Multiple-gene Panel Research Articles

A Chinese family affected by lynch syndrome caused by MLH1 mutation

BackgroundLynch syndrome (LS) is caused by mutations in DNA mismatch repair (MMR) genes, which accounts for 3–5% of colorectal cancer. The risks of several types of cancer are greatly increased among individuals with LS. In this study, 4 members of a Chinese family with a MLH1 pathogenic variant, resulting in colonic carcinoma, was reported.Case presentationA 52-year-old colon cancer female was brought to us with a family history of colon cancer. Genetic counseling traced 4 members in her family with colon cancer (mother and 3 siblings including the proband) as well as other cancer types. Next generation sequencing (NGS) with a multiple gene panel including MMR genes showed a germline mutation in MLH1 (c.1852_1854delAAG, p.K618del) in all 3 affected family members and confirmed the diagnosis of Lynch syndrome. In addition, this mutation was also identified in a asymptomatic offspring, who was then recommended to a prophylactic measure against cancer. A personalized health care plan was implemented for monitoring the condition and progression of the affected individuals.ConclusionBased on public database searching followed by pedigree verification, p.K618del variant in MLH1 is a pathogenic mutation, which supported the diagnosis of LS. This case highlights the importance of diagnosis and management in patients with hereditary cancer syndromes, particularly for asymptomatic family members.

A panel consisting of three novel circulating lncRNAs, is it a predictive tool for gastric cancer?

Early detection is vital for prolonging 5‐year survival for patients with gastric cancer (GC). Numerous studies indicate that circulating long non‐coding RNAs (lncRNAs) can be used to diagnose malignant tumours. This study aimed to investigate the capacity of novel lncRNAs for diagnosing GC. A lncRNA microarray assay was used to screen differentially expressed lncRNAs between plasma of patients with GC and healthy controls. Plasma samples from 100 patients with healthy controls were used to construct a multiple‐gene panel. An additional 50 pairs of GC patients with healthy controls were used to evaluate the diagnostic accuracy of the panel. Expression levels of lncRNAs were quantified through real‐time polymerase chain reaction. The receiver operating characteristic curve and area under curve (AUC) were used to estimate the diagnostic capacity. We identified three lncRNAs, CTC‐501O10.1, AC100830.4 and RP11‐210K20.5 that were up‐regulated in the plasma of GC patients with AUCs 0.724, 0.730 and 0.737, respectively (P < .01). Based on the logistic regression model, the combined AUC of the three lncRNAs was 0.764. The AUC of the panel was 0.700 in the validation cohort. These findings indicate that plasma lncRNAs can serve as potential biomarkers for detection of GC.

Abstract PD1-10: Multi-gene panel testing results in patients with multiple breast cancer primaries

Abstract Background: Every woman diagnosed with breast cancer has a risk to develop another breast primary throughout their lifetime. This risk is significantly elevated in individuals with a BRCA1 or BRCA2 mutation. For these individuals, the risk of a second primary breast cancer is 15% within 5 years of their initial cancer and the lifetime risk could be as high as 44%. Currently, the NCCN guidelines recommend testing of the BRCA1 and BRCA2 genes for individuals with multiple breast primaries, if their first diagnosis was under the age of 50. With the advent of Next Generation Sequencing and multiple gene panels, testing for hereditary breast cancer genes outside of BRCA1 and BRCA2 has become more prevalent. Although there are currently no guidelines that dictate when multiple gene panel testing should be ordered, recent studies have shown that there may be some associations between non-BRCA breast cancer genes such as ATM, CDH1, CHEK2, PALB2, PTEN, and TP53, in individuals with multiple primary breast cancers. Our study aimed to look at our institution's cohort of individuals with multiple primary breast cancers that underwent panel testing, to determine the rates of pathogenic mutations in non-BRCA genes. Methods: Sixty-five patients that had multiple breast cancer primaries and underwent a multi-gene breast cancer panel test were identified using MD Anderson's Clinical Cancer Genetics Database. The genetic testing results for each of these patients was reviewed and analyzed. Results: Out of the sixty-five patients found to have multiple breast cancer primaries and had a multiple gene panel test, 23 (29%) tested positive for a pathogenic mutation in a breast cancer predisposition gene: 6 (26%) BRCA1, 3 (13%) BRCA2, 4 (17%) ATM, 3 (13%) CHEK2, 1 PALB2 (4%), 1 PTEN (4%), 1 TP53 (4%). Overall, 15% of this cohort tested positive for a mutation in a non-BRCA breast cancer predisposition gene. The average age of first breast cancer diagnosis in these positive patients was 42 (range 26-75), which was similar to the average age in patients that tested negative or were found to have a variant of uncertain significance (VUS), 42 (range26-65). The average age of the first breast cancer diagnosis in patients positive for non-BRCA breast cancer genes was 46 (range 28-75). Conclusion: In our cohort, 29% of patients with multiple breast primaries who underwent panel testing were found to have a germline mutation in a breast cancer predisposition gene. Interestingly, 15% of our cohort were found to have a mutation in a non-BRCA breast cancer gene. There was no difference between age of onset in those that tested positive versus those that tested negative or were found to have a VUS. The high positive rate for all individuals with multiple breast cancers, regardless of age, for both BRCA1/2 and non-BRCA genes suggests that panel testing for patients with multiple breast cancer primaries should be considered. This finding should be validated in larger cohorts in order to help clarify whether all patients meeting guidelines for BRCA1 and BRCA2 genetic testing due to multiple breast cancer primaries would benefit from a multiple gene panel test. Citation Format: Ross JL, Woodson AH, Gutierrez Barrera AM, Litton JK, Arun B. Multi-gene panel testing results in patients with multiple breast cancer primaries [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 PD1-10.

Germline deleterious mutations in genes other than BRCA2 are infrequent in male breast cancer.

Male breast cancer (MBC) is a rare cancer entity, with mutations in BRCA1 and BRCA2 genes accounting for~10% of patients. Multiple-gene sequencing has already entered clinical practice for female breast cancer, whereas the performance of panel testing in MBC has not been studied extensively. Therefore, the aim of this study was to evaluate the clinical utility of panel testing for MBC, by the largest gene panel used so far, through investigation of patients deriving from a population with known founder effects. Genomic DNA from one hundred and two Greek MBC patients, unselected for age and family history, was used to prepare libraries which capture the entire coding regions of 94 cancer genes. Loss-of-function (LoF) mutations were found in 12.7% of the cases, distributed in six genes: BRCA2, ATM, BRCA1, CHEK2, PMS2, and FANCL. BRCA2 mutations were the most frequent, followed by ATM mutations, accounting for 6.9 and 2%, respectively, while mutations in other genes were detected in single cases. Age at diagnosis or family history was not predictive of mutation status. Beyond mutations in established breast cancer predisposing genes, LoF mutations in PMS2 and FANCL among MBC patients are reported here for the first time. Our findings, using the largest gene panel for MBC patients so far, indicate that BRCA testing should be the primary concern for MBC patients. Until sufficient evidence arises from larger studies, multiple-gene panels may be of limited benefit for MBC and their families, at least for MBC patients of specific descent.

Clinical and molecular characterization of KCNT1-related severe early-onset epilepsy.

ObjectiveTo characterize the phenotypic spectrum, molecular genetic findings, and functional consequences of pathogenic variants in early-onset KCNT1 epilepsy.MethodsWe identified a cohort of 31 patients with epilepsy of infancy with migrating focal seizures (EIMFS) and screened for variants in KCNT1 using direct Sanger sequencing, a multiple-gene next-generation sequencing panel, and whole-exome sequencing. Additional patients with non-EIMFS early-onset epilepsy in whom we identified KCNT1 variants on local diagnostic multiple gene panel testing were also included. When possible, we performed homology modeling to predict the putative effects of variants on protein structure and function. We undertook electrophysiologic assessment of mutant KCNT1 channels in a xenopus oocyte model system.ResultsWe identified pathogenic variants in KCNT1 in 12 patients, 4 of which are novel. Most variants occurred de novo. Ten patients had a clinical diagnosis of EIMFS, and the other 2 presented with early-onset severe nocturnal frontal lobe seizures. Three patients had a trial of quinidine with good clinical response in 1 patient. Computational modeling analysis implicates abnormal pore function (F346L) and impaired tetramer formation (F502V) as putative disease mechanisms. All evaluated KCNT1 variants resulted in marked gain of function with significantly increased channel amplitude and variable blockade by quinidine.ConclusionsGain-of-function KCNT1 pathogenic variants cause a spectrum of severe focal epilepsies with onset in early infancy. Currently, genotype-phenotype correlations are unclear, although clinical outcome is poor for the majority of cases. Further elucidation of disease mechanisms may facilitate the development of targeted treatments, much needed for this pharmacoresistant genetic epilepsy.

Clinical evaluation of a multiple-gene sequencing panel for hypoparathyroidism

Clinical evaluation of a multiple-gene sequencing panel for hypoparathyroidism

P 44 Brisk jerk reflexes in a CMT case – novel heterozygous variant c.785T>C; p.Leu262Pro in KIF5A explaining the mixed phenotype

Introduction Charcot-Marie-Tooth (CMT) disease is a progressively disabling syndrome phenotypically comprising distal muscle weakness and atrophy, foot deformities, sensory loss, and reduced or absent tendon reflexes. In spastic paraplegia (SPG), a hereditary disorder affecting the upper motor neuron only, pareses are spastic, and deep tendon reflexes increased. Mixed forms between both diseases have been previously described ( Liu et al., 2014 ). By multiple gene panel based analysis using next-generation-sequencing (NGS), we herein identified the novel variant c.785T>C; p.Leu262Pro in KIF5A as the putative cause of a mixed CMT and SPG phenotype. Methods The patient’s examination took place in the neuromuscular outpatient clinic of the RWTH Aachen University hospital. After obtaining the patient’s informed consent, the molecular genetic analysis of an NGS-based panel comprising 84 genes in total was performed following the commercialized standard procedures established by CeGaT GmbH. The pathogenicity of each variant was evaluated according to the international ACMG criteria ( Richards et al., 2015 ). Case report At the age of 44 years, the now 48-year-old male patient with a negative family history noticed the first signs of gait unsteadiness. In the course, he developed profound symmetric calf atrophies, high arched feet, claw toes, and steppage gait. Except for the absent ankle jerk reflex, the deep tendon reflexes where surprisingly brisk. Sensory loss turned out comparably mild. Nerve conduction studies showed an axonal motor neuropathy in the legs, but were normal in the arms. The molecular genetic analysis revealed the heterozygous variant c.785T>C; p.Leu262Pro in the KIF5A gene, which has been described in association to SPG10 and/or an axonal CMT subtype following an autosomal dominant inheritance. The variant c.785T>C; p.Leu262Pro affects a highly conserved amino acid position within a functionally relevant domain. A change of secondary protein structure is conceivable as the linear leucine is replaced by proline, a cyclic amino acid. Several other missense mutations are described in the very close vicinity. The variant is predicted to be pathogenic by all available prediction programs. Its allele frequency in the healthy reference population is unknown. Unfortunately, co-segregation analyses could be performed since further family members were not available. For further evaluation, functional tests would be required. Discussion On the current state of knowledge, the novel variant c.785T>C; p.Leu262Pro in KIF5A is evaluated as being a variant of uncertain significance. Due to the well matching phenotype ( Liu et al., 2014 ), however, we consider it to be putatively pathogenic. This example underlines the necessity of precise phenotyping in the context of NGS-based multigene panels.

Performance of mutation risk prediction models in a racially diverse multi-gene panel testing cohort.

1523 Background: Mutation carrier prediction models are clinically useful tools for identifying candidates for genetic counseling and testing. Consensus guidelines recommend germline genetic testing for those with a carrier probability (CP) of approximately 5% or higher. However, prediction models may perform less well among racial/ethnic minorities. Our hypothesis is that pathogenic mutations (PM) are identifiable in a clinically meaningful fraction of racially/ethnically diverse patients with a CP of &lt; 5%. Methods: We conducted a multicenter prospective clinical trial of patients undergoing cancer-risk assessment using a 25 gene panel, which include APC, ATM, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDH1, CDK4, CDKN2A, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD51C, RAD51D, SMAD4, STK11, TP53. Patients were recruited from August 2014 to November 2016 at three centers. Patients were enrolled if they met standard clinical criteria for genetic testing or were predicted to have a ≥2.5% probability of inherited cancer susceptibility using validated prediction models. We evaluated the CP of patients with a PM in BRCA1, BRCA2, and/or a mismatch repair (MMR) gene using the following models: (1) BRCApro, (2) MMRpro and (3) PREMM1,2,6. Results: Of 2000 patients enrolled in this cohort, 80.6% are female (n = 1612). Regarding race/ethnicity, the cohort is 40.1% Non-Hispanic White (n = 802), 37.4% Hispanic (n = 748), 11.5% Asian (n = 230), 3.9% Black (n = 78), and 7.1% Other (n = 142). Among 241 (12.1%) patients who tested positive for a pathogenic mutation, 76 (31.5%) patients had a BRCA1 or BRCA2 mutation. Of those, 52 (68.4%) patients had a BRCApro CP of &lt; 5%. Thirty-eight (15.8%) patients had a pathogenic mutation in an MMR gene: 19 (50.0%) had an MMRpro CP of &lt; 5%, while 13 (34.2%) had a PREMM1,2,6 CP of &lt; 5%. The racial/ethnic distribution of BRCA1/2 or MMR mutation carriers is similar to that of the whole cohort. Conclusions: In a diverse cohort of patients undergoing 25-gene multiple-gene panel testing, half or more carriers of BRCA1/2 or MMR mutations had a CP of &lt; 5%, the consensus guideline-recommended cutoff for genetic testing. These results support a lower threshold for genetic testing guidelines. Clinical trial information: NCT02324062.

Pathogenic germline mutations in emerging cancer genes: What happens after panel testing?

1528 Background: Next-generation sequencing technology enables more comprehensive germline genetic testing, including genes whose cancer risks are less well-characterized (particularly among patients with less striking family histories). Little is known about patient outcomes, particularly adherence to risk-reducing recommendations and family testing. Methods: We attempted a phone interview ≥3 times with each adult patient who had a germline pathogenic or likely pathogenic mutation found in an emerging cancer gene (defined as any gene other than BRCA1/2 or the Lynch Syndrome genes MLH1, MSH2/6, PMS2) at a single academic cancer genetics clinic from January 2013-July 2016. Results: Of 143 eligible patients, 53 (37%) were successfully contacted and all consented to participate. Median follow-up was 677 days (range 247–1401) and age was 52 years (21-82). Two-thirds (68%) had personal cancer history and 93% had a first-degree relative with cancer. Mutations in genes associated with named syndromes ( APC=5 , CDH1=3 , TP53=3, PTEN=2) were found in 23% (many of whom lacked family history typical of these syndromes) whereas 77% had mutations in less well-characterized genes ( MYH=10, CHEK2=10, ATM=6, PALB2=6 , NBN=3, RAD51C=2, RAD51D=2, SDHB=1, CDKN2A=1, MRE11A=1, RAD50=1, FLCN=1). Conclusions: Two years after panel testing, patients with germline mutations in less well-characterized genes reported high rates of adherence to recommendations, family communication and testing. Limitations include a relatively low response rate and a single academic center; this may bias toward a “best-case” scenario. Larger, population-based studies will be crucial to understand the real-world outcomes of germline multiple-gene panel testing and its contribution to precision oncology. [Table: see text]

Gaps in Incorporating Germline Genetic Testing Into Treatment Decision-Making for Early-Stage Breast Cancer.

Purpose Genetic testing for breast cancer risk is evolving rapidly, with growing use of multiple-gene panels that can yield uncertain results. However, little is known about the context of such testing or its impact on treatment. Methods A population-based sample of patients with breast cancer diagnosed in 2014 to 2015 and identified by two SEER registries (Georgia and Los Angeles) were surveyed about genetic testing experiences (N = 3,672; response rate, 68%). Responses were merged with SEER data. A patient subgroup at higher pretest risk of pathogenic mutation carriage was defined according to genetic testing guidelines. Patients' attending surgeons were surveyed about genetic testing and results management. We examined patterns and correlates of genetic counseling and testing and the impact of results on bilateral mastectomy (BLM) use. Results Six hundred sixty-six patients reported genetic testing. Although two thirds of patients were tested before surgical treatment, patients without private insurance more often experienced delays. Approximately half of patients (57% at higher pretest risk, 42% at average risk) discussed results with a genetic counselor. Patients with pathogenic mutations in BRCA1/2 or another gene had the highest rates of BLM (higher risk, 80%; average risk, 85%); however, BLM was also common among patients with genetic variants of uncertain significance (VUS; higher risk, 43%; average risk, 51%). Surgeons' confidence in discussing testing increased with volume of patients with breast cancer, but many surgeons (higher volume, 24%; lower volume, 50%) managed patients with BRCA1/2 VUS the same as patients with BRCA1/2 pathogenic mutations. Conclusion Many patients with breast cancer are tested without ever seeing a genetic counselor. Half of average-risk patients with VUS undergo BLM, suggesting a limited understanding of results that some surgeons share. These findings emphasize the need to address challenges in personalized communication about genetic testing.

Multiple-gene panel analysis in a case series of 255 women with hereditary breast and ovarian cancer

As new genes predisposing to breast (BC) and ovarian cancer (OC) are constantly emerging, the use of panels of genes analyzed by Next-Generation Sequencing (NGS) is increasing in clinical diagnostics. The identification of a large number of new germline mutations allows for deeper knowledge of cancer predisposition, although raising many questions about patient management.BC and OC patients recruited by our counseling service between 2012-2015 were included in this study. DNA was extracted from peripheral blood and a panel of 94 genes involved in hereditary tumors was analyzed by NGS. Patient clinical features of BC and OC and cancer family history were collected and compared to the patient genetic profile.A total of 255 women were analyzed, 57 of whom had a pathogenic mutation in BRCA1/2 genes, and 17 carried pathogenic mutations in other genes, such as PALB2, ATM, BRIP1, RAD51D, MSH6, PPM1D, RECQL4, ERCC3, TSC2, SLX4 and other Fanconi anemia genes.Patients with a pathogenic mutation in genes other than BRCA1 and BRCA2 showed no significant difference from the BRCA1/2-mutated carriers with respect to age at diagnosis and clinical features, suggesting that mutations in other genes could pose a high risk of cancer development.These patients had a much higher percentage of bilateral breast cancer (BBC) and a lower rate of OC than BRCA-mutated patients and patients with no pathogenic mutations: as a consequence, the surveillance protocol should be customized to the patient genetic characteristics.

Gaps in integrating genetic testing into management of breast cancer.

160 Background: Genetic testing for breast cancer risk is evolving rapidly, with surging use of multiple-gene panels. However, little is known about the extent to which testing is effectively integrated into management after diagnosis of breast cancer. Methods: A population-based sample of 3930 patients diagnosed with breast cancer in 2014-15 and identified by two SEER registries (Georgia and Los Angeles) were sent surveys 2 months after surgery and responses merged to SEER data. A subgroup at higher pre-test risk of pathogenic mutation carriage (vs average risk) was defined according to testing guidelines. Results: Among 2502 eligible patients with unilateral breast cancer (response rate 70%), 666 (27%) reported genetic testing. The Table shows wide variability in patient report of which professional ordered the test and discussed the results. Few (18-21%) patients had testing ordered by a genetic counselor and approximately half (57% high-risk, 42% average-risk) discussed results with one. One third of patient received testing after they had surgery. In a multivariable model adjusted for age, race, education, pre-test risk of mutation carriage, stage, co-morbidities and study site, the only factor significantly associated with delayed testing was insurance status: Compared to private insurance, patients were more likely to be tested after surgery if they had Medicare (OR 2.1, 95% CI 1.1-4.2) or no insurance (OR 3.0, CI 1.6-5.3). Conclusions: There is wide variability in which professionals order genetic testing and discuss results. Many breast cancer patients who receive genetic testing never see a genetic counselor. Many patients do not get tested early enough to consider the results in surgery management. These findings suggest enormous challenges in personalizing communication about genetic testing after diagnosis of breast cancer. [Table: see text]

Abstract PD8-06: Multiple-gene panel testing for hereditary cancer risk reveals a racial/ethnic disparity in genetic information

Abstract Background: Multiple-gene germline sequencing panels are increasingly used to evaluate hereditary cancer risk. However, little is known about the results of such testing in racially/ethnically diverse populations. Methods: Patients who presented to the Stanford University Clinical Cancer Genetics Program from 1/1/2013 to 12/31/2015 and underwent multiple-gene panel testing were included in the cohort (N=1,483). Information on demographics, personal and family history of cancer, and tumor characteristics was collected at time of clinic visit. Odds ratios and 95% confidence intervals were calculated for mutation status by different patient and tumor characteristics, including race/ethnicity. Results were compared using the chi-square test and considered significant if P&amp;lt;0.05 after Bonferroni correction for multiple hypothesis testing. Results: Most patients (92%) were female. Patients were 51% Non-Hispanic White (NHW), 19% Asian, 14% Hispanic, 10% Ashkenazi Jewish, 5% other, and 1% unknown. Eighty-nine genes were tested in at least one patient; panel size ranged from six to 62 genes, with a median of 25 genes. The frequency of pathogenic or likely pathogenic mutations was 15% for any panel-tested gene, 5.5% for BRCA1/2, and 5.3% for other breast cancer-associated genes; mutation frequencies were similar between NHW, Asian, Hispanic, and Ashkenazi Jewish patients. Variables significantly associated with the carriage of a pathogenic BRCA1/2 mutation included personal or family history of ovarian cancer and personal history of triple-negative breast cancer (TNBC). No variable was significantly associated with the presence of a pathogenic mutation in the other breast cancer genes. The odds ratios for carrying a BRCA1/2 mutation with personal history of ovarian cancer (4.1 [2.2-7.3]), family history of ovarian cancer (3.1 [1.9-4.9]), and TNBC relative to other breast cancer subtypes (6.0 [2.9-12.4]) did not differ significantly between NHWs and non-Whites. The frequency of variants of unknown significance (VUS) in any panel-tested gene was higher in non-Whites (36%) than in NHWs (27%) (P=2E-4), with the highest odds ratio relative to NHWs among Asians (2.0 [1.5-2.7], vs 1.3 [0.9-1.7] among Hispanics and 1.2 [0.8-1.7] among Ashkenazi Jews). The odds ratio of finding a VUS for non-Whites compared to NHWs was similar for any panel (1.5 [1.2-1.9]), for BRCA1/2 (1.3 [0.8-2.3]), and for other known breast cancer-associated genes (1.5 [1.1-1.9]). Conclusions: In this diverse cohort tested for hereditary cancer risk with multiple-gene panels, frequencies of pathogenic mutations were similar between racial/ethnic groups. By contrast, frequencies of VUS were significantly higher among non-Whites compared to NHWs. This higher VUS rate renders multiple-gene panel testing less informative for non-White patients. Efforts toward VUS re-classification, particular among non-Whites, are urgently needed to address this genetic information disparity. Citation Format: Caswell-Jin* JL, Gupta* T, Hall E, Petrovchich IM, Mills MA, Kingham KE, Koff R, Chun NM, Levonian P, Lebensohn AP, Ford JM, Kurian AW. Multiple-gene panel testing for hereditary cancer risk reveals a racial/ethnic disparity in genetic information [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr PD8-06.

Abstract P2-02-06: Genetic counseling, germline genetic testing, and impact of results in patients with newly diagnosed breast cancer

Abstract The surge in BRCA1/2 and multiple-gene panel testing after a diagnosis of breast cancer has fueled concerns about how genetic testing results will be integrated into patient management. However, there is virtually no research about the timing or extent of genetic counseling before or after testing or the impact of genetic results on bilateral mastectomy (BLM) use since the advent of more widespread testing. Methods: A population-based sample of 3600 patients newly diagnosed with breast cancer identified by two SEER registries (Georgia and Los Angeles County) were sent surveys two months after surgery (Dx dates 2014-15) about their genetic testing and treatment experiences. Survey information was merged with SEER data. We examined patterns and correlates of counseling and genetic testing and the impact of results on patient preferences for BLM and receipt of BLM. Results: Among 2388 patients with unilateral breast cancer (response 70%), 697 (29.2%) had elevated pre-test risk of a germline mutation (based on age, family cancer history, ancestry, and tumor subtype). One-quarter of these higher risk patients (25.6%) did not discuss whether to have testing with any provider, 26.1% discussed it with clinicians only, and 48.3% had a visit with a genetic counselor. Half of patients with elevated pre-test risk (51.2%) were tested: 6.6% before diagnosis, 65.4% after diagnosis but before surgery and 28.0% after surgery. Higher risk patients who underwent testing were younger (p&amp;lt;.001) and had higher income (p=.029) but rates did not differ significantly by race, education, insurance, marital status, cancer stage, comorbidities, or geographic site after controlling for all covariates. There was wide variation in the type of professional who discussed test results with patients: discussed with surgeon only (17.8%), medical oncologist only (19.7%), both physicians but no counselor (4.8%), or genetic counselors (56.8%). Among all testers in the total sample (n=667), 54 (9.4%) reported a pathogenic mutation (12.1% of higher risk patients vs 5.7% of low risk patients) and 59 (10.0%) reported a variant of unknown significance (VUS) (10.2% of higher risk patients vs 9.9% of lower risk patients), p=.027 for differences between groups. Two-thirds (60.4%) of patients with pathogenic mutations reported that the test made them more interested in BLM vs 8.8% of those with a VUS, and 11.4% of those with negative tests, p&amp;lt;.001. Two-thirds (69.2%) of those with pathogenic mutations received BLM vs 21.9% of those with VUS and 27.9% of those with negative tests, p&amp;lt;.001. Conclusions: Many patients newly diagnosed with breast cancer at higher risk of carrying a pathogenic mutation do not receive pre-test counseling or genetic testing and disparities are observed. There is wide variability in the timing of genetic testing after diagnosis and with which clinician the findings are discussed. Taken together, these results suggest that germline genetic testing after a diagnosis of breast cancer is poorly integrated into practice. However, the impact of genetic test results on patient attitudes and receipt of bilateral mastectomy suggests that genetic testing does help target prevention to a patient's future risk for a new primary breast cancer. Citation Format: Katz SJ, Morrow M, Jagsi R, Kurian A. Genetic counseling, germline genetic testing, and impact of results in patients with newly diagnosed breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-02-06.

Germline mutations in Japanese familial pancreatic cancer patients.

Clinicopathologic and genetic features of familial pancreatic cancer (FPC) in Asian countries remain largely unknown. The main purpose of this study was to determine the prevalence of FPC and to define causative FPC-predisposition genes in a Japanese cohort with pancreatic ductal adenocarcinoma (PDAC). We reviewed 1,197 patients with a pathologically proven PDAC and found that 88 (7.3%) were FPC patients who had at least one first-degree relative with PDAC. There were no significant differences between the FPC cases and sporadic cases in terms of gender, age, tumor location, stage, family history of any cancer except PDAC, and personal history of smoking, other cancers, diabetes mellitus and chronic pancreatitis. In the FPC patients, we then investigated the prevalence of germline mutations in 21 genes associated with hereditary predispositions for pancreatic, breast and ovarian cancers by means of the next-generation sequencing using a custom multiple-gene panel. We found that eight (14.5%) of the 54 FPC patients with available germline DNA carried deleterious mutations in BRCA2, PALB2, ATM, or MLH1. These results indicate that a significant fraction of patients with PDAC in Japan have a family history of pancreatic cancer, and some of them harbor deleterious causative mutations in known FPC predisposition genes.

Magnitude of invasive breast cancer (BC) risk associated with mutations detected by multiple-gene germline sequencing in 95,561 women.

1512Background: Using a multiple-gene sequencing panel to assess hereditary BC risk increases the detection rate of clinically significant mutations. However, the magnitude of BC risk with mutation...

Refining Breast Cancer Risk Stratification: Additional Genes, Additional Information.

Recent advances in genomic technology have enabled far more rapid, less expensive sequencing of multiple genes than was possible only a few years ago. Advances in bioinformatics also facilitate the interpretation of large amounts of genomic data. New strategies for cancer genetic risk assessment include multiplex sequencing panels of 5 to more than 100 genes (in which rare mutations are often associated with at least two times the average risk of developing breast cancer) and panels of common single-nucleotide polymorphisms (SNPs), combinations of which are generally associated with more modest cancer risks (more than twofold). Although these new multiple-gene panel tests are used in oncology practice, questions remain about the clinical validity and the clinical utility of their results. To translate this increasingly complex genetic information for clinical use, cancer risk prediction tools are under development that consider the joint effects of all susceptibility genes, together with other established breast cancer risk factors. Risk-adapted screening and prevention protocols are underway, with ongoing refinement as genetic knowledge grows. Priority areas for future research include the clinical validity and clinical utility of emerging genetic tests; the accuracy of developing cancer risk prediction models; and the long-term outcomes of risk-adapted screening and prevention protocols, in terms of patients' experiences and survival.

Gene panel testing for hereditary breast cancer.

Inherited predisposition to breast cancer is explained only in part by mutations in the BRCA1 and BRCA2 genes. Most families with an apparent familial clustering of breast cancer who are investigated through Australia's network of genetic services and familial cancer centres do not have mutations in either of these genes. More recently, additional breast cancer predisposition genes, such as PALB2, have been identified. New genetic technology allows a panel of multiple genes to be tested for mutations in a single test. This enables more women and their families to have risk assessment and risk management, in a preventive approach to predictable breast cancer. Predictive testing for a known family-specific mutation in a breast cancer predisposition gene provides personalised risk assessment and evidence-based risk management. Breast cancer predisposition gene panel tests have a greater diagnostic yield than conventional testing of only the BRCA1 and BRCA2 genes. The clinical validity and utility of some of the putative breast cancer predisposition genes is not yet clear. Ethical issues warrant consideration, as multiple gene panel testing has the potential to identify secondary findings not originally sought by the test requested. Multiple gene panel tests may provide an affordable and effective way to investigate the heritability of breast cancer.

Abstract P2-09-05: Multiple-gene panel sequencing prompts no change in care compared to BRCA1 and BRCA2 testing in male breast cancer patients and their families

Abstract Male breast cancer is a rare cancer entity, representing just 1% of all cancers diagnosed in men. It shares clinical and biological characteristics with post-menopausal female breast cancer, although recent reports showed that they are not identical. Approximately 10% of unselected male breast cancer cases carry BRCA1 &amp; BRCA2 mutations, with the most frequently mutated gene being BRCA2. Multiple-gene sequencing has already entered clinical practice and leads in detection of potential pathogenic variants in other cancer predisposition genes, in as many as 15% female breast cancer patients without BRCA1 &amp; BRCA2 mutations. We evaluated the performance of a customized panel for cancer risk assessment in a representative sample of male breast cancer patients. Ninety eight male individuals diagnosed with breast cancer (mean age 59y, range 38y-81y) and referred for genetic counseling between 2010 and 2015 were invited to donate a research blood sample. Patients were eligible irrespectively of family history and age at diagnosis. Genomic DNAs were used to prepare libraries for the capture of the entire coding regions of twenty six known -or suspected- breast cancer genes. These were: BRCA1, BRCA2, TP53, STK11, CDH1, PTEN, PALB2, ATM, CHEK2, NBN, BRIP1, BARD1, RAD51C, RAD51D, RAD50, BLM, SLX4, MRE11A, FAM175A, MLH1, MSH2, EPCAM, MHS6, PMS2, MUTYH, NF1. Loss-of-function mutations have been found in three genes; BRCA2, BRCA1 and PMS2. Not surprisingly, the most frequently mutated gene was BRCA2 accounting for 5% of the cases, while BRCA1 and PMS2 mutations have been detected in single cases, accounting each for 1%. Interestingly, no mutations were identified in any of other genes that have been reported in female breast-ovarian cancer families (PALB2, TP53, ATM, CDH1, RAD51C, RAD51D, etc). Compared to BRCA1 &amp; BRCA2 testing, gene panel prompted consideration of change in care (early colon cancer screening) in a single family (1%). This is the first evaluation of the performance a multiple-gene panel in male patients with breast cancer. Our findings confirm that genetic counseling and BRCA1 &amp; BRCA2 should be the primary concern for these patients and their families. Mutations in other genes been reported in female breast-ovarian cancer families were not identified in this cohort. If larger studies confirm our results, then multiple-gene sequencing panels may be of limited benefit for male breast cancer patients and their families. Citation Format: Fostira F, Saloustros E, Konstantopoulou I, Tryfonopoulos D, Barbounis V, Mauroudis D, Georgoulias V, Fountzilas G, Yannoukakos D. Multiple-gene panel sequencing prompts no change in care compared to BRCA1 and BRCA2 testing in male breast cancer patients and their families. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-09-05.

Advances in the Understanding of the Genetic Causes of Hearing Loss in Children Inform a Rational Approach to Evaluation.

Hearing loss represents the most common sensory disability of children. Remarkable advances in the identification of genes underlying nonsyndromic and syndromic hearing loss in just the last 2 decades have led to the ability to determine the specific genetic cause of hearing loss in many children. Surprisingly one gene, GJB2, encoding the protein connexin-26, accounts for about 20% of sensorineural hearing loss (including in India) and is considered the first tier test in evaluating an infant with unexplained congenital hearing loss. Using the knowledge of the etiology of hearing loss, the authors propose a diagnostic reasoning process for the assessment of a child in the pediatric setting. Second tier testing consists of the multiple gene panels using whole exome sequencing strategies, and is becoming available in some regions of the world including the US. Referral to medical genetics is always a consideration in a child with no explanation for the hearing loss and in families with questions about recurrence risk.