HBC gene were identified in 7.7% of cases (7.8% of invasive and 6.1% of in situ BC) with 5.2% having an actionable mutation in an HR pathway gene (BRCA1, BRCA2, PALB2 and RAD51C). Most cases with pathogenic variants showed bi-allelic inactivation in the tumour. All BRCA1, BRCA2 and PALB2 tumours showed high HRDetect and/or HRD scores consistent with loss of HR repair function, indicating them to be the underlying hereditary driver of the BC. One BC with a pathogenic PMS2 variant showed retention of the wild-type allele with no evidence of a mismatch repair mutational signature suggesting PMS2 was not the driver of this BC. Of the 157 BC in phase one that underwent WGS and did not have a germline pathogenic HBC gene variant, 16% (18/117 invasive and 3/13 DCIS) had an HRDetect score of >0.7 indicative of a homologous recombination repair defect and therefore biologically a “BRCA-like” tumour. Of these 21 BRCA-like cases, only 3 invasive BCs had clear somatic bi-allelic inactivation of an HBC gene that could explain the high HRDetect score (2 BRCA1 and 1 BRCA2). One of the 21 BRCA-like cases had a germline variant of unknown significance (VUS) in an HBC gene (a BRCA2 missense variant in an ER+ tumour. The tumour showed loss of the wild-type allele). Of the BRCA-like cases, 71% were ER positive which included 3 invasive lobular cancers. Conclusion: Tumour sequencing identified three times as many cases that might be eligible for HR repair defect targeted therapy than germline testing alone (16% versus 5.2%). Unlike a previous study (Ann Oncol., 2019 30:1071-1079), the majority of the BRCA-like BCs were ER+ with no evidence of a VUS in a known HBC gene suggesting these are driven by novel germline or somatic mutations in genes involved in DNA HR repair. Citation Format: Ian Campbell, Lisa Devereux, Kirsten Hogg, Luxi Lal, Michelle Sinclair, Lesley Stafford, Magnus Zethoven, Anita Skandarajah, Paul James, Geoffrey Lindeman, Bruce Mann, Dilanka De Silva. The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-08-11.

Familial Medullary Thyroid Cancer: Five-year Review of the Most Frequent Mutations in the RET Gene: An Update

Background: Familial Medullary Thyroid Cancer (FMTC) is hereditary in 25% of cases. Patients with an inherited form of FMTC usually have a germline mutation in the RET proto-oncogene (10q11.2); these mutations generally occur in exons 10 (codons 618 and 620) and 11 (codons 630, 631, and 634).
 Methods: A narrative review of articles focused on the pathology of familial medullary thyroid cancer was carried out using the next databases PubMed, ScienceDirect, BMC, Springer, Frontiers, PMC, Wiley Online Library, Cold Spring Harbor and ELSEVIER. This search was carried out between August and September 2021.
 Results: 19 studies were selected in which the following mutations were found: five studies (26.31%) reported mutation in exon 10; three studies (15.78%) in exon 11; three studies in exon 13 (one of them associated with a rare mutation in exon 7) (10.52% plus 5.26%); three studies (15.78%) in exon 14; two studies (10.52%) in exon 15; two (10.52%) in exon 16; and one (5.26%) rare FMTC NO RET. The two most frequent mutations were in codons 620 of exon 10 and 804 of exon 14.
 Conclusion: The findings of this review are consistent with the medical literature, finding the most common RET mutations in exon 10 and codon 620. It is essential that in patients with a presumptive diagnosis, genetic studies (identification of germline mutations in the RET proto-oncogene, located on chromosome 10q11.2) be performed.

Identification of Germline Mutations in East-Asian Young Never-Smokers with Lung Adenocarcinoma by Whole-Exome Sequencing.

The online version contains supplementary material available at 10.1007/s43657-022-00062-1.

TBIO-12. Screening for Cancer Predisposition Syndromes in Pediatric Neuro-Oncology Patients: a Single Institution Experience

BACKGROUND: Traditional screening for cancer predisposition syndromes centers on family history, phenotypic features, and tumor histology. With expanded accessibility of next generation sequencing, identification of de novo germline mutations is increasing and the predictive value of family history has become less clear. While identification of germline mutations often affects care of pediatric neuro-oncology patients, germline sequencing is not currently standard of care. We hypothesize that routine screening for germline mutations in pediatric neuro-oncology patients reveals unsuspected cancer predisposition syndromes and impacts care. METHODS: A retrospective analysis was performed on pediatric neuro-oncology patients at a single institution who had targeted next generation sequencing of approximately 500-cancer associated genes (UCSF500) on tumor and paired germline DNA. We determined the proportion of patients with germline mutations and assessed impact on future screening and current tumor treatment. We interrogated clinical notes, family history, and interviewed treating physicians to determine if predispositions were previously suspected. RESULTS: Between June 2015-December 2019, 187 patients had paired testing; of these 29 (16%) harbored germlines mutations that were pathogenic or likely pathogenic. Germline mutations were found in patients with high-grade glioma (n=12), low-grade glioma (n=7), medulloblastoma (n=4), ATRT (n=2), and choroid plexus papilloma (n=1). Known cancer predisposition syndromes were identified or confirmed in 18 patients. Of these, the most common alterations were in TP53 (n=6), CHEK2 (2), NF1 (n=2), SMARCB1 (n=2), and PTEN (n=2). Patients were referred to genetic counseling in 26 cases and malignancy screenings were implemented in 25 cases. Germline findings affected malignancy treatment in 10 cases, most often through use of targeted therapeutics or avoidance of radiation. CONCLUSIONS: In our series, we found that 16% of pediatric neuro-oncology patients harbored germline mutations, the majority of which were associated with cancer predisposition syndromes. These results support standardizing screening for pathogenic germline mutations in pediatric neuro-oncology patients.

Clinical utility of widespread germline testing of cancer patients in a diverse community cancer clinic.

e18537 Background: Identification of germline mutations can determine prognosis, inform targeted therapies, allow risk-reducing interventions, and suggest additional cancer screenings in patients and their biological relatives. Large prospective cohort studies have been historically skewed towards wealthier socioeconomic populations that lack ethnic diversity and vastly underrepresent African Americans. Recently, small studies outside of standard clinical guidelines reveal detection of pathogenic variants in germline testing with significant clinical ramifications. We present our single center experience of prospective germline testing in a small community clinic in suburban and rural South Carolina with understudied real-world populations. Methods: We performed germline testing, outside of guidelines, in patients presenting at earlier age or with either rare tumors, or recurrent/multiple malignancies. This prospective, observational cohort included a suburban and rural underserved population where approximately 30% identify as African American. Patients were counselled about testing that performed outside of guidelines. Results: We identified 67 individuals outside the guidelines concordance, compromising of 45 male and 22 female patients, within the first 6 months of this prospective, observational cohort. Patients reported race as African American (14), White (50), or Asian American (3). Rare germline findings included Li Fraumeni syndrome, Fanconi’s syndrome, Perelman’s disease, and Von Hippel Lindau’s disease. We summarize our findings in the attached table. Conclusions: There are limited studies that report prevalence of germline findings in cancer patients who are unselected by clinical practice guidelines. Studies also lack representation of ethnic minorities. Recently published data on the clinical utility of broad-based germline testing of all incoming patients suggest current practice of guidelines and genetic counselor recommended testing should be re-examined for broader testing for all incoming cancer patients in a more inclusive manner.[Table: see text]

Identification of Germline Mutations in Genes Involved in Classic FAP in Patients from Northern Brazil.

Colorectal cancer is a common cancer worldwide, with 5-10% of cases being hereditary. Familial adenomatous polyposis syndrome (FAP) is caused by germline mutations in the APC gene or rarely in the MUTYH gene. This work did not identify germline mutations in the MUTYH, NTHL1, POLD1 and POLE genes in 15 individuals belonging to five families with classic FAP, who had the mutation in the APC gene confirmed in a previous study. Our results support mutations in the APC gene as the main genetic contribution of classical FAP with severe phenotype. In the family that had the most aggressive form of the disease, we performed an array-based Comparative Genomic Hybridization analysis and identified the germinal loss of an allele of the NOTCH2 and BMPR2 genes in the mother (proband) and daughter. In order to validate the involvement of these genes in the other four families of this study, we analyzed the DNA copy number variation in the peripheral blood of the 15 participants. FAP is a syndrome with considerable genetic and phenotypic heterogeneity and this phenomenon may explain the presence of secondary genetic alterations, such as the allelic loss of NOTCH2 and BMPR2 genes, found only in one family in this study. The CNV analysis confirmed that only the two members of the FAP2 family (patient 02H and 02F) had a deletion of these two genes, as the aCGH methodology had found. The other study participants did not show allelic loss for these two genes. Validation in a larger number of families could confirm the presence of these new genetic alterations in classic FAP and improve understanding of the different types of aggressiveness of the disease.

Identification of Germline Mutations in Upper Tract Urothelial Carcinoma With Suspected Lynch Syndrome

ObjectiveWhole-exon sequencing (WES) is a commercially available tool for hereditary disease testing. However, little is known about hereditary upper-tract urothelial carcinoma (UTUC) in the Chinese population. This study aims to investigate the prevalence of Lynch syndrome (LS) in UTUC patients with high-risk features and identify the germline mutations of genetic predisposition gene mutations in those patients.MethodsIn total, 354 consecutive UTUC patients undergoing surgery were universally recruited, of whom 108 patients under 60 years old or with a personal/family history of cancer underwent universal immunohistochemistry staining to detect the expression of mismatch repair (MMR) proteins (MLH1, MSH2, MSH6 and PMS2). Patients with deficient or weak MMR protein staining or meeting the Amsterdam II criterion were defined as suspected LS patients, who further experienced microsatellite instability (MSI) (BAT25, BAT26, BAT40, D2S123, D5S346, D17S250) detection and performed WES analysis to explore germline pathogenic/likely pathogenic (P/LP) alterations.ResultsOf 108 patients, 90 (83.3%) cases were included due to younger than 60 years, and 18 cases due to personal/family history. IHC staining identified 21 patients with deficient MMR protein staining and 15 cases with weak MMR protein staining. Three cases met the Amsterdam II criterion but with proficient MMR protein staining. Finally, WES analysis was performed in 38 suspected LS patients and P/LP germline mutations were identified in 22 individuals. Genetic testing confirmed 5 LS cases, including 3 cases with novel mutations. MSI-harboring tumor was discovered in 4 LS cases, one of whom had weak MMR protein staining. Germline P/LP variants in DNA damage repair genes were found in 11 cases. In addition, we found that 11 patients had high- or moderate- penetrance P/LP mutations other than MMR genes. The common P/LP variants in high- or moderate-penetrance genes were 4 in ATM, 3 in MSH6 and KIT, and 2 in APC, NF1 and DICER.ConclusionsWe identified approximately 11% of UTUC cases as suspected LS and at least 1.4% patients with confirmed LS-associated UTUC. In addition, broader germline genetic testing could be considered to screen for cancer severity in hereditary UTUC patients.

Germline mutations in Black women with ovarian, fallopian tube and primary peritoneal carcinomas

Routine genetic testing for ovarian cancer and identification of germline mutations can help improve early detection of cancer as well as guide treatment. Knowledge of genetic counseling and referral rates for genetic testing has been lower for Black women, compared to Caucasian women. We aimed to describe the demographics and presence of germline mutations in Black women with ovarian, fallopian tube or peritoneal carcinoma at two large academic institutions.

P70.05 Identification of Germline Mutations in Young Never Smokers With Lung Adenocarcinoma by Whole Exome Sequencing

Recently, an increasing number of young never-smokers were diagnosed with lung cancer. Although environmental risk factors such as second-hand smoke, radon, and indoor air pollutants might cause never-smoking lung cancer, a large proportion of these patients do not have a definite association with established environmental risk factors. The aim of this study was to investigate the genetic predisposition of lung cancer in these patients and discover candidate pathogenic variants for lung adenocarcinoma in young never-smokers.

Monogenic Epilepsies: Disease Mechanisms, Clinical Phenotypes, and Targeted Therapies.

A monogenic etiology can be identified in up to 40% of people with severe epilepsy. To address earlier and more appropriate treatment strategies, clinicians are required to know the implications that specific genetic causes might have on pathophysiology, natural history, comorbidities, and treatment choices. In this narrative review, we summarize concepts on the genetic epilepsies based on the underlying pathophysiologic mechanisms and present the current knowledge on treatment options based on evidence provided by controlled trials or studies with lower classification of evidence. Overall, evidence robust enough to guide antiseizure medication (ASM) choices in genetic epilepsies remains limited to the more frequent conditions for which controlled trials and observational studies have been possible. Most monogenic disorders are very rare and ASM choices for them are still based on inferences drawn from observational studies and early, often anecdotal, experiences with precision therapies. Precision medicine remains applicable to only a narrow number of patients with monogenic epilepsies and may target only part of the actual functional defects. Phenotypic heterogeneity is remarkable, and some genetic mutations activate epileptogenesis through their developmental effects, which may not be reversed postnatally. Other genes seem to have pure functional consequences on excitability, acting through either loss- or gain-of-function effects, and these may have opposite treatment implications. In addition, the functional consequences of missense mutations may be difficult to predict, making precision treatment approaches considerably more complex than estimated by deterministic interpretations. Knowledge of genetic etiologies can influence the approach to surgical treatment of focal epilepsies. Identification of germline mutations in specific genes contraindicates surgery while mutations in other genes do not. Identification, quantification, and functional characterization of specific somatic mutations before surgery using CSF liquid biopsy or after surgery in brain specimens will likely be integrated in planning surgical strategies and reintervention after a first unsuccessful surgery as initial evidence suggests that mutational load may correlate with the epileptogenic zone. Promising future directions include gene manipulation by DNA or mRNA targeting; although most are still far from clinical use, some are in early phase clinical development.

Germline mutations in Black patients with ovarian, fallopian tube and primary peritoneal carcinomas

ObjectiveRoutine genetic testing for ovarian cancer and identification of germline mutations can help improve early detection of cancer as well as guide treatment. Knowledge of genetic counseling and referral rates for genetic testing has been lower for Black patients, compared to White patients. We aimed to describe the demographics and presence of germline mutations in Black individuals with ovarian, fallopian tube or peritoneal carcinoma at two large academic institutions. MethodsFifty-one Black patients with invasive epithelial ovarian, fallopian tube, or primary peritoneal carcinoma were identified via institutional tissue banks over a 20-year time-period. Germline DNA was sequenced using BROCA, a targeted capture and parallel sequencing assay that identified pathogenic germline mutations in ovarian carcinoma susceptibility genes. ResultsGermline mutations in ovarian cancer susceptibility genes were found in 25.5% of women, most commonly BRCA1 and BRCA2. This mutation frequency mirrors those previously described among predominantly White populations. Our data suggests there may be an advantage in survival among those with germline mutations, although this was not statistically significant. ConclusionsGiven similar frequencies of germline mutations between Black and White patients with ovarian cancer, we conclude that there are not major differences in the genetic predisposition to ovarian carcinoma. Equitable access to genomic advancements including germline and tumor sequencing would facilitate equal access to PARP inhibitors, the standard of care for patients with BRCA mutated advanced ovarian cancer.

Germline mutations in RAD51C and RAD51D and hereditary predisposition to ovarian cancer.

Ovarian cancer is one of the most common gynecologic cancers with the highest mortality rate over a long period. Genetic predisposition to ovarian cancer is unusually high. In the Czech Republic, causal mutation in any ovarian cancer predisposition gene is identified in approximately 30% of the ovarian cancer patients. Therefore, according to the current guidelines, all ovarian cancer patients should be provided with genetic testing. The BRCA1 and BRCA2 are the two major ovarian cancer predisposition genes. Nevertheless, mutations in other predisposition genes, including RAD51C and RAD51D, are associated with high ovarian cancer risk. Mutations in RAD51C and RAD51D are found in 1% of ovarian cancer patients in each respective gene. Currently, identification of germline mutation in RAD51C and RAD51D is primarily of preventive importance but it potentially could make a prognostic difference. The aim of this review is to summarize the recent RAD51C and RAD51D knowledge, including the biological function, cancer risks associated with germline mutations, and recommendations for mutation carriers.

Abstract PO-034: A collaborative approach to increase germline testing and counseling uptake within New York City’s underserved patient population

Abstract Background: Understanding the role of genetic drivers in cancer is a fundamental component of precision medicine. Further, identification of germline mutations provides important clinical data for patients. Understanding the risk conferred by inheriting certain mutations can guide treatment and screening behaviors for both patients and their family members. Despite the importance of testing, minority patients are less likely to undergo germline testing. Patient and physician reported barriers include limited or no knowledge of genetic tests, limited knowledge of hereditary cancer syndromes, lack of educational materials, time constraints, lack of genetic counselors, and out-of-pocket costs. Objective: To describe how an academic-community collaboration between local healthcare institutions addresses some known barriers to germline testing and counseling in a typically underrepresented patient population. Methods: The Cancer Health Equity Research Program (CHERP) at Memorial Sloan Kettering (MSK) partners with local community hospitals, which serve diverse populations, to provide somatic and germline testing to their cancer patients under the research protocol, MSK-IMPACT™ (Integrated Mutation Profiling of Actionable Cancer Targets). Testing and counseling are provided by the Center for Molecular Oncology and Clinical Genetics Service at MSK. Site clinicians are trained on study procedures to ensure they are prepared to educate their patients on the purpose of genetic testing. Non-clinical MSK research staff (NCMRS) are trained as consenting professionals and delegated to a site to address clinic time constraints. NCMRS facilitate the collection, shipment, and tracking of biospecimens and collaborate with MSK’s Clinical Genetics Service on behalf of the sites. To address both educational and language barriers, a subtitled video on germline testing, translated informed consents, and translated educational brochures are provided to each site. Results: Since March 2018, 270 patients from our CHERP sites agreed to germline testing. Self-reported race is as follows: 35 Asian (13.0%), 123 Black (45.6%), 25 Caucasian (9.3%), 1 Pacific Islander (0.4%), 11 Other (4.1%), and 75 Unknown (27.8%). Additionally, 99 (36.7%) patients identified as Hispanic and Hispanics represent 90.7% of self-reported Unknown race and 100% of the self-reported Other race. Of the 270 patients, 201 have had successful germline testing (62 patients ineligible and 7 pending results) with 26 (12.9%) having a positive finding. Genetic counseling was provided for 17 (65.4%) of these patients, with 6 sessions in-person and 11 telegenetic sessions. Conclusion: Disparities in genetic testing are well documented and efforts to expand access to testing and counseling for minority patients are urgently needed. In partnership with local hospitals, CHERP addresses many of the barriers that contribute to these disparities and demonstrated success in providing germline testing and counseling for minority patients. Citation Format: Kenya P. Vado, Thomas Reynolds, Kellie Jack, Linda Bulone, Margaret Kemeny, Jason Gonsky, Lewis Kampel, Shadai Mcmillan, Anna Maio, Margaret Sheehan, Erin Salo-Mullen, Sandy Naupari, Jesse Galle, Alisha Williams, Zsofia Stadler, Mark Robson, David Solit, Paul Sabbatini, Carol Brown. A collaborative approach to increase germline testing and counseling uptake within New York City’s underserved patient population [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-034.

Identification of Germline Mutations in Melanoma Patients with Early Onset, Double Primary Tumors, or Family Cancer History by NGS Analysis of 217 Genes.

Cutaneous melanoma is the deadliest skin malignity with a rising prevalence worldwide. Patients carrying germline mutations in melanoma-susceptibility genes face an increased risk of melanoma and other cancers. To assess the spectrum of germline variants, we analyzed 264 Czech melanoma patients indicated for testing due to early melanoma (at <25 years) or the presence of multiple primary melanoma/melanoma and other cancer in their personal and/or family history. All patients were analyzed by panel next-generation sequencing targeting 217 genes in four groups: high-to-moderate melanoma risk genes, low melanoma risk genes, cancer syndrome genes, and other genes with an uncertain melanoma risk. Population frequencies were assessed in 1479 population-matched controls. Selected POT1 and CHEK2 variants were characterized by functional assays. Mutations in clinically relevant genes were significantly more frequent in melanoma patients than in controls (31/264; 11.7% vs. 58/1479; 3.9%; p = 2.0 × 10−6). A total of 9 patients (3.4%) carried mutations in high-to-moderate melanoma risk genes (CDKN2A, POT1, ACD) and 22 (8.3%) patients in other cancer syndrome genes (NBN, BRCA1/2, CHEK2, ATM, WRN, RB1). Mutations in high-to-moderate melanoma risk genes (OR = 52.2; 95%CI 6.6–413.1; p = 3.2 × 10−7) and in other cancer syndrome genes (OR = 2.3; 95%CI 1.4–3.8; p = 0.003) were significantly associated with melanoma risk. We found an increased potential to carry these mutations (OR = 2.9; 95%CI 1.2–6.8) in patients with double primary melanoma, melanoma and other primary cancer, but not in patients with early age at onset. The analysis revealed affected genes in Czech melanoma patients and identified individuals who may benefit from genetic testing and future surveillance management of mutation carriers.

MP09-03 GERMLINE MUTATIONS IN HIGH RISK PROSTATE CANCER PATIENTS

INTRODUCTION AND OBJECTIVE:Genetic testing is an integral guideline-directed component of prostate cancer care. We summarize our experience with identification of germline mutations in men at a ter...

Clinical Utility of Next-Generation Sequencing in Acute Myeloid Leukemia.

Acute myeloid leukemia (AML) is a genetically heterogeneous disease that, even with current advancements in therapy, continues to have a poor prognosis. Recurrent somatic mutations have been identified in a core set of pathogenic genes including FLT3 (25-30% prevalence), NPM1 (25-30%), DNMT3A (25-30%), IDH1/2 (5-15%), and TET2 (5-15%), with direct diagnostic, prognostic, and targeted therapeutic implications. Advances in the understanding of the complex mechanisms of AML leukemogenesis have led to the development and recent US Food and Drug Administration (FDA) approval of several targeted therapies: midostaurin and gilteritinib targeting activated FLT3, and ivosidenib and enasidenib targeting mutated IDH1/2. Several additional drug candidates targeting other recurrently mutated gene pathways in AML are also being actively developed. Furthermore, outside of the realm of predicting responses to targeted therapies, many other mutated genes, which comprise the so-called long tail of oncogenic drivers in AML, have been shown to provide clinically useful diagnostic and prognostic information for AML patients. Many of these recurrently mutated genes have also been shown to be excellent biomarkers for post-treatment minimal residual disease (MRD) monitoring for assessing treatment response and predicting future relapse. In addition, the identification of germline mutations in a set of genes predisposing to myeloid malignancies may directly inform treatment decisions (particularly stem cell transplantation) and impact other family members. Recent advances in sequencing technology have made it practically and economically feasible to evaluate many genes simultaneously using next-generation sequencing (NGS). Mutation screening with NGS panels has been recommended by national and international professional guidelines as the standard of care for AML patients. NGS-based detection of the heterogeneous genes commonly mutated in AML has practical clinical utility for disease diagnosis, prognosis, prediction of targeted therapy response, and MRD monitoring.

Familial Clustering of Hematological Malignancies: Harbingers of Wider Germline Cancer Susceptibility

Introduction. The Australian Familial Haematological Cancer Study (AFHCS) was founded in 2004 when only one familial haematological malignancy (FHM) gene was known, RUNX1 causing thrombocytopenia and predominantly an MDS/AML HM phenotype. Today, there are over a dozen known FHM genes, mostly characterized as predisposing to myeloid malignancies. Within our AFHCS cohort of over 200 families, this is also true with a significant proportion of families with predisposition to myeloid malignancies solved with our identification of germline mutations in genes such as GATA2, RUNX1,CEBPA and DDX41. In contrast the majority of unsolved families have a predominance of lymphoid malignancies, most commonly non-Hodgkin lymphoma and chronic lymphocytic leukaemia. In several of these families we have found known pathogenic mutations in genes involved in regulation of the homologous recombination (HR) DNA damage repair (DDR) pathway (e.g. BRCA2 Y1710fs* and PALB2 K142*) that are previously characterised with regard to their known solid tumour predisposition. In the AFHCS families with these mutations we observe a mixture of hematological tumors of mostly lymphoid origin as well as non-hematological tumours. This led us to hypothesise that there is a subset of families for which the predisposition to malignancy includes a spectrum of different malignancies, i.e. pan-cancer predisposition. Further, we hypothesise that these are associated with mutations in genes with roles in HR DNA repair. In light of this we undertook a review of the phenotypic and genetic characteristics of families in our AFHCS cohort. Methods. Malignancy phenotype data, with regard to the different tumor types observed in each AFHCS family was annotated and aggregated. Covariance matrix analysis was then used to compare the number of times different tumor types were observed occurring together in a family pedigree. Genetic data: we curated whole exome sequence data for damaging mutations in genes with a known role in HR DNA damage repair. Results. A phenotype review of our cohort found 52% of assessable FHM families also had multiple types of solid tumour and/or individuals with diagnosis of multiple malignancies, indicative of a 'pan-cancer' phenotype. Covariance analysis showed that Hodgkin and non-Hodgkin lymphoma most often occurred together and also co-occurred with non-HM tumors breast, melanoma, colorectal, prostate and ovarian subtypes, implying a possible shared genetic etiology (Figure 1A). Assessment of AFHCS families for mutations in DDR genes including DNA repair (e.g. FANC/BRCA pathway genes) and chromosome cohesion (RAD21 and related) identified 18 variants segregating with malignancy including 5 frameshift or stopgain mutations. These high impact mutations included genes previously characterised in the context of autosomal recessive predisposition to hematological malignancy such as PALB2/BRCA2 family (Fanconi Anemia, see Figure 1B), NBN1 (Nijmegen Breakage Syndrome), DDX11 (Warsaw Syndrome) and others. A further 18 variants segregated in families where pan-cancer status is still under investigation. Conclusions. Phenotypic and genetic analysis of unsolved HM predisposed families have identified that familial clustering of lymphoma in actuality identifies families with pan-cancer germline genetic susceptibility, characterised by mutations in DNA damage response genes. Collectively these mutations may have a significant impact on our understanding of germline cancer predisposition, a finding supported by recent genetic population studies on sporadic cohorts, including pediatric cancer cohorts, opening the door for the application of rational therapies as evidenced by the BRCA/PARP inhibitor paradigm. However, as each individual gene mutation is rare, international collaborative studies will be essential for accurate measurements of risk and prognostication to assist individuals in the clinic. Disclosures Branford: Novartis: Consultancy, Honoraria, Research Funding, Speakers Bureau; Bristol-Myers Squibb: Honoraria, Speakers Bureau; Qiagen: Consultancy, Honoraria; Cepheid: Consultancy, Honoraria. Scott:Celgene: Honoraria.

Abstract 621: Germline testing in African American women with invasive breast cancer

Abstract Background: Although African ancestry is not included in the NCCN guidelines for identifying women with invasive breast cancer who may benefit from genetic testing, African American women (AAW) are at increased risk of being diagnosed at a young age and/or with triple negative breast cancer, both factors that do meet NCCN criteria for genetic testing. Because AAW represent a frequently underserved population, we evaluated the utilization and results of germline testing of cancer predisposition genes in AAW with invasive breast cancer. Methods: 546 self-described AAW with invasive breast cancer enrolled in the Clinical Breast Care Project from 2001-2017). Eligibility status for genetic testing was assessed using the NCCN guidelines version 1.2019. In patients without clinical panel testing performed and with an available genomic DNA sample, targeted sequencing across 94 cancer predisposition genes was performed. Variants were classified as pathogenic, likely pathogenic, uncertain significance (VUS), likely benign or benign using ClinVar. Results: 60% of the patients were eligible for genetic testing of which 37% of underwent clinical testing. Within the high-risk women who pursued clinical testing, the mutation frequency was 13% and included mutations in ATM (n=2), BRCA1 (n=7), BRCA2 (n=5) and TP53 (n=1). High-risk women who were tested only in the research setting had a mutation frequency of 9% including BRCA1 (n=2) and BRCA2 (n=2) and single carriers of mutations in BLM, CHEK2, MLH1, MUTYH, PALB2, PMS2 and RECQL4. Within the 111 women who did not meet NCCN criteria, the mutation frequency was 5% with mutations in BRCA2 (n=3), PMS2 (n=1), SBHD (n=1) and TSC2 (n=1). Six women had previously unreported variants in BRCA1, BRCA2, TP53, ALK and RB1 and 29% of the women had VUS in genes including BRCA1 and BRCA2. Conclusions: Under current NCCN guidelines, the majority of AAW with invasive breast cancer were eligible for genetic testing; however, translating eligibility into pursuit of germline testing remains a challenge. For example, 33% of the high-risk women underwent clinical testing and 40% of the mutation carriers within the high-risk group were detected in the research setting. Furthermore, 5% of low-risk women, not currently eligible for genetic testing, were mutation carriers. In addition, while the majority (66%) of mutations detected were in BRCA1 or BRCA2, multi-gene testing allowed for an additional 50% of mutation carriers to be identified. Because identification of germline mutations may alter patient management and prevent secondary cancers, it is critical to identify and address barriers, such as evolving NCCN guidelines, cost, and patient preference, to testing and optimize the selection of AAW for genetic testing. The views expressed in this abstract are those of the author and do not reflect the official policy of the Department of Army/Navy/Air Force, Department of Defense, or U.S. Government. Citation Format: Leann A. Lovejoy, Seth K. Rummel, Craig D. Shriver, Rachel E. Ellsworth. Germline testing in African American women with invasive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 621.

Abstract 4227: Salvage genetic testing on buccal swab samples using liquid in situ amplification identifies genetic mutations from previous test failures

Abstract Background: NCCN guidelines version 2.2019 address BRCA1/2 testing for men with a personal history of prostate cancer limited to Gleason ≥7 and specific family history features. Inherited genetic mutations have been identified in up to 12% of metastatic prostate cancer, primarily in DNA repair genes. Here we report liquid in situ amplification (LISA) technique followed by hereditary testing on buccal swab samples that had previously failed to yield a genetic testing result. Methods: Previously failed buccal swab samples from another CLIA-certified laboratory were re-prepared using LISA. Qubit quantification following LISA revealed goodDNA concentrations even for these poor-quality swab samples ranging from 5 to 70 ng/uL, which is sufficient for next-generation sequencing analysis (NGS). Coding regions of ATM, BRCA1, BRCA2, CHEK2, PALB2, and RAD51D genes were amplified by a panel of specific primer pools followed by massively parallel sequencing for the identification of germline mutations. Minimal sequencing coverage was set as 50X, and pathogenic, likely pathogenic, and variants of unknown significance (VUS) were classified and reported. Results: Buccal swab samples from 29 men with at least intermediate-risk prostate cancer were received as low-yield, low-quality DNA (n=12), pre-cut swabs in preservation solution (n=6), and aged swab samples (n=11). LISA and subsequent NGS testing was able to salvage results for 24/29 (82.8%) (failed samples included 4 aged swab and 1 pre-cut swab). 1 patient had a pathogenic BRCA1 mutation (c.4309delT) and 3 patients had VUS (BRCA1 c.4776C&amp;gt;G, BRCA1 c.1846_1848delTCT, and RAD51D c.268G&amp;gt;A). The remaining 20/29 (69.0%) samples have either benign or likely benign variants. Conclusions: LISA applied to these previously failed samples was able to salvage results for over 80% of cases, including the identification of a pathogenic BRCA1 mutation which led cascade hereditary testing for immediate family members. It also provided confirmation for nearly 70% of cases about the absence of hereditary risk for the genes on the panel. Citation Format: Glen J. Weiss, Andrew Ford, Charmaine Brown, Elizabeth Caver, Matthew Vallejo, Claribel Adeyemi, Forrest Collins, Chen-Hsiung Yeh. Salvage genetic testing on buccal swab samples using liquid in situ amplification identifies genetic mutations from previous test failures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4227.

Low likelihood that potential germline findings identified during somatic tumor testing are evaluated: Room for improvement.

e13037 Background: Genomic testing, useful for treatment planning, may indicate the presence of a germline mutation. We evaluate the incidence of potentially actionable germline mutations detected via genomic testing and determined rates of follow-up referrals for genetic counseling and germline testing among patients with potential germline mutations. Methods: This was a retrospective chart review of patients who underwent genomic testing at The University of Vermont Cancer Center (UVMCC). Test reports were reviewed for mutations in 24 genes associated with hereditary cancer and recognized as clinically actionable by the American College of Medical Genetics. Medical record review was performed to identify patients referred for genetic counseling and results of germline testing. Results: Between 8/2009 and 9/2016 157 patients underwent genomic testing at UVMCC. Eighty-one percent (127/157) had a mutation in ≥ 1 gene associated with hereditary cancer (range 0-4 mutations per patient), and 46% (73/157) had mutations in more than one gene. Potential germline mutations were most commonly identified in TP53, CDKN2A, RB1, PTEN, STK11 and APC (each with mutations in &gt; 10% of patients). To date only 12% (15/127) of patients with potential germline mutations have been referred for genetic counseling. Two were referred for evaluation of findings seen on genomic testing others being referred for personal or family history of cancer. The majority (11/15) of referred patients have undergone genetic testing with 27% (3/11) having germline mutations identified; 2/3 of which were also identified on genomic testing. Conclusions: Genomic testing can be an important tool for identifying hereditary cancer syndromes. While the majority (81%) of patient’s undergoing genomic testing had mutations genes associated with hereditary cancer, the low rate of referral (12%) for genetic counseling to determine if these are truly germline represents a significant missed opportunity. Identification of germline mutations has implications for both the patient (for treatment and risk of second cancers) and their family. Patients and their providers should be aware of the potential for germline findings when genomic testing is performed.