Highlights of Recent Work and Literature

The Division of Clinical Cancer Genomics staff have authored a number of journal articles in publications such as Genetics in Medicine, American Journal of Human Genetics, Cancer Genetics, Journal of Genetic Counseling, Familial Cancer, Breast Cancer Research and Treatment, JAMA, Journal of Cancer Education, and Journal of Clinical Oncology.
Founder effect and a high prevalence of BRCA1 mutations among young Mexican triple-negative breast cancer (TNBC) patients. A podium presentation at the ASCO 50th Annual Meeting 2014.
Villarreal-Garza CM, Weitzel JN, Sifuentes E, Llacuachaqui M, Herzog J, et al.  May 30 - June 3, 2014; Chicago, IL.
Previous studies have shown that the prevalence of BRCA mutations among young TNBC patients is elevated. Current guidelines recommend that women ≤60 years with TNBC be referred for genetic counseling. Different studies in Mexico have shown an early age of onset of BC and a high prevalence of TNBC, which suggests that BRCA mutations may account for a higher proportion of breast cancers in this population. However, there is limited information regarding BRCA mutation prevalence mainly due to lack of access to clinical BRCA gene analyses in Mexico. Methods: The purpose of this study is to analyze BRCA mutation frequency in a cohort of young Mexican TNBC patients using a panel assay of 114 recurrent BRCA mutations found in women of Hispanic ancestry (HISPANEL) on the Sequenom platform. Mexican women diagnosed with TNBC at or before age 50 were prospectively recruited from the National Cancer Institute in Mexico City. Patients were screened by HISPANEL and by PCR for the Mexican founder BRCA1 ex9-12del large rearrangement.
Results: Among 190 consecutive TNBC cases, the median age of diagnosis was 42 years old and 69% were younger than 45 years. The majority of patients presented with locally advanced disease (69%). A BRCA mutation was detected in 43/190 (23%) of patients (42-BRCA1, 1-BRCA2), and BRCA1 ex9-12del accounted for 42% of the mutations. Only 45% of the BRCA mutation carriers had a family history of breast and/or ovarian cancer. Samples were processed in a two-week period, with a total cost of $4,000 USD.
Conclusions: There is a remarkable prevalence of BRCA1 mutations among young TNBC patients in our population. The first documented Mexican founder mutation, BRCA1 ex9-12del, was the most frequent BRCA mutation and is likely responsible for a significant burden of disease in women from Southern Mexico. The HISPANEL can be completed within 72 hours from sample collection, at a modest cost of $20 USD per sample, and implementation among women of Mexican ancestry could reduce overall genotyping cost and increase access to cancer prevention among underserved women in Mexico and the U.S.
Phase II trial of single agent PARP inhibitor ABT-888 (veliparib [vel]) followed by post-progression therapy of vel with carboplatin (carb) in patients (pts) with stage BRCA-associated metastatic breast cancer (MBC). California cancer consortium trial PhII-96. A podium presentation at the American Society of Clinical Oncology Annual Meeting 2014.
Somlo G, Frankel P, Luu T, Ma C, Arun B, et al.  May 30 - June 3, 2014; Chicago, IL.
Background:  We reported on a phase I trial showing 54% confirmed partial response (PR) with carb + vel.  Here we describe single agent vel activity and, upon progression, the feasibility and efficacy of continuing administration of vel + carb.
Methods:  Pts  with MBC with BRCA1 or 2 mutations, an ECOG performance status of ≤ 2, and measurable disease were eligible. Prior PARP-inhibitor therapy (Rx) , platinum Rx for MBC, or central nervous system metastasis requiring Rx were exclusions. Vel was administered orally at 400 mg twice daily (BID).  Cohorts (BRCA1 and BRCA2) were studied independently: 2 or more PRs to vel out of 10 pts were required to proceed to accrual of 22 pts per cohort. Upon progression, carb (AUC of 5) iv every 21 days, and vel  150 mg orally BID were prescribed.
Results:  Between 10/2012 and 1/2014, 44 pts enrolled (41 treated) carrying BRCA1 (N=21) or BRCA2 (N=20)  mutations. The median age was 43-years (range; 28-68); 50% of pts had hormone receptor + BC.  Pts received 3 prior chemo-regimens (0-7). The current PR rate in pts with at least 4 cycles of follow-up  is 2/12 (17%) for BRCA1 and 3/13 (23%) for BRCA2.  Three pts withdrew from treatment during the first cycle of vel due to grade 2 seizure (1), grade 3 thrombocytopenia (PLT [1]), grade  2 PLT and neutropenia (1).   Time to failure (TTF) on vel is 2.0 months (0-10.5+), and 5.1 months (0.9-10.3+) for the two cohorts (BRCA1, BRCA2, respectively). Twenty pts are still on vel (8 BRCA1, 12 BRCA2).  Of the 10 pts to proceed to vel + carb so far, 1 PR in a BRCA1 pt was observed.
Conclusions:  Vel is active when given at 400 mg BID daily. Further trials are indicated to assess its benefit whether in combination or as a single agent in both BRCA1 and BRCA2-associated BC.
BRCA1 and BRCA2 (BRCA) gene analyses on an economic platform: A global consortium to demonstrate the feasibility of a shared, dedicated workflow for non-optical next generation sequencing (NGS) with a custom BRCA AmpliSeq kit on the Ion Torrent PGM™. A podium presentation at the American Society of Human Genetics Annual 63rd Annual Meeting.
Weitzel J, Costa J, Mensenkamp A, Ekici A, Herzog J, et al. 2013 October 22-26; Boston, MA.
While the “Jolie effect ” has refocused attention on the central role of BRCA gene analyses in the diagnosis and prevention of hereditary breast and ovarian cancer, there is a global disparity in access to affordable testing. The development of bench top NGS technologies holds promise for faster, more comprehensive and cost-effective methodologies than Sanger sequencing. We describe here a global consortium developing and demonstrating the feasibility of a shared, dedicated workflow for clinical grade BRCA gene analyses using Ion AmpliSeq ™ multiplex PCR technology combined with Ion PGM ™ System. The non-overlapping primers were designed to provide 1) 100% coverage of all coding exons and exon-intron boundaries; 2) overlapping amplicons covering exons; 3) no SNPs in the last five nucleotides of primer; and 4) maximum of three non-validated SNPs per primer. The technical protocol was developed and piloted by centers in the Netherlands and Portugal, and the current phase III testing includes 5 additional centers (California, USA; D.F., Mexico; Glasgow, Scotland; Erlangen, Germany; Ontario, Canada). More than 200 different known germline BRCA mutation positive cases were selected (~30 per center), many representative of a given region, with the aim to assess the ability to detect and call the full spectrum of mutation types, with additional cases in or within close proximity to homopolymer regions. Data analyses include independent and blind evaluation and power estimation of the new methodology. All samples were studied using both Sanger sequencing and the Ion PGM ™ System. For data-analysis various software packages were evaluated, with an aim to harmonize the analyses as a custom workflow on Ion Reporter to facilitate use in widely disparate settings. The technical platform has been established in all 7 centers, with excellent performance characteristics: 100% coverage of the targeted regions; >100x coverage across all but 1 amplicon in BRCA2 (>40x), while using barcoding to analyze 8 cases simultaneously on a 316 chip. There was high sensitivity and specificity; technical challenges in the bioinformatic component and emerging copy number variation detection methods will be discussed. This work demonstrates the potential for mutational screening of BRCA1 and BRCA2 using the Ion AmpliSeq ™ technology combined with the Ion Torrent PGM, and the feasibility of deploying a common protocol to diverse geographic settings, with a close collaboration among peers.
Efficacy of The Combination of ABT-888 (veliparib) and Carboplatin in Patients BRCA-Associated Breast Cancer. A poster presentation at the American Society of Clinical Oncology annual meeting, 2013.
Somlo G, Frankel P, Luu T, Ma C, Arun B, et al.. 2013 May 31-June 4; Chicago, IL. .
Platinum and PARP inhibitors have both shown single agent activity in BRCA-associated breast cancer patients  (Silver et al. J Clin Oncol 2010; Tutt et al. Lancet 2010). However, data on combining these two classes of agents are limited, and the optimal dose, frequency, and duration have not been defined. 
In line with the concept of synthetic lethality (Rehman et al. Nat Rev 2010),  we designed a trial to treat women with BRCA-associated stage IV breast cancer. We planned to compare carboplatin and ABT-888 vs. single agent ABT-888. Precinical data suggest synergism between platinum agents and ABT-888 (Clark CC et al. Mol Cancer Ther. 2012).
Since neither the dose-limiting toxicity (DLT) nor the maximum tolerated dose(MTD)  of daily ABT-888 has been firmly established, we conducted a phase I trial of carboplatin  and escalating doses of ABT-888.
We report on the MTD and observed DLTs of this combination, and early efficacy data in 28 patients accrued as part of a California Cancer Consortium-lead trial with participation from multiple NO-1-supported consortia.
Hispanic MMR Mutations: A Multi-Institutional Report from Southwestern United States and Puerto Rico. A poster presentation at the 17th Annual Meeting Collaborative Group of the Americas on Inherited Colorectal Cancer.
Sunga A, Ricker C, Espenschied C, Herzog J, Bannon S, et al.; 2013 October 7-8; Anaheim, CA.
Background:  Knowledge of founder mutations can enable efficient and cost-effective strategies for genetic testing, a potential benefit for populations with limited access to services.  We have shown several BRCA mutations, most of Spanish origin, to be founder mutations in Hispanic populations.  We hypothesized that the same population factors may be operative in Lynch syndrome.  There is limited literature on the spectrum of mutations in mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) in Hispanic populations.  The goal of this study was to identify recurrent MMR mutations in Hispanic patients and explore potential ancestral origins of identified mutations. 
Methods:  Subjects included Hispanic patients seen for genetic cancer risk assessment at City of Hope Clinical Cancer Genetics Community Research Network collaborating institutions, MD Anderson Cancer Center, USC Norris Comprehensive Cancer Center and the University of Puerto Rico Comprehensive Cancer Center.  A total of 120 patients underwent genotyping for mutations in one or more of the four MMR genes due to abnormal MSI, loss of MMR protein(s) on IHC, and/or strong family history.  A comprehensive review of the literature and of multiple MMR variant databases was conducted for all identified mutations. 
Results:  Sixty unrelated Hispanic families were found to have at least one MMR gene mutation and among these, 49 different mutations were identified (33-MLH1, 19-MSH2, 6-MSH6, and 2-PMS2).  Nine mutations were observed two or more times: MLH1 350C>T, 1790del2ins9, 2041G>A, 1852del3, 1024del16, and IVS7+5G>A; and MSH2 1216C>T, 425C>G, and 1705delGA. Most (6/9) recurrent mutations were detected in separate institutions.  MSH2 1216C>T, MSH2 1705delGA, and MLH1 1852del3 were each seen three times and have been reported multiple times in various European populations. MLH1 350C>T, 2041G>A, 332C>T, and 676C>T and MSH2 1216C>T, deletion of exons 4-8, and deletion of exon 8 have all been reported previously in Spain.  The MSH2 deletion of exons 4-8 was seen in one Mexican family in our series and has been reported as a Spanish founder mutation.  Though seen twice at one center in our series, to our knowledge, MLH1 1790del2ins9 has not been previously reported in the literature or MMR mutation databases, nor have 18 other mutations identified in our cohort. 
Conclusion:  Our finding, that three of the nine recurrent mutations and the MSH2 deletion of exon 8 identified in our cohort were previously reported in Spain, supports the hypothesis of the likely influence of Spanish ancestral heritage on MMR gene mutations in Hispanic populations.  While this is the largest reported cohort of Hispanic patients with MMR mutations in North America, a larger sample and haplotype analyses are needed to  better define the spectrum and origin of MMR mutations in Hispanic populations.
Searching for Recurrent MMR Mutations in Hispanic Patients. A poster presentation at the NSGC 32nd Annual Education Conference.
Espenschied C, Sunga A, Herzog J, Bannon S, Lynch P, et al. ; 2013 October 9-12; Anaheim, CA.
Knowledge of founder mutations can enable efficient and cost-effective strategies for genetic testing, a potential benefit for populations with otherwise limited access to services.  We have shown several BRCA mutations, most of Spanish origin, to be founder mutations in Hispanic populations.  We hypothesized that the same population factors may be operative in Lynch syndrome.  There is limited literature on the spectrum of mismatch repair (MMR) gene mutations (MLH1, MSH2, MSH6, and PMS2) in Hispanic populations.  This study aims to identify recurrent MMR mutations in Hispanic patients and explore potential ancestral origins of mutations identified.  Subjects included Hispanic patients seen for genetic cancer risk assessment at City of Hope Clinical Cancer Genetics Community Research Network collaborating institutions and at MD Anderson Cancer Center.  Literature review was performed for all mutations identified.  Among 30 unrelated Hispanic families, 26 different MMR mutations were identified.  MLH1 350C>T and MLH1 1790del2ins9 were each seen in two families and MSH2 1216C>T was seen in three families in our cohort.  Literature review revealed that MLH1 350C>T and MSH2 1216C>T have been reported in the Spanish and other European populations.  We found no previous reports of MLH11790del2ins9.  A deletion of exons 4-8 in MSH2 was seen in one Mexican family and has been reported as a Spanish founder mutation.  Given that two of three recurrent mutations in our cohort were previously reported in the Spanish population, and an additional large deletion has been reported as a Spanish founder mutation, this provides evidence of population factors similar to those previously described among BRCA carriers.  To our knowledge, this is the largest reported cohort of Hispanic patients with MMR mutations in North America; however, the sample is small and further studies are needed to expand and better define the spectrum and origin of MMR mutations in Hispanic populations.
Next-generation Sequencing for Genetic Cancer Risk Assessment. A poster presentation at the ASCO annual meeting.
Blazer KR, Espenschied C, Weissman S, Sand S, Weitzel JN. ; 2013 May 31-June 4; Chicago, Illinois.
Background: Current standard-of-care practice for genetic cancer risk assessment (GCRA) focuses on single-gene testing for specific hereditary cancer syndromes. Next-generation sequencing (NGS) technologies recently became available for clinical applications. This study explored the perspectives and experiences of community-based clinicians regarding NGS testing for personalized GCRA.
Methods: A 27-item survey was developed and administered online to 325 members of an interdisciplinary nationwide clinical cancer genetics community of practice. Results: Of 94 (29%) respondents, 25 (27%) have ordered at least one multi-gene panel and only 2 (2.1%) have ordered a whole exome or genome test from a commercial vendor for GCRA. Concerns about clinical utility, the challenge of interpreting and communicating results, lack of knowledge about and potential costs were most often cited as reasons for not pursuing NGS testing. Respondents were significantly more confident about their ability to interpret and counsel about single gene test results compared with multi-gene panels or whole exome/genome sequencing; and about multi-gene panels over whole exome/genome sequencing (p<.0001 for all comparisons).
Conclusions: Findings suggest that while NGS tests are entering the realm of GCRA, multidisciplinary genomics education and clinical support resources are needed to address barriers to utilization and promote successful integration of NGS testing into community-based GCRA practice settings.
Prevalence and type of BRCA mutations in Hispanics undergoing genetic cancer risk assessment in the southwestern United States: a report from the Clinical Cancer Genetics Community Research Network.
Weitzel JN, Clague J, Martir-Negron A, Ogaz R, Herzog J, et al. (2013) Journal of Clinical Oncology 31: 210-216.
Purpose: To determine the prevalence and type of BRCA1 and BRCA2 (BRCA) mutations among Hispanics in the Southwestern United States and their potential impact on genetic cancer risk assessment (GCRA).
Patients and Methods: Hispanics (n = 746) with a personal or family history of breast and/or ovarian cancer were enrolled in an institutional review board–approved registry and received GCRA and BRCA testing within a consortium of 14 clinics. Population-based Hispanic breast cancer cases (n = 492) enrolled in the Northern California Breast Cancer Family Registry, negative by sequencing for BRCA mutations, were analyzed for the presence of the BRCA1 ex9-12del large rearrangement.
Results: Deleterious BRCA mutations were detected in 189 (25%) of 746 familial clinic patients (124 BRCA1, 65 BRCA2); 21 (11%) of 189 were large rearrangement mutations, of which 62% (13 of 21) were BRCA1 ex9-12del. Nine recurrent mutations accounted for 53% of the total. Among these, BRCA1 ex9-12del seems to be a Mexican founder mutation and represents 10% to 12% of all BRCA1 mutations in clinic- and population-based cohorts in the United States.
Conclusion: BRCA mutations were prevalent in the largest study of Hispanic breast and/or ovarian cancer families in the United States to date, and a significant proportion were large rearrangement mutations. The high frequency of large rearrangement mutations warrants screening in every case. We document the first Mexican founder mutation (BRCA1 ex9-12del), which, along with other recurrent mutations, suggests the potential for a cost-effective panel approach to ancestry-informed GCRA.
Impact of Web-based Case Conferencing on Cancer Genetics Training Outcomes for Community-based Clinicians.
Blazer, K. R., Christie, C., Uman, G., & Weitzel, J. N. (2012) Journal of Cancer Education; 27: 217-225.
Introduction: Technology and market forces are driving the demand for cancer risk assessment services in the community setting, where few clinicians are trained to order and interpret predictive genetic tests. City of Hope conducts a three-phase course in genetic cancer risk assessment (GCRA) for community-based clinicians, comprised of distance didactics, face-to-face workshops and 12 months of professional development. As designed, the course cannot meet increasing demands for GCRA training. Action research identified face-to-face workshops as a barrier to increasing course capacity. This study compared the learning effectiveness of Web-based case conferencing to face-to-face training.
Methods: A quasi-experimental design compared pre-post knowledge, skills and professional self-efficacy outcomes from 2009-2010 course cohorts (n=96). The intervention group (n=52) engaged in Web-based case conferences during distance learning; the comparison group (n=44) participated in the course as originally designed.
Results: Both groups and all practice disciplines demonstrated significant pre-to-post increases on all measures. Knowledge increases were higher for the intervention group (p < .015); skills and self-efficacy increases were comparable between groups (p < .33 and p < .30, respectively).
Discussion: Findings support the learning utility of Web-based case conferencing. Further studies may inform the development of tools to assess the impact of Web-based case conferencing on practice change and patient outcomes, in alignment with the highest standards of continuing professional development.
Closing the Loop: Action research in a multimodal hereditary cancer patient conference is an effective tool to assess and address patient needs.
Espenschied, C. R., MacDonald, D. J., Culver, J. O., Sand, S., Hurley, K., Banks, K. C., Weitzel, J. N., Blazer, K. R.. (2012) Journal of Cancer Education; 27: 467-477.
This paper describes the use of action research in a patient conference to provide updated hereditary cancer information, explore patient and family member needs and experiences related to genetic cancer risk assessment (GCRA), elicit feedback on how to improve the GCRA process, and inform future research efforts. Invitees completed GCRA at City of Hope or collaborating facilities and had a BRCA mutation or a strong personal or family history of breast cancer. Action research activities were facilitated by surveys, roundtable discussions, and Reflection Time to engage participants, faculty, and researchers in multiple cycles of reciprocal feedback. The multimodal action research design effectively engaged conference participants to share their experiences, needs, and ideas for improvements to the GCRA process. Participants indicated that they highly valued the information and resources provided and desired similar future conferences. The use of action research in a patient conference is an innovative and effective approach to provide health education, elicit experiences, and needs of high-risk patients and their family members, and generate research hypotheses. Insights gained yielded valuable feedback to inform clinical care, future health services research, and Continuing Medical Education.
Reflex Immunohistochemistry and Microsatellite Instability Testing of Colorectal Tumors for Lynch Syndrome among US Cancer Programs and Follow-up of Abnormal Results.
Beamer, L., Grant, M., Huizenga, C., Blazer, K.R., Hampel, H., Weitzel, J.N., MacDonald, D.J. (2012) Journal of Clinical Oncology; 30: 1058-1063.
Background: Immunohistochemistry (IHC) for MLH1, MSH2, MSH6, and PMS2 protein expression and microsatellite instability (MSI) are well-established tools to screen for Lynch Syndrome (LS). While many cancer centers have adopted these tools as reflex LS-screening following a colorectal cancer diagnosis, to date the standard of care has not been established and no formal studies have described this practice in the U.S.
Purpose: To describe the prevalent practices regarding IHC/MSI reflex testing for LS in the U.S. and subsequent follow-up of abnormal results.
Methods: A 12-item survey was developed following interdisciplinary expert input. A letter of invitation, survey, and online-survey option was sent to a contact at each cancer program. A modified Dillman’s strategy was used to maximize response rate. The sample included 39 NCI-designated Comprehensive Cancer Centers (NCI-CCC), 50 randomly-selected ACS-accredited Community Hospital Comprehensive Cancer Programs (COMPs) and 50 Community Hospital Cancer Programs (CHCPs).
Results: The overall response rate was 50%. Seventy-one percent of NCI-CCCs, 36% of COMPs, and 15% of CHCPs were conducting reflex IHC/MSI for LS; 48% used IHC, 14% used MSI and 38% used both. One program used a pre-surgical information packet, four offered an opt-out option, and none required written consent.
Conclusion: While most NCI-CCCs use reflex IHC/MSI to screen for LS, this practice is not well-adopted by community hospitals. These findings may indicate an emerging standard of care and diffusion from NCI-CCC to community cancer programs. Our findings also describe an important trend away from requiring written patient consent for screening.
Genetics, Genomics and Cancer Risk Assessment: State of the art and future directions in the era of personalized medicine.
Weitzel, J. N., Blazer, K. R., MacDonald, D. J., Culver, J. O., & Offit, K. (2011) CA-Cancer J Clin, 61(5), 327-359
Scientific and technologic advances are revolutionizing our approach to genetic cancer risk assessment, cancer screening and prevention, and targeted therapy, fulfilling the promise of personalized medicine. In this monograph we review the evolution of scientific discovery in cancer genetics and genomics, and describe current approaches, benefits and barriers to the translation of this information to the practice of preventive medicine. Summaries of known hereditary cancer syndromes and highly penetrant genes are provided and contrasted with recently-discovered genomic variants associated with modest increases in cancer risk. We describe the scope of knowledge, tools, and expertise required for the translation of complex genetic and genomic test information into clinical practice. The challenges of genomic counseling include the need for genetics and genomics professional education and multidisciplinary team training, the need for evidence-based information regarding the clinical utility of testing for genomic variants, the potential dangers posed by premature marketing of first-generation genomic profiles, and the need for new clinical models to improve access to and responsible communication of complex disease-risk information. We conclude that given the experiences and lessons learned in the genetics era, the multidisciplinary model of genetic cancer risk assessment and management will serve as a solid foundation to support the integration of personalized genomic information into the practice of cancer medicine.
Personalized cancer genetics training for personalized medicine: Improving community-based healthcare through a genetically literate workforce.
Blazer, K. R., MacDonald, D. J., Culver, J. O., Huizenga, C. R., Morgan, R. J., Uman, G. C., Weitzel, J. N. (2011) Genet Med, 13(9), 832-840.
Purpose: To assess the impact of a multimodal interdisciplinary course on genetic cancer risk assessment and research collaboration for community-based clinicians. Clinicians are increasingly requested to conduct genetic cancer risk assessment, but many are inadequately prepared to provide these services.
Methods: A prospective analysis of 131 participants (48 physicians, 41 advanced-practice nurses, and 42 genetic counselors) from community settings across the United States. The course was delivered in three phases: distance didactic learning, face-to-face training, and 12 months of web-based professional development activities to support integration of skills into practice. Cancer genetics knowledge, skills, professional self-efficacy, and practice changes were measured at baseline, immediate, and 14 months post-course.
Results: Knowledge, skills, and self-efficacy scores were significantly different between practice disciplines; however, post-scores increased significantly overall and for each discipline (P < 0.001). Fourteen-month practice outcomes reflect significant increases in provision of genetic cancer risk assessment services (P = 0.018), dissemination of cancer prevention information (P = 0.005) and high-risk screening recommendations (P = 0.004) to patients, patient enrollment in research (P = 0.013), and educational outreach about genetic cancer risk assessment (P = 0.003).
Conclusions: Results support the efficacy of the multimodal course as a tool to develop a genetically literate workforce. Sustained alumni participation in web-based professional development activities has evolved into a distance-mediated community of practice in clinical cancer genetics, modeling the lifelong learning goals envisioned by leading continuing medical education stakeholders.