Variants Of Undetermined Significance Research Articles

Outcomes of retesting BRCA-negative patients using multigene panels.

23 Background: New technologies for identifying hereditary predisposition to breast cancer have led to the discovery of novel genes associated with cancer risk. This has prompted re-evaluation of patients who previously tested negative for BRCA1/2 gene mutations, with a possibility of discovering new genes which may impact management. This study reports on the results of retesting patients who previously were negative for BRCA1/2. Methods: Patients who tested negative for BRCA1/2 mutations who had significant personal and family history were referred back to the Cancer Genetics Center between February 1, 2012 and May 30, 2105 for discussion of additional testing. A detailed personal and family history was reviewed, and patients were counseled about the genetics and clinical implications of panel testing for multiple breast cancer genes. Panel testing using next generation sequencing technologies was ordered. Patients were seen in follow up for discussion of results and management. Results: A total of 12 pathogenic mutations were identified during the study period. The genes and frequencies of these mutations were: CHEK2(3), PALB2(3), ATM(2), APC(1), BARD(1), CDH(1), MUTYH(1). There were 33 variants of undetermined significance(VUS) in 27 patients. 5 of these were seen in patients with a known pathogenic mutation; 3 others were later classified as benign. The frequencies of these VUSs were: ATM (9), PALB2(3), BARD1 (3), PTEN(3), PMS2(3), MSH6(2), CHEK2 (1), MYH(1), RAD51(1), BRIP1(2), NF1(1), BMPR1A(1). Of the 46 patients who had their initial BRCA testing and repeat panel testing between February 1, 2012 and May 30, 2015, 6 (13%) tested positive for a pathogenic mutation. Conclusions: This study demonstrates the feasibility and potential clinical benefit of retesting individuals who previously tested negative for BRCA1/2 mutation. This approach had a significant management impact on patients and their families, with a 13% detection rate of pathogenic mutations. The success of retesting is predicated upon an infrastructure of provider and patient education, pre and post genetic counseling and serves as a model for other centers.

Abstract 3892: Somatic genetic profiling in pheochromocytomas and paragangliomas

Abstract Approximately one quarter of pheochromocytomas and paragangliomas (PCC/PGLs) are malignant, defined as having distant metastases, which can be present at initial diagnosis or develop even 20 years later. Patients with malignant PCC/PGL only have a 50% five year survival rate. This poor prognosis and potential long latency period emphasizes the need for biomarkers of aggressive disease and novel targets for therapeutic intervention. More than eleven known susceptibility genes have been identified. Nevertheless, very little is known about the activated cellular pathways or the somatic genetic and genomic changes leading to tumor development and progression to malignancy. We aimed to characterize the somatic genetic profile in clinically benign and clinically aggressive PCC/PGLs in order to identify alterations leading to tumorigenesis and malignant potential. We performed exome sequencing on matched germline and tumor DNA from 21 PCC/PGLs including five VHL-associated PCCs representing clinically benign disease, seven SDHB-associated PCC/PGLs representing clinically aggressive disease, and two SDHD-associated and seven sporadic PCC/PGLs representing a mix of clinical behavior. Three hundred and twenty-one protein altering variants were identified. There were seven truncating mutations (nonsense variants and frameshifts) and twelve variants affecting splice sites. The vast majority of variants were non-synonymous variants of undetermined significance. Three of the seven sporadic tumors had somatic NF1 mutations, but no somatic mutations in any of the other known susceptibility genes were observed. In addition to somatic ATRX mutations which we have previously reported, there were a number of cancer associated genes with somatic variants including SHH, FANCD2, CTNND1, MACC1, FGFR1, GADD45A, and RBBP6. Pathway analysis identified a broad range of disrupted pathways including the WNT and cadherin signaling pathways. For tumors with a known inherited mutations in VHL or SDHx, copy number variation analysis identified loss of heterozygosity as the second hit. In summary, we performed a comprehensive somatic exome sequencing analysis of a large set of PCC/PGLs, and we identified several cancer associated genes not previously reported to be altered in PCC/PGLs. These data not only expand upon the limited prior knowledge of somatic alterations in PCC/PGLs but may also serve to identify potential targets for therapeutic intervention. Citation Format: Lauren Fishbein, Sanika Khare, Bradley Wubbenhorst, Virginia LiVolsi, Kathleen Montone, Douglas Fraker, Debbie L. Cohen, Katherine L. Nathanson. Somatic genetic profiling in pheochromocytomas and paragangliomas. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3892. doi:10.1158/1538-7445.AM2015-3892

Decreased frequency of FBN1 missense variants in Ghent criteria-positive Marfan syndrome and characterization of novel FBN1 variants.

The diagnosis of Marfan syndrome (MFS) remains challenging despite the 2010 revision to Ghent nosology criteria, and there is a lack of published information regarding FBN1 genotype associations in patients since the update in Ghent criteria. Applying revised Ghent criteria, we reviewed consecutive proband cases (n=292) submitted for FBN1 sequencing. Testing yielded 207 pathogenic or likely pathogenic FBN1 variants, with 114/207 (55%) missense, 67/207 (32%) non-sense or frameshift, and 28/207 (13%) splicing. There were 130 novel FBN1 variants predicted as pathogenic or likely pathogenic (n=109) or variant of undetermined significance (n=21). Of the 104 patients who met 2010 revised Ghent criteria, 87/104 (82%) had a pathogenic or likely pathogenic variant. There was a significantly lower frequency of missense variants (41 vs 89%; P<0.0001) observed in the Ghent-positive (vs Ghent-negative) patients, and this association held true in age-based groupings. Previously described genotype associations with ectopia lentis and early onset/'neonatal' MFS were confirmed in our cohort. Overall, our study points to the imperfect nature of relying solely on clinical criteria to diagnose MFS as well as the potential importance of truncating/splicing variants in Ghent-positive cases. Furthermore, the description of numerous novel variants and associated clinical findings may be useful for future clinical interpretation of FBN1 genotype in patients with suspected MFS.

Data Disclosure Crucial After DNA Patent Verdict

The Supreme Court's recent decision in Association for Molecular Pathology v. Myriad Genetics ([ 1 ][1]) was widely regarded for its conclusion that patents could not be held over isolated DNA. However, Myriad maintains a confidential library of BRCA variants of undetermined significance (VUSs) ([ 2

Unique genetic characteristics of BRCA mutation carriers in a cohort of Arab American women.

1541 Background: Worldwide ethnic variations in the distribution of BRCA1 and BRCA2 mutations of breast cancer patients have been recently recognized. This has led to investigations of the epidemiology, genetics and clinical characteristics of BRCA positive individuals within specific populations. This study aims to describe the findings of BRCA genetic testing in a cohort of Arab American women. Methods: A total of 73 women of Arab ancestry were evaluated in the Beaumont Cancer Genetics Program from Jan 2008 to Jan 2013. Criteria for genetic testing included a personal or family history suggestive of Hereditary Breast and Ovarian Cancer Syndrome (HBOC). Patients underwent comprehensive genetic counseling, followed by full sequence analysis for germline mutations in BRCA1 and BRCA2. Results: 63 women of Arab ancestry underwent genetic testing for BRCA1 and BRCA2. 13 (21%) patients were found to be mutation carriers, of whom 10 (16%) of the 63 had deleterious mutations (7 in BRCA2, and 3 in BRCA1), and 3 (5%) had variants of undetermined significance (VUS) in BRCA2. Of the 10 patients with deleterious mutations, 4 (40%) unrelated individuals had the same mutation, 5804del4, in exon 11 of BRCA2. The remaining patients had deleterious mutations in exon 2, exon 20, and exon 13 of BRCA2; one patient had a BRCA1 and BRCA2 mutation (exon 18). 7 of 10 patients with deleterious mutations had a cancer diagnosis, of which 5 had breast cancer, 1 had ovarian cancer, 1 had pancreatic cancer, and 3 were unaffected. Conclusions: This study demonstrates that BRCA mutations (predominantly in BRCA2) were seen in a significant proportion of Arab American women undergoing genetic testing for HBOC. A mutation in BRCA2, 5804del4, was seen in nearly half (4/10) of the carriers of deleterious mutations. This mutation, in exon 11, has not previously been associated with Arab ethnicity and may represent a founder mutation. Knowledge of the genetic spectrum, frequency, and clinical characteristics of BRCA mutation carriers will lead to greater understanding of hereditary cancer in Arab American women.

Abstract PD09-06: Two phase I trials exploring different dosing schedules of carboplatin (C), paclitaxel (P), and the poly-ADP-ribose polymerase (PARP) inhibitor, veliparib (ABT-888) (V) with activity in triple negative breast cancer (TNBC)

Abstract Background: The histopathologic and molecular similarities between TNBC and BRCA-1 mutation related breast cancer provide rationale for the use of PARP inhibitors in treating sporadic TNBC. C and P are established drugs in the treatment of advanced breast cancer. In order to determine the recommend phase II dose (RP2D) of V in combination with C and P, two separate phase I trials evaluated the combination of V with C and P dosed weekly (q1wk) and every 3 weeks (q3wk). Methods: Both phase I trials were a standard 3+3 dose escalation design of C, P, and V open to patients (pts) with advanced solid tumors and enriched for pts with TNBC. In the q1wk trial, C was given weekly on day 3 at an AUC of 2, P was given weekly on day 3 at a dose of 80 mg/m2, and V was escalated from 50 mg twice daily (BID) to a maximum of 200 mg BID on days 1–5 every week over 4 dose levels. In the q3wk trial, C was given on day 3 every 21 days at an AUC of 6, P was given on day 3 every 21 days with the dose escalated from 150 mg/m2 to a dose of 200 mg/m2, and V was given on days 1–7 every 21 days and escalated from 10 mg BID to a dose of 120 mg BID over 9 dose levels. Toxicity was assessed by CTCAE v. 4 and response was determined using RECIST criteria. Results: The q1wk trial enrolled a total of 18 pts, 12 of whom had BC, and 10 had TNBC. One TNBC pt was BRCA-1+ and the remainder were sporadic. The trial will be completed with the enrollment of one additional patient on dose level 4. Ten breast cancer pts are evaluable for response. DLT's included thrombocytopenia on dose levels 3 (V at 150 mg BID) and 4 (V at 200mg BID), and both occurred in TNBC pts. The range of cycles administered to TNBC pts was 1–11. The q3wk trial enrolled a total of 75 pts, 14 had BC (12 evaluable for response), and 9 had TNBC. One of these pts had a BRCA mutation; 2 pts had a variant of undetermined significance. Three DLT's were observed on this schedule: febrile neutropenia (C at AUC 6, P at 200 mg/m2, V at 40 mg BID, 100 mg BID, and 120 mg BID) and grade 3 hyponatremia. No DLT's occurred in TNBC pts. The established RP2D for the q3wk schedule is C (AUC6), P (200mg/m2) and V (100mg bid) and additional pts are being accrued to an expansion cohort. The range of cycles administered to TNBC pts was 1–14. The clinical activity in TNBC is summarized in Table 1. Responses occurred in pts who had been previously treated both in the adjuvant and metastatic settings, as well as in those who received prior taxanes. Conclusion: There is evidence of promising clinical activity and acceptable tolerability with carboplatin, paclitaxel, and veliparib on both dosing schedules. An additional 12 pts with TNBC will be accrued to the q1wk trial with pre- and post-treatment biopsies to further evaluate underlying mechanisms of sensitivity and response with regards to DNA repair pathways. Based on our phase I experience, further randomized trials are warranted in breast cancer, particularly TNBC. Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD09-06.

Thirty-Nine-Year-Old With Familial Colon Cancer, and Variant of Undetermined Significance in MSH6

Thirty-Nine-Year-Old With Familial Colon Cancer, and Variant of Undetermined Significance in MSH6

A simplified method for segregation analysis (SISA) to determine penetrance and expression of a genetic variant in a family

A method for SImplified rapid Segregation Analysis (SISA) to assess penetrance and expression of genetic variants in pedigrees of any complexity is presented. For this purpose the probability for recombination between the variant and the gene is zero. An assumption is that the variant of undetermined significance (VUS) is introduced into the family once only. If so, all family members in between two members demonstrated to carry a VUS, are obligate carriers. Probabilities for cosegregation of disease and VUS by chance, penetrance, and expression, may be calculated. SISA return values do not include person identifiers and need no explicit informed consent. There will be no ethical complications in submitting SISA return values to central databases. Values for several families may be combined. Values for a family may be updated by the contributor. SISA is used to consider penetrance whenever sequencing demonstrates a VUS in the known cancer-predisposing genes. Any family structure at hand in a genetic clinic may be used. One may include an extended lineage in a family through demonstrating the same VUS in a distant relative, and thereby identifying all obligate carriers in between. Such extension is a way to escape the selection biases through expanding the families outside the clusters used to select the families.