Search

This study demonstrates the replication and validation of a prior model of women’s pathways to prison that was initially developed in California Women’s prisons and subsequently implemented in the Massachusetts Department of Correction (MADOC) women’s prison in 2013. The following four main pathways were identified: (1) Quasi-normal, least disturbed, drug and situational offending; (2) lifelong abused and depressed drug abusing women; (3) socialized subcultural women, with chronic crimes and drug abuse; and (4) abused and aggressive, early onset and multi-need women with severe drugs, crime, and mental health issues. Since 2013, this model has routinely functioned in MADOC women’s prison as an internal classification (IC) for women detainees. Using a newly extracted sample of approximately 1,800 cases from MADOC, several forms of replication and validation were conducted; these demonstrated cross-sample stability, cross-method stability, and stability across time and region. Implications for theory, treatment planning, and implementation are discussed.

Genomic alterations in lung adenocarcinoma displayed in Figure 2A.

Focal amplification and activating point mutation of the MET gene are well-characterized oncogenic drivers that confer susceptibility to targeted MET inhibitors. Recurrent somatic splice site alterations at MET exon 14 (METex14) that result in exon skipping and MET activation have been characterized, but their full diversity and prevalence across tumor types are unknown. Here, we report analysis of tumor genomic profiles from 38,028 patients to identify 221 cases with METex14 mutations (0.6%), including 126 distinct sequence variants. METex14 mutations are detected most frequently in lung adenocarcinoma (3%), but also frequently in other lung neoplasms (2.3%), brain glioma (0.4%), and tumors of unknown primary origin (0.4%). Further in vitro studies demonstrate sensitivity to MET inhibitors in cells harboring METex14 alterations. We also report three new patient cases with METex14 alterations in lung or histiocytic sarcoma tumors that showed durable response to two different MET-targeted therapies. The diversity of METex14 mutations indicates that diagnostic testing via comprehensive genomic profiling is necessary for detection in a clinical setting.Significance: Here we report the identification of diverse exon 14 splice site alterations in MET that result in constitutive activity of this receptor and oncogenic transformation in vitro. Patients whose tumors harbored these alterations derived meaningful clinical benefit from MET inhibitors. Collectively, these data support the role of METex14 alterations as drivers of tumorigenesis, and identify a unique subset of patients likely to derive benefit from MET inhibitors. Cancer Discov; 5(8); 850–9. ©2015 AACR.See related commentary by Ma, p. 802.See related article by Paik et al., p. 842.This article is highlighted in the In This Issue feature, p. 783

To summarize current guidance and best practices surrounding non-orthopedic medical concerns in baseball.Discussion of COVID19-related practice changes pertaining to the prevention and screening of communicable respiratory illness, concussion protocol updates, the enhanced role of a multi-disciplinary team of mental health professionals. Prevention, appropriate screening, and early identification remain cornerstones of effective primary care both within the general population as well as for the baseball athlete.

Acute myeloid leukemia (AML) is the most common diagnosed leukemia. In older adults, AML confers an adverse outcome1,2. AML originates from a dominant mutation, then acquires collaborative transformative mutations leading to myeloid transformation and clinical/biological heterogeneity. Currently, AML treatment is initiated rapidly, precluding the ability to consider the mutational profile of a patient’s leukemia for treatment decisions. Untreated patients with AML ≥ 60 years were prospectively enrolled on the ongoing Beat AML trial (ClinicalTrials.gov NCT03013998 ), which aims to provide cytogenetic and mutational data within 7 days (d) from sample receipt and before treatment selection, followed by treatment assignment to a sub-study based on the dominant clone. A total of 487 patients with suspected AML were enrolled; 395 were eligible. Median age was 72 years (range 60–92 years; 38% ≥75 years); 374 patients (94.7%) had genetic and cytogenetic analysis completed within 7 d and were centrally assigned to a Beat AML sub-study; 224 (56.7%) were enrolled on a Beat AML sub-study. The remaining 171 patients elected standard of care (SOC) (103), investigational therapy (28) or palliative care (40); 9 died before treatment assignment. Demographic, laboratory and molecular characteristics were not significantly different between patients on the Beat AML sub-studies and those receiving SOC (induction with cytarabine + daunorubicin (7 + 3 or equivalent) or hypomethylation agent). Thirty-day mortality was less frequent and overall survival was significantly longer for patients enrolled on the Beat AML sub-studies versus those who elected SOC. A precision medicine therapy strategy in AML is feasible within 7 d, allowing patients and physicians to rapidly incorporate genomic data into treatment decisions without increasing early death or adversely impacting overall survival. Preliminary results from the Beat AML umbrella trial demonstrates the feasibility and efficacy of applying prospective genomic profiling for matching newly diagnosed patients with AML with targeted therapies.

Genomic profiling of circulating tumor DNA derived from cell-free DNA (cfDNA) in blood can provide a noninvasive method for detecting genomic biomarkers to guide clinical decision making for cancer patients. We developed a hybrid capture–based next-generation sequencing assay for genomic profiling of circulating tumor DNA from blood (FoundationACT). High-sequencing coverage and molecular barcode–based error detection enabled accurate detection of genomic alterations, including short variants (base substitutions, short insertions/deletions) and genomic re-arrangements at low allele frequencies (AFs), and copy number amplifications. Analytical validation was performed on 2666 reference alterations. The assay achieved >99% overall sensitivity (95% CI, 99.1%–99.4%) for short variants at AF >0.5%, >95% sensitivity (95% CI, 94.2%–95.7%) for AF 0.25% to 0.5%, and 70% sensitivity (95% CI, 68.2%–71.5%) for AF 0.125% to 0.25%. No false positives were detected in 62 samples from healthy volunteers. Genomic alterations detected by FoundationACT demonstrated high concordance with orthogonal assays run on the same clinical cfDNA samples. In 860 routine clinical FoundationACT cases, genomic alterations were detected in cfDNA at comparable frequencies to tissue; for the subset of cases with temporally matched tissue and blood samples, 75% of genomic alterations and 83% of short variant mutations detected in tissue were also detected in cfDNA. On the basis of analytical validation results, FoundationACT has been approved for use in our Clinical Laboratory Improvement Amendments–certified/College of American Pathologists–accredited/New York State–approved laboratory.

Background Gangliogliomas are slow-growing, low-grade central nervous system tumors affecting children and young adults. However, some patients will experience tumor recurrence and/or malignant progression. This article reports on the clinical history, molecular findings, and treatment response in a patient with BRAF V600-mutated high-grade glioma arising from ganglioglioma. Methods Hematoxylin-eosin staining and comprehensive genomic profiling via Foundation One were performed on the tumor sample from a male patient undergoing treatment at the Department of Neuro-Oncology at Baylor University Medical Center. Results The patient was eligible for participation in a clinical trial (ClinicalTrials.gov identifier: NCT00916409) of a tumor treatment fields (TTFields) device, NovoTTF-100A, with concurrent radiation and chemotherapy (CCRT). His disease relapsed 4 months after completion of his CCRT, with MRI showing areas of enhancement. Temozolomide was discontinued and he was offered dabrafenib, an oral selective inhibitor of BRAF V600E, with continued use of NovoTTF. At the time of this report, after 2 years of treatment with dabrafenib and TTFields, the patient shows a durable complete response in all areas with no active lesions or new areas of enhancement. Conclusions This report suggests that TTFields delivered in combination with targeted therapy dabrafenib yielded a remarkable clinical and radiologic response in this recurrent high-grade glioma. Targeted therapy matched to genomic alterations combined with TTFields treatment could provide clinical benefit and should be prospectively explored in the near future.

The spectrum of somatic alterations in hematologic malignancies includes substitutions, insertions/deletions (indels), copy number alterations (CNAs), and a wide range of gene fusions; no current clinically available single assay captures the different types of alterations. We developed a novel next-generation sequencing-based assay to identify all classes of genomic alterations using archived formalin-fixed paraffin-embedded blood and bone marrow samples with high accuracy in a clinically relevant time frame, which is performed in our Clinical Laboratory Improvement Amendments-certified College of American Pathologists-accredited laboratory. Targeted capture of DNA/RNA and next-generation sequencing reliably identifies substitutions, indels, CNAs, and gene fusions, with similar accuracy to lower-throughput assays that focus on specific genes and types of genomic alterations. Profiling of 3696 samples identified recurrent somatic alterations that impact diagnosis, prognosis, and therapy selection. This comprehensive genomic profiling approach has proved effective in detecting all types of genomic alterations, including fusion transcripts, which increases the ability to identify clinically relevant genomic alterations with therapeutic relevance.

Cisplatin-based neoadjuvant chemotherapy (NAC) before cystectomy is the standard of care for muscle-invasive bladder cancer (MIBC), with 25-50% of patients expected to achieve a pathologic response. Validated biomarkers predictive of response are currently lacking.To discover and validate biomarkers predictive of response to NAC for MIBC.Pretreatment MIBC samples prospectively collected from patients treated in two separate clinical trials of cisplatin-based NAC provided the discovery and validation sets. DNA from pretreatment tumor tissue was sequenced for all coding exons of 287 cancer-related genes and was analyzed for base substitutions, indels, copy number alterations, and selected rearrangements in a Clinical Laboratory Improvements Amendments-certified laboratory.The mean number of variants and variant status for each gene were correlated with response. Variant data from the discovery cohort were used to create a classification tree to discriminate responders from nonresponders. The resulting decision rule was then tested in the independent validation set.Patients with a pathologic complete response had more alterations than those with residual tumor in both the discovery (p=0.024) and validation (p=0.018) sets. In the discovery set, alteration in one or more of the three DNA repair genes ATM, RB1, and FANCC predicted pathologic response (p0.001; 87% sensitivity, 100% specificity) and better overall survival (p=0.007). This test remained predictive for pathologic response in the validation set (p=0.033), with a trend towards better overall survival (p=0.055). These results require further validation in additional sample sets.Genomic alterations in the DNA repair-associated genes ATM, RB1, and FANCC predict response and clinical benefit after cisplatin-based chemotherapy for MIBC. The results suggest that defective DNA repair renders tumors sensitive to cisplatin.Chemotherapy given before bladder removal (cystectomy) improves the chance of cure for some but not all patients with muscle-invasive bladder cancer. We found a set of genetic mutations that when present in tumor tissue predict benefit from neoadjuvant chemotherapy, suggesting that testing before chemotherapy may help in selecting patients for whom this approach is recommended.

From rudimentary conceptions of risk in the late 18th century, risk assessment slowly evolved toward a more multifaceted conceptualization of risk and progressed to more sophisticated methods to calibrate offender risk levels. This story largely involves the struggles in criminology and applied agencies to achieve a successful “science-to-practice” advancement in risk technologies to support criminal justice decision making. This has involved scientific measurement issues such as reliability, predictive validity, construct validity, and ways to assess the accuracy of predictions and to effectively implement risk assessment methods. The urgent call for higher predictive accuracy from criminal justice policymakers has constantly motivated such change. Over time, the concept of risk has fragmented as diverse agencies, including pretrial release, probation, courts, and jails, have sought to assess specific risk outcomes that are critical for their policy goals. Most agencies are engaged in both risk assessment and risk reduction, with the latter requiring a deeper assessment of explanatory factors. Currently, risk assessment in criminal justice faces several turbulent challenges. The explosive trends in information technology regarding data access, computer memories, and processing speed are combining with new predictive analytic methods that may challenge the currently dominant techniques of risk assessment. A final challenge is that there is, as yet, insufficient standardization of risk assessment methods; nor are there any common language or definitions for offender risk categories. Thus, recent proposals for standardization are examined.

*equal contribution of AB, RLL, BD and JCB Background: Acute myeloid leukemia (AML) is common with increasing age, and older adults with AML rarely achieve long-term remission with chemotherapy. Gene discovery studies in older adults with AML have shown that this malignancy is characterized by a multitude of somatic genomic alterations beginning with initiating somatic events followed by acquisition of collaborative transforming mutations. Despite these important biologic insights, current therapeutic approaches to AML remain limited, particularly in adults ≥ 60 years of age. The Beat AML trial was designed to assess the feasibility of using genetic profiling to assign patients (pts) to molecularly defined, subtype-specific therapies within 7 days of the initial diagnosis in a multi-center clinical trial setting, and to delineate the role of molecularly informed first-line treatment of AML with mechanism based novel therapies. Methods: Treatment-naïve patients with AML were enrolled in this prospective trial which offered accelerated cytogenetic and comprehensive mutational testing within 7 days followed by treatment assignment using these molecular data. Pt eligibility included age ≥ 60 years with non-APML AML, no known CNS leukemia, no prior hypomethylating agent (HMA) therapy and no clinical need for emergent therapy. Eligible pts were profiled by local cytogenetics analysis and using a central next generation sequencing (NGS) assay (Foundation Medicine, Inc.) with all molecular data required for treatment assignment (TA) obtained < 7 days. TA was made centrally using a pre-determined algorithm considering somatic cytogenetic and molecular alterations in the dominant clone, available targeted therapeutics for specific AML subsets, and the likelihood of cure with intensive chemotherapy. Results: From November 2016 to January 2019, 487 pts with a suspected diagnosis of AML had enrolled at 14 clinical sites; 395 were eligible for the study (77% of the patients not eligible for the study had an alternative diagnosis). The median age of eligible patients was 72 years (range: 60 to 92) with 38% being≥ 75 years and 16% with treatment-related AML. From the 395 eligible patients, 374 (94.7%) were centrally assigned to the different cytogenetic/genomic groups within 7 days. The most common groups were TP53 mutated (19%) and marker negative (18%) molecular groups. The Beat AML trial is dynamic by design, thereby allowing different arms to open over time; all trial arms are designed to evaluate for substantial clinical efficacy in small, molecularly defined patient subsets. As shown in Figure 1, 224 patients (57%) had a TA and consented to a BEAT AML sub-study. Of the remaining 171 patients, 103 received standard therapy defined as induction therapy (7+3) or hypomethylation agent (25 before TA and 78 after TA), 28 received an alternative investigational agent (5 before TA and 23 after TA), 38 received palliative care, and 2 had an unknown treatment status and are grouped with the palliative care patients in subsequent analyses; 9 patients died before TA (2 who received standard therapy and 7 in the palliative care group). Demographic, clinical, performance and molecular characteristics were not largely different between pts who elected targeted therapy as part of the BEAT AML trial versus those who elected standard therapy. As shown in Figure 2, the overall survival was significantly longer for patients enrolled in a targeted therapy arm as part of the BEAT AML trial compared to those who elected standard therapy. (p Conclusion: Our data support the feasibility of a rapid precision medicine approach in older patients with previously untreated AML. Patients with AML who elected treatment assigned based upon cytogenetic and molecular alterations in the dominant clone using a novel precision medicine approach had significantly improved overall survival versus those who elected standard of care treatment. Disclosures Levine: Gilead: Consultancy; Prelude Therapeutics: Research Funding; Celgene: Consultancy, Research Funding; Novartis: Consultancy; Isoplexis: Membership on an entity's Board of Directors or advisory committees; Roche: Consultancy, Research Funding; Qiagen: Membership on an entity's Board of Directors or advisory committees; Loxo: Membership on an entity's Board of Directors or advisory committees; Imago Biosciences: Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Membership on an entity's Board of Directors or advisory committees; Amgen: Honoraria; Lilly: Honoraria. Mims:Abbvie: Membership on an entity's Board of Directors or advisory committees; Agios Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Astellas Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; PTC Therapeutics: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Borate:Novartis: Consultancy; Takeda: Consultancy; Pfizer: Consultancy; Daiichi Sankyo: Consultancy; AbbVie: Consultancy. Stein:Agios: Consultancy, Membership on an entity's Board of Directors or advisory committees; Astellas Pharma US, Inc: Membership on an entity's Board of Directors or advisory committees; Celgene Corporation: Membership on an entity's Board of Directors or advisory committees; PTC Therapeutics: Membership on an entity's Board of Directors or advisory committees; Syros: Membership on an entity's Board of Directors or advisory committees; Daiichi Sankyo, Inc.: Membership on an entity's Board of Directors or advisory committees; Bioline: Membership on an entity's Board of Directors or advisory committees; Genentech: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees. Patel:France Foundation: Honoraria; Dava Oncology: Honoraria; Celgene: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Baer:Takeda: Research Funding; Incyte: Research Funding; Kite: Research Funding; Forma: Research Funding; AI Therapeutics: Research Funding; Abbvie: Research Funding; Astellas: Research Funding. Stock:Daiichi: Membership on an entity's Board of Directors or advisory committees; Agios: Membership on an entity's Board of Directors or advisory committees; Astellas: Membership on an entity's Board of Directors or advisory committees; Research to Practice: Honoraria; UpToDate: Honoraria; Kite, a Gilead Company: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees. Deininger:Pfizer: Consultancy, Honoraria, Research Funding; Ascentage Pharma: Consultancy, Honoraria; TRM: Consultancy; Sangoma: Consultancy; Fusion Pharma: Consultancy; Adelphi: Consultancy; Takeda: Honoraria, Membership on an entity's Board of Directors or advisory committees; Humana: Honoraria; Incyte: Honoraria; Novartis: Honoraria; Sangamo: Consultancy; Blueprint: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees. Blum:Boehringer Ingelheim: Research Funding; Celgene: Research Funding; Astellas,: Research Funding; Xencor: Research Funding; Forma: Research Funding; AmerisourceBergen: Consultancy. Schiller:Amgen: Other, Research Funding; Agios: Research Funding, Speakers Bureau; Celgene: Research Funding, Speakers Bureau; Constellation Pharmaceutical: Research Funding; Daiichi Sankyo: Research Funding; Eli Lilly and Company: Research Funding; FujiFilm: Research Funding; Genzyme: Research Funding; Gilead: Research Funding; Incyte: Research Funding; J&J: Research Funding; Jazz Pharmaceuticals: Honoraria, Research Funding; Karyopharm: Research Funding; Novartis: Research Funding; Onconova: Research Funding; Pfizer Pharmaceuticals: Equity Ownership, Research Funding; Sangamo Therapeutics: Research Funding; Bristol Myer Squibb: Research Funding; Astellas: Research Funding; Biomed Valley Discoveries: Research Funding. Olin:Daiichi Sankyo: Research Funding; Astellas: Research Funding; Genentech: Consultancy, Research Funding; Pfizer: Research Funding; Jazz Pharmaceuticals: Consultancy, Honoraria; Revolution Medicine: Consultancy; AstraZeneca: Research Funding; Clovis: Research Funding; Ignyta: Research Funding; MedImmune: Research Funding; Mirati Therapeutics: Research Funding; Novartis: Research Funding; Spectrum: Research Funding. Foran:Agios: Honoraria, Research Funding. Lin:Pfizer: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Honoraria. Traer:AbbVie: Consultancy; Agios: Consultancy; Astellas: Consultancy; Daiichi Sankyo: Consultancy; Notable Labs: Equity Ownership. Odenike:AbbVie: Consultancy, Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Incyte: Research Funding; Astra Zeneca: Research Funding; Astex Pharmaceuticals: Research Funding; NS Pharma: Research Funding; Gilead Sciences: Research Funding; Janssen Oncology: Research Funding; Oncotherapy: Research Funding; Agios: Research Funding; CTI/Baxalta: Research Funding. Arellano:Gilead: Consultancy. Vergilio:Roche Holding AG: Equity Ownership; Foundation Medicine: Employment. Brennan:Foundation Medicine: Employment. Vietz:Foundation Medicine: Employment. Druker:ALLCRON: Membership on an entity's Board of Directors or advisory committees; Pfizer: Research Funding; Aileron Therapeutics: #2573, Constructs and cell lines harboring various mutations in TNK2 and PTPN11, licensing fees , Membership on an entity's Board of Directors or advisory committees; Bristol-Myers Squibb: Patents & Royalties, Research Funding; Burroughs Wellcome Fund: Membership on an entity's Board of Directors or advisory committees; Cepheid: Consultancy, Honoraria; The RUNX1 Research Program: Membership on an entity's Board of Directors or advisory committees; GRAIL: Equity Ownership, Other: former member of Scientific Advisory Board; Patient True Talk: Consultancy; Dana-Farber Cancer Institute (antibody royalty): Patents & Royalties: #2524, antibody royalty; Pfizer: Other: PI or co-investigator on clinical trial(s) funded via contract with OHSU., Research Funding; Merck & Co: Patents & Royalties: Dana-Farber Cancer Institute license #2063, Monoclonal antiphosphotyrosine antibody 4G10, exclusive commercial license to Merck & Co; OHSU (licensing fees): Patents & Royalties: #2573, Constructs and cell lines harboring various mutations in TNK2 and PTPN11, licensing fees ; Amgen: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Aptose Biosciences: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Beta Cat: Membership on an entity's Board of Directors or advisory committees, Other: Stock options; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees, Other: Stock options; Beat AML LLC: Other: Service on joint steering committee; CureOne: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy; Gilead Sciences: Other: former member of Scientific Advisory Board; ICON: Other: Scientific Founder of Molecular MD, which was acquired by ICON in Feb. 2019; Monojul: Other: former consultant; Novartis: Other: PI or co-investigator on clinical trial(s) funded via contract with OHSU., Patents & Royalties: Patent 6958335, Treatment of Gastrointestinal Stromal Tumors, exclusively licensed to Novartis, Research Funding; Bristol-Myers Squibb: Other: PI or co-investigator on clinical trial(s) funded via contract with OHSU., Research Funding. Byrd:Novartis: Other: Travel Expenses, Speakers Bureau; BeiGene: Research Funding; Pharmacyclics LLC, an AbbVie Company: Other: Travel Expenses, Research Funding, Speakers Bureau; Acerta: Research Funding; Ohio State University: Patents & Royalties: OSU-2S; Genentech: Research Funding; Gilead: Other: Travel Expenses, Research Funding, Speakers Bureau; TG Therapeutics: Other: Travel Expenses, Research Funding, Speakers Bureau; Janssen: Consultancy, Other: Travel Expenses, Research Funding, Speakers Bureau.

Background. FNAC are generated during the FNA procedure - for example, commonly used in conjunction with endobronchial ultrasound (EBUS-FNA) as a minimally invasive tool for the diagnosis and management of non small-cell lung cancer (NSCLC) - as a histologic QC for the presence of malignant cells. Formalin-fixed core biopsies and aspirate cell blocks (FNACB) are then created for comprehensive genomic profiling (CGP). However, the routine pathology workup may render the FNACB unable to generate a CGP result, while the FNAC remain in reserve. In the current study we performed a retrospective multi-cancer, multi-institutional analysis of FNAC performance, including computed tumor purity analysis, using a regulated commercial grade CGP assay. Experimental procedures. 119 FNAC met minimum specimen cellularity (10K total cellularity) and DNA extraction (50ng) criteria for CGP. Extracted DNA from FNACS underwent hybrid-capture-based CGP for all classes of genomic alterations in 315 genes. Tumor mutational burden (TMB) was determined on 1.1 Mbp of sequenced DNA and microsatellite instability (MSI) was determined on 114 loci. A comparison set of 182 FNACB specimens underwent the same CGP assay. Individual specimen CGPs were annotated as Pass, Fail, or Qualified per computational biology standard procedures that factor in sequencing quality metrics such as mean target coverage and computational tumor purity modeling. Results. The 119 FNAC, collected at 14 different medical facilities, encompassed 44 distinct tumor disease ontologies (DO) from 17 unique anatomic biopsy sites. 105 of 119 FNACS (88%) received a passing report, 10 (8%) were qualified, and 4 (3%) failed. In the FNACB comparison group, 155 of 182 reports were pass (85%), 22 qualified (12%), and 5 failed (3%). The number of passing reports in FNACS versus FNACB was equivalent (P=0.5). The FNAC had a significantly higher mean target coverage than FNACB (703 vs 665; P= 0.04995). The average computational tumor purity metric was significantly higher in FNACS than in FNACB (57.9% vs. 45.3%; P=0.00001). Conclusions. This study provides new data from FNAC that further support their utility for clinical testing. FNAC derived from multiple medical facilities, biopsy sites, and tumor types were found to be equivalent or superior to FNACB for CGP. Finally, the relative cellular homogeneity and high tumor cell content of both FNAC and FNACB likely confirms the discohesiveness of malignant cells and enables CGP without required enrichment given that macrodissection would be challenging for these samples in a daily practice setting. Citation Format: Jonathan K. Killian, Dean Pavlick, Lindsay Croshier, John Truesdell, Chris Wright, Tim Brennan, Vera Banning, Lazaro Garcia, Laurie Gay, Gene Stirchak, Jo-Anne Vergilio, Christine Malboeuf, Nhu Ngo, Julia Elvin, Siraj Ali, Vince Miller, Jeffrey S. Ross. A multi-institutional, multi-tumor analysis of fine needle aspiration (FNA) cytology smear (FNAC) performance in clinical comprehensive genomic profiling [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 1694.

We view Berk and Bleich’s (2013, this issue) article as potentially an important contribution to both criminology and practical criminal justice decision making. Although it is focused on new machine learning (ML) methods for forecasting, the article ramifies into several general problems that challenge the dominant, widely used standardized methods in criminology. The initial challenge raised by Berk and Bleich concerns the complexity of the data underlying many substantive and theoretical issues in criminology and criminal justice (e.g., multidimensionality, nonlinearity, complex interactions, feedback loops, and multimodality). Second, this challenge leads to the question of whether our standard parametric methods for predictive forecasting (e.g., logistic regression) are mismatched to the complexity and nonlinear decision boundaries found in many research and practical situations. Third, althoughMLmethods seem to have substantial forecasting advantages in dealing with complex data, several current evaluative studies in criminal justice have suggested that ML methods have little predictive advantage over our standard parametric forecasting methods. Berk and Bleich explore reasons for these conclusions and conduct new comparative evaluations between two ML forecasting methods (random forests [RF] and stochastic gradient boosting) compared against logistic regression. In this policy essay, we examine some implications of the complexity issue for criminal justice method, theory, and practice, and we elaborate on several key issues raised by Berk and Bleich.

Qualitative approaches for identifying and characterizing women’s pathways to crime are being augmented by quantitative methods. This study applies quantitative taxonomic methods in disaggregating a large sample of women offenders from a prison population to identify diverse pathway prototypes. An array of gender-responsive and gender-neutral factors and full criminal histories was used to characterize each pathway. Cross-sample and cross-method replication tests demonstrated the stable replication of these pathways. The identified prototypes were related to the prior literature, including Daly’s pathway models, Moffitt’s developmental taxonomy, and several prior taxonomic studies of women’s pathways. Eight reliable pathways were identified that were nested within four broad, superordinate pathway categories. Substantial links to the prior pathways literature were noted, although greater complexity was found to exist in the eight identified pathways.

Introduction: The BeatAML master trial is evaluating the use of precision medicine via genomically guided therapy in acute myeloid leukemia (AML). A variety of assays are used to test patient samples including cytogenetic karyotyping, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS)-based approaches to analyze genomic alterations. We developed an algorithm to extract karyotype information from NGS-based genomic sequencing data in the BeatAML cohort. We also utilized this algorithm to retrospectively study 1603 unique AML samples collected during routine clinical care. Methods: Comprehensive genomic profiling (CGP) was performed using a CLIA/CAP/NYS approved DNA and RNA hybrid capture-based next-generation sequencing assay that sequences 426 genes in DNA and 265 genes to capture fusions by RNA. We analyzed aneuploidy by comparing the log ratio of read counts in tumor DNA to a process matched normal control and developed signal to noise metrics to measure chromosome arm copy number. A chromosome arm was considered altered if >50% of the arm was altered. Chromosome (chr) 5q was also considered lost if only chr5q31 (containing EGR1) was lost. Based on the noise metrics of each sample, we also calculated a per sample limit of detection, which was defined as the lowest percentage of cells that could have a single copy gain or loss and be detected. We validated chr5q loss, chr7q loss, and chr8 gain using FISH results obtained from available BeatAML samples as the gold standard. To better understand the genomic landscape of AML, we also included 1603 samples run in standard clinical practice. False discovery rate (FDR) was assessed using the Bonferroni method. Results: We developed a method to analyze chr5q loss, chr7q loss and chr8 gain that had 95% concordance across all chromosomes compared to the FISH gold standard. The median limit of detection was 10.1% (percentage of cells required to have a single copy gain/loss to be detected). Overall concordance adjusted for limit of detection was 97% with 92% sensitivity (55/60 chromosomes) and 99% specificity (162/164 chromosomes) with similar performance across chromosomes. For chr7q loss and chr8 gain, over 50% of the chromosomal region was altered. However, the size of the loss on chr5q varied widely from the entire arm to a single gene (EGR1). We next applied the algorithm to 1603 unique patient samples analyzed by CGP during routine clinical care. We detected loss of chr5q in 10.9% (174), loss of chr7q in 10.4% (166), and gain of chr8 in 9.2% (147) of AML samples. Frequently altered genes in this cohort included FLT3 (21%, 337), RUNX1 (20.5%, 328), DNMT3A (17.5% 280), and TP53 (17.5%, 280). To further explore the genomic landscape, we analyzed the cooccurrence of each chromosomal alteration with all genes assayed. All three chromosomal aberrations exhibited significant cooccurrence with each other and TP53 (FDR P < 0.05). TP53 was altered in 75% (130/174) of chr5q loss samples 49% (82/166) of chr7q loss samples and 37% (55/147) of chr8 gain samples. Loss of chr5q also exhibited significant mutual exclusivities with FLT3, DNMT3A, NPM1, SRSF2, ASXL1, CEBPA, and WT1 (FDR P < 0.05). Loss of chr7q exhibited a slightly different mutual exclusivity profile with FLT3, NPM1, and PTPN11 (FDR P < 0.05). The difference in the cooccurrence profile between chr5q and chr7q was not a matter of p-value cutoffs since the magnitude of effect varied widely between groups. Conclusions: We demonstrated an NGS-based algorithm to determine karyotype that has a high concordance with FISH results. Limit of detection was equivalent to karyotyping by metaphase analysis but slightly worse than FISH assays on freshly prepared samples. We identified a previously described genomic stratification of TP53-aneuploidy since chromosomal aberrations and TP53 exhibited significant cooccurrence. However, only 50% of samples with loss of chr5q exhibited loss of chr7q and vice versa. While both were mutually exclusive with FLT3 and NPM1, loss of chr5q was mutually exclusive with several genes of prognostic significance including chromatin factors (DNMT3A) and splice factors (SRSF2). This study shows how NGS-based approaches can capture both chromosome arm level copy number alterations as well as all four categories of genomic alterations, thereby enabling risk stratification and identification of potential treatment options as defined in current NCCN guidelines. Disclosures Pavlick: Foundation Medicine Inc: Employment. Montesion:Foundation Medicine Inc: Employment. Severson:Foundation Medicine Inc: Employment. Brennan:Foundation Medicine Inc: Employment. Frampton:Foundation Medicine Inc: Employment, Other: Employee and stockholder. He:Foundation Medicine Inc: Employment. Levine:Roche: Consultancy, Research Funding; Epizyme: Patents & Royalties; Celgene: Consultancy, Research Funding; Isoplexis: Equity Ownership; Prelude: Research Funding; Qiagen: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Gilead: Honoraria; Janssen: Consultancy, Honoraria; Novartis: Consultancy; C4 Therapeutics: Equity Ownership; Imago: Equity Ownership; Loxo: Consultancy, Equity Ownership. Vergilio:Foundation Medicine Inc: Employment. Albacker:Foundation Medicine Inc: Employment; Foundation Medicine Inc: Employment.

A multitude of somatic genomic alterations contribute to the pathogenesis of acute myeloid leukemia (AML). Despite these important biologic insights, current therapeutic approaches to AML remain limited, particularly in adults ≥ 60. The Leukemia & Lymphoma Society (LLS)-led Beat AML trial was designed to assess whether a multi-center clinical trial could use genetic profiling to assign patients (pts) to molecularly defined, subtype-specific therapies within 7 days, and to delineate the role of new therapies in the first-line treatment of AML, with the goal of improving outcomes in older pts with AML through the use of mechanism based novel therapies. Pt eligibility included age ≥ 60 years with non-APML AML, no CNS leukemia, no prior hypomethylating agent (HMA) therapy and no clinical need for emergent therapy. Eligible pts were profiled using local cytogenetics and next generation sequencing (NGS) assay (Foundation Medicine, Inc.) with all molecular data required for treatment assignment (TA) obtained ≤ 7 days. TA was made centrally using a prioritization schema incorporating cytogenetics [t(8;21], inv(16), MLL rearrangement, complex karyotype ≥ 3 abn) and somatic mutations present in a dominant AML clone with a variant allele frequency (VAF) >0.3. If no cytogenetic abnormality or mutation with VAF ≥ 0.3 was observed, VAF ≥ 0.2 was used for TA. The trial opened with 3 arms but currently has 11 treatment arms with 7 novel agents (NA) shown in Table 1. Treatment among different arms include either NA followed by combination of NA + HMA if no response, upfront combination of NA + HMA, or NA + intensive chemotherapy for select groups. Current treatment prioritization and TA based upon enrollment are shown in Table 2. Enrollment began November 2016 with a data cut off of April 30, 2018. At data cutoff, 268 pts have enrolled with a median age of 72 years (range: 60 to 92) and 38% being ≥ 75 years; 43% were female; median WBC was 4.8 x 109/L (range: 0.5 to 194.1) and WBC > 50 x 109/L in 9.3%; median Hgb was 8.4 g/dL (range: 3.9 to 15); median platelet count was 61 x 109/L (range: 7 to 649). Of the 268 patients, 210 had AML with TA. 53 pts were ineligible for enrollment, most commonly due to an alternative diagnosis, and 5 pts have a treatment decision pending. All pts had cytogenetic results available by 7 days. We achieved TA within 7 days in 106 of the 109 (97.2%) pts in the feasibility phase, and 200/210 (95.2%) of the overall cohort, meeting feasibility requirements. Of the 10 pts with delayed treatment assignment, 1 pt had suboptimal specimen quality whereas 9 pts had delayed TA due to technical (7/10) or instrumentation failure (2/10). All pts had cytogenetics available by 7 days. TA is shown in Table 2. These data confirm the feasibility of a precision medicine TA trial in newly diagnosed pts with AML. The Beat AML trial is dynamic by design, with different arms opening over time and all trial arms designed to detect for substantive clinical efficacy. As shown in Figure 1, of the 210 eligible AML pts enrolled, 7 pts (3.3%) died during the first 7 days prior to TA, 12 pts (5.7%) received alternative treatments prior to TA and 81 pts (38.6%) received an alternative treatment after TA. At time of analysis, weekly safety calls assessed that 23 pts went on an alternative clinical trial deemed better for them than Beat AML, and 40 pts received other standard-of-care therapies, 13 pts received palliative care and 5 pts were not specified. Special events of interest (disease worsening or progression) were assessed in 19 (9.0%) of pts. Of those going onto treatment, 110 pts (52.4%) received treatment on one of the Beat AML sub-studies. At time of abstract submission, one sub-study had completed phase 2 enrollment with positive results using monotherapy as measured by CR/CRi attainment (Study S3 with enasidenib +/- HMA: 43% CR/Cri rate) and is currently in expansion to further assess efficacy of this NA in newly diagnosed AML. Three additional studies have completed phase 1b dose escalation for combined NA + HMA therapy. An update including overall (for all enrolled pts) survival, sub-study-specific survival, and survival of patients receiving alternative treatment will be presented. Our data support the feasibility of a rapid precision medicine approach in older pts with previously untreated AML. The Beat AML trial is a model for dynamic, mechanism- based clinical trials in blood cancers where genomic analysis may inform, accelerate, and improve drug development. Disclosures Levine: Roche: Consultancy, Research Funding; Novartis: Consultancy; Isoplexis: Equity Ownership; Janssen: Consultancy, Honoraria; Prelude: Research Funding; Imago: Equity Ownership; Epizyme: Patents & Royalties; Celgene: Consultancy, Research Funding; C4 Therapeutics: Equity Ownership; Qiagen: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Gilead: Honoraria; Loxo: Consultancy, Equity Ownership. Mims:Agios Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Abbvie Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy. Borate:Agios: Consultancy; Novartis: Consultancy. Stein:Novartis: Consultancy; Daiichi Sankyo: Consultancy; Pfizer: Consultancy; Celgene: Consultancy; Bayer: Consultancy; Agios: Consultancy. Patel:Celgene: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; France Foundation: Honoraria; Dava Oncology: Honoraria. Stock:Jazz Pharmaceuticals: Consultancy. Deininger:Pfizer: Consultancy, Membership on an entity's Board of Directors or advisory committees; Blueprint: Consultancy. Vergilio:Foundation Medicine Inc: Employment. Brennan:Foundation: Employment, Equity Ownership. Vietz:Foundation Medicine: Employment, Equity Ownership. Druker:ARIAD: Research Funding; Oregon Health & Science University: Patents & Royalties; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Aileron Therapeutics: Consultancy; ALLCRON: Consultancy, Membership on an entity's Board of Directors or advisory committees; Millipore: Patents & Royalties; Celgene: Consultancy; Bristol-Meyers Squibb: Research Funding; McGraw Hill: Patents & Royalties; Third Coast Therapeutics: Membership on an entity's Board of Directors or advisory committees; Novartis Pharmaceuticals: Research Funding; Monojul: Consultancy; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; GRAIL: Consultancy, Membership on an entity's Board of Directors or advisory committees; Beta Cat: Membership on an entity's Board of Directors or advisory committees; Patient True Talk: Consultancy; Henry Stewart Talks: Patents & Royalties; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees; Fred Hutchinson Cancer Research Center: Research Funding; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Aptose Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees.

This study examines the statistical validation of a recently developed, fourth-generation (4G) risk—need assessment system (Correctional Offender Management Profiling for Alternative Sanctions; COMPAS) that incorporates a range of theoretically relevant criminogenic factors and key factors emerging from meta-analytic studies of recidivism. COMPAS's automated scoring provides decision support for correctional agencies for placement decisions, offender management, and treatment planning. The article describes the basic features of COMPAS and then examines the predictive validity of the COMPAS risk scales by fitting Cox proportional hazards models to recidivism outcomes in a sample of presentence investigation and probation intake cases ( N = 2,328). Results indicate that the predictive validities for the COMPAS recidivism risk model, as assessed by the area under the receiver operating characteristic curve (AUC), equal or exceed similar 4G instruments. The AUCs ranged from .66 to .80 for diverse offender subpopulations across three outcome criteria, with a majority of these exceeding .70.

Gene testing in primary immune deficiencies (PIDs) once was limited to expert academic laboratories, but now is easily available to physicians with a broad range of clinical expertise. Such testing can establish or confirm a suspected diagnosis and also may predict future disease risk in advance of clinical signs and symptoms, inform reproductive decision making, and guide clinicians in selecting the most appropriate therapeutic options. This article, based on the authors' experience and a review of the published literature, discusses some of the advances and challenges currently encountered in the clinical molecular genetic diagnosis of PIDs.

Taxonomic structure is examined in two large samples of delinquent youth in a domain of socio-psychological and personality factors. This paper offers a partial empirical test of the overlapping theoretical taxonomies of Moffitt (Pshycol Rev 100:674–701, 1993), Lykken (The antisocial personalities, 1995) and Mealey (1995). The first sample consisted of juvenile offenders (n = 1,572) from three state systems. Multiple cluster analysis methods were applied (Wards method, standard K-means, bootstrapped K-means and a semi-supervised pattern recognition technique). Core or exemplar cases were identified by means of a voting procedure. Seven clusters recurrently emerged across replications. While clear analogues of Moffitt’s two main categories were found, several additional stable subtypes emerged that were clearly reminiscent of Lykken’s sociopathic, neurotic-internalizing and “normal” types. However, boundaries between types were fuzzy and unstable, and many unclassified cases existed. Internal validation was assessed by cross-method verification. External validation assessed type differentiation on several delinquent behaviors. Finally, generalizability was assessed by repeating the clustering on a large replication sample (n = 1,453) from another state. Six of the seven initial types re-emerged.

Recurrent, metastatic mesenchymal myxoid tumors of the gynecologic tract present a management challenge as there is minimal evidence to guide systemic therapy. Such tumors also present a diagnostic dilemma, as myxoid features are observed in leiomyosarcomas, inflammatory myofibroblastic tumors (IMT), and mesenchymal myxoid tumors. Comprehensive genomic profiling was performed in the course of clinical care on a case of a recurrent, metastatic myxoid uterine malignancy (initially diagnosed as smooth muscle tumor of uncertain malignant potential (STUMP)), to guide identify targeted therapeutic options. To our knowledge, this case represents the first report of clinical response to targeted therapy in a tumor harboring a DCTN1-ALK fusion protein. Hybridization capture of 315 cancer-related genes plus introns from 28 genes often rearranged or altered in cancer was applied to >50 ng of DNA extracted from this sample and sequenced to high, uniform coverage. Therapy was given in the context of a phase I clinical trial ClinicalTrials.gov Identifier: ( NCT01548144 ). Immunostains showed diffuse positivity for ALK1 expression and comprehensive genomic profiling identified an in frame DCTN1-ALK gene fusion. The diagnosis of STUMP was revised to that of an IMT with myxoid features. The patient was enrolled in a clinical trial and treated with an anaplastic lymphoma kinase (ALK) inhibitor (crizotinib/Xalkori®) and a multikinase VEGF inhibitor (pazopanib/Votrient®). The patient experienced an ongoing partial response (6+ months) by response evaluation criteria in solid tumors (RECIST) 1.1 criteria. For myxoid tumors of the gynecologic tract, comprehensive genomic profiling can identify clinical relevant genomic alterations that both direct treatment targeted therapy and help discriminate between similar diagnostic entities.

Focal amplification and activating point mutation of the MET gene are well-characterized oncogenic drivers that confer susceptibility to targeted MET inhibitors. Recurrent somatic splice site alterations at MET exon 14 (METex14) that result in exon skipping and MET activation have been characterized, but their full diversity and prevalence across tumor types are unknown. Here, we report analysis of tumor genomic profiles from 38,028 patients to identify 221 cases with METex14 mutations (0.6%), including 126 distinct sequence variants. METex14 mutations are detected most frequently in lung adenocarcinoma (3%), but also frequently in other lung neoplasms (2.3%), brain glioma (0.4%), and tumors of unknown primary origin (0.4%). Further in vitro studies demonstrate sensitivity to MET inhibitors in cells harboring METex14 alterations. We also report three new patient cases with METex14 alterations in lung or histiocytic sarcoma tumors that showed durable response to two different MET-targeted therapies. The diversity of METex14 mutations indicates that diagnostic testing via comprehensive genomic profiling is necessary for detection in a clinical setting. Significance: Here we report the identification of diverse exon 14 splice site alterations in MET that result in constitutive activity of this receptor and oncogenic transformation in vitro. Patients whose tumors harbored these alterations derived meaningful clinical benefit from MET inhibitors. Collectively, these data support the role of METex14 alterations as drivers of tumorigenesis, and identify a unique subset of patients likely to derive benefit from MET inhibitors. Cancer Discov; 5(8); 850–9. ©2015 AACR. See related commentary by Ma, p. 802. See related article by Paik et al., p. 842. This article is highlighted in the In This Issue feature, p. 783

Purpose Neoadjuvant cisplatin-based chemotherapy is standard of care for muscle-invasive bladder cancer (MIBC); however, it is infrequently adopted in practice because of concerns regarding toxicity and delay to cystectomy. We hypothesized that three cycles of neoadjuvant accelerated methotrexate, vinblastine, doxorubicin, and cisplatin (AMVAC) would be safe, shorten the time to surgery, and yield similar pathologic complete response (pT0) rates compared with historical controls. Patients and Methods Patients with cT2-T4a and N0-N1 MIBC were eligible and received three cycles of AMVAC with pegfilgrastim followed by radical cystectomy with lymph node dissection. The primary end point was pT0 rate. Telomere length (TL) and p53 mutation status were correlated with response and toxicity. Results Forty-four patients were accrued; 60% had stage III to IV disease; median age was 64 years. Forty patients were evaluable for response, with 15 (38%; 95% CI, 23% to 53%) showing pT0 at cystectomy, meeting the primary end point of the study. Another six patients (14%) were downstaged to non–muscle invasive disease. Most (82%) experienced only grade 1 to 2 treatment-related toxicities. There were no grade 3 or 4 renal toxicities and no treatment-related deaths. One patient developed metastases and thus did not undergo cystectomy; all others (n = 43) proceeded to cystectomy within 8 weeks after last chemotherapy administration. Median time from start of chemotherapy to cystectomy was 9.7 weeks. TL and p53 mutation did not predict response or toxicity. Conclusion AMVAC is well tolerated and results in similar pT0 rates with 6 weeks of treatment compared with standard 12-week regimens. Further analysis is ongoing to ascertain whether molecular alterations in tumor samples can predict response to chemotherapy.

Several researchers have discussed the need to define "outcomes" in health care more holistically, particularly from women's health, chronic illness, and self-care perspectives. Interstitial cystitis (IC), a chronic illness that primarily affects women, is a poorly understood condition that can produce hopelessness and suicidal ideation. Management of IC usually requires behavioral changes in all life dimensions. Multidimensional health outcomes were examined in a survey of 138 women with IC. Item-item and item-factor correlations were used to identify relationships between indicators of health outcomes and self-reported effectiveness of more than 300 self-care strategies used to manage IC. The effectiveness of behavioral and cognitive self-care strategies correlated differentially with dimensions of health. Uncertainty correlated most strongly with the quality of relationships with health care providers. Psychiatric nurses are well prepared to address the complex body-mind phenomena of IC, promoting effective self-care strategies while maintaining a supportive therapeutic relationship.

Purpose: NTRK1-3 fusions are oncogenic drivers in lung and other carcinomas in adults, suggest benefit from targeted therapy. We examined a large series of pediatric/adolescent advanced cancer cases to identify those with NTRK fusions. Background: The NTRK, neurotrophic tyrosine kinase receptor, genes encode proteins essential for normal neuronal growth and development. Fusions of NTRK family members have recently been linked to oncogenesis as well as identified as potential targets of therapy. In this study, a hybrid capture based comprehensive genomic profiling (CGP) assay was used to study a large series of pediatric solid tumors to search for NTRK gene fusions. Methods: CGP using hybridization capture of at least 3,320 exons from 182 cancer-related genes and 37 introns of 14 genes commonly rearranged in cancer (previous version of the test) was applied to ≥ 50ng of DNA extracted from 1351 pediatric/adolescent/young adult tumors ( Results:, From 1351 pediatric/adolescent young adult advanced cancer patients, 7 (0.52%) harbored NTRK family member fusions. Of these, 5 were pediatric ( Conclusions: 0.5% pediatric/adolescent/young advanced cancers harbor NTRK1 and NTRK3 fusions, and all such tumors are mesenchymal in origin. Of these, an index case benefitted from crizotinib treatment, suggesting pathways to clinical benefit for such cases. Citation Format: Dean Pavlick, Siraj Mahamed Ali, Julia A. Elvin, Phil J. Stephens, Vincent A. Miller, Jeffrey S. Ross, James H. Suh, Jo-Anne Vergilio, Juliann Chmielecki, Tim Brennan, John R. Crawford, Denise M. Malicki, Hyunah Ahn, Victor N. Wong. Identification of NTRK fusions in pediatric tumors via comprehensive genomic profiling. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Pediatric Cancer Research: From Mechanisms and Models to Treatment and Survivorship; 2015 Nov 9-12; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(5 Suppl):Abstract nr A46.

477 Background: NSGCT, the most common solid malignancy in U.S. men ages 18-35, has a > 95% 5-year survival due to exquisite chemosensitivity; however, chemoresistant recurrences still contribute to 400 NSGCT deaths/year. We queried CGP results of the largest collection to date of recurrent NSGCT (n = 28) to identify targeted therapy options for this subset of high risk patients. Methods: DNA was extracted from 28 FFPE NSGCT clinical specimens. Hybridization captured libraries of 236 (FoundationOne, n = 20) or 305 (FoundationOne, n = 8) genes, plus select introns frequently rearranged in cancer were sequenced to high ( > 605x), uniform coverage. All classes of genomic alterations (GA; base subs, in/dels, rearrangements, and copy number alterations) were evaluated. CRGA were defined as GA associated with on-label targeted therapies and targeted therapies in mechanism-driven clinical trials. CGP coverage data was used to assess for chromosome 12p arm amplifications. Results: 28 samples (29% primary, 71% metastasis) from patients (avg 33.7 y) with recurrent NSGCT of predominant pattern of yolk sac tumor (43%), embryonal carcinoma (18%), choriocarcinoma (18%), or unspecified/mixed (21%) were profiled. 57% of NSGCT had chromosome 12p amplification ( > 6 copies). 89% had at least one GA not localized to chromosome 12p, including CRGA of CRKL (11%), MCL1 (11%), MDM2 (11%), GNAS (11%), KRAS (SV 7%), AURKA (7%), KIT (7%). CRGA in each of: AKT1, AKT2, BRAF, ERBB2, NF1, PIK3R2, PDGFRA, STK11 were identified in a single case. To date, we are aware of one patient in whom treatment with everolimus was initiated on the basis of the CGP results (inactivating point mutations in STK11 and PIK3R2) and who experienced marker stabilization lasting 5 months suggesting a biologic effect of this therapy. Conclusions: GA not accounted for by 12p amplification are present at a higher frequency than previously reported in recurrent or treatment-resistant NSGCT. The prevalence of CRGA and clinical response to targeted therapy in one such patient support the utility of CGP to identify additional therapeutic options for high risk NSGCT and warrants additional study.

The key structural feature in Boceprevir, Merck’s new drug treatment for hepatitis C, is the bicyclic [3.1.0]proline moiety “P2”. During the discovery and development stages, the P2 fragment was produced by a classical resolution approach. As the drug candidate advanced through clinical trials and approached regulatory approval and commercialization, Codexis and Schering–Plough (now Merck) jointly developed a chemoenzymatic asymmetric synthesis of P2 where the net reaction was an oxidative Strecker reaction. The key part of this reaction sequence is an enzymatic oxidative desymmetrization of the prochiral amine substrate.

Acute Lymphoblastic Leukemia (ALL) is the most common malignancy observed in the pediatric population. Recent genomic studies have made considerable strides in improving our understanding of the molecular pathogenesis of pediatric B-cell ALL. This includes the discovery of recurrent somatic alterations targeting B-cell transcription factors, mutations in epigenetic regulators, and oncogenic mutations which activate signaling effectors, including in Ph-like B-ALL. However, the molecular pathogenesis of adult B-cell ALL has been less well studied, and there is a need to identify novel therapeutic targets in adult B-ALL. We therefore performed detailed genomic profiling in adults with B-cell ALL. We performed targeted DNA/RNA capture and sequencing of 189 patients with B-cell ALL enrolled on the ECOG E2993 clinical trial. All samples were taken at the time of diagnosis before patients were treated with multi-agent chemotherapy and followed for clinical outcomes including overall survival and remission/relapse duration and kinetics. We used the FoundationOne® Heme assay for our genomics study. This platform allows us to identify short events (point substitutions, short insertions/deletions) copy number and fusion events present in DNA and/or RNA. Of the 203 samples profiled, 189 had sufficient quality genomic data with a median coverage of 435 on DNA sequencing and 7.85 million on target distinct reads per case on RNA sequencing. In all, we identified cancer-related mutations in 108 genes, 55 of these genes being mutated in more than one sample. We identified a median of 2.98 genomic alterations per sample (standard deviation of 1.78) in the target gene set, which included all genes known to be altered in B-ALL and in other hematologic malignancies. The most common genomic events were the BCR-ABL1 fusion (69 samples, 36.5%), followed by CDKN2A loss (57 samples, 30%), CDKN2B loss (35 samples, 18%), NRAS and KRAS point mutations (32 samples, 16.9%), and MLL fusion genes with a spectrum of partners (25 samples, 13.2%). Notably, we found that BCR-ABL1 fusion are mutually exclusive with both RAS mutations (p We next investigated the spectrum and frequency of alterations observed in different classes of oncogenes/tumor suppressors. We identified mutations which result in activation of oncogenic signaling pathways in 130 cases or 68.7% of our cohort. This included known mutations/fusions, such as BCR-ABL, RAS-MAPK pathway mutations, and JAK-STAT pathway alterations, and included missense alleles, insertion/deletion events, and fusion genes targeting a spectrum of genes including ABL, PDGFRB, and CRLF2. In aggregate, 33.8% of the cohort had mutations which activate signaling exclusive of BCR-ABL, demonstrating the high prevalence of the Ph-like B-ALL subtype in adult B-ALL. We identified mutations affecting key transcription factors, including PAX5 and IKZF1, in 31.2% of our cohort including missense, nonsense and deletion events. To confirm our ability to detect small deletions of PAX5 and IKZF1, we performed array CGH of 50 cases and compared copy number calls using high-throughput sequencing and CGH. Of note, all deletions targeting PAX5 and IKZF1 identified by NGS were confirmed by CGH. We also identified mutations in epigenetic regulators in 30.6% of cases, including MLL fusions, mutations in the DNA methylation/hydroxymethylation the pathway (DNMT3A, TET1, TET2), and mutations targeted chromatin modulators. Detailed analyses of the mutational spectra and their relationship to clinical outcome will be presented at the meeting. Taken together, these data show we can use a clinically validated sequencing assay to identify known and novel somatic mutations in adult B-ALL, including sequence alterations, rearrangements and copy number aberrations. These data demonstrate the feasibility of combined DNA and RNA study to identify a complex landscape of fusions and short mutations with prognostic and therapeutic relevance, and inform the use of genomic profiling in B-ALL in the clinical context. Figure 1. Figure 1. Disclosures He: Foundation Medicine, Inc.: Employment, Equity Ownership. Brennan:Foundation Medicine, Inc.: Employment, Equity Ownership. Nahas:Foundation Medicine, Inc.: Employment, Equity Ownership. Balassubramanian:Foundation Medicine, Inc.: Employment, Equity Ownership. Otto:Foundation Medicine, Inc.: Employment, Equity Ownership. Lipson:Foundation Medicine, Inc.: Employment, Equity Ownership. Stephens:Foundation Medicine, Inc.: Employment, Equity Ownership. Miller:Foundation Medicine, Inc.: Employment, Equity Ownership. van den Brink:Boehringer Ingelheim: Consultancy, Other: Advisory board attendee; Merck: Honoraria; Regeneron: Honoraria; Novartis: Consultancy, Membership on an entity's Board of Directors or advisory committees; Tobira Therapeutics: Other: Advisory board attendee. Rowe:Amgen: Consultancy; BioSight Ltd.: Consultancy, Membership on an entity's Board of Directors or advisory committees; BioLineRx Ltd.: Consultancy. Levine:Foundation Medicine: Consultancy; CTI BioPharma: Membership on an entity's Board of Directors or advisory committees; Loxo Oncology: Membership on an entity's Board of Directors or advisory committees.

Interstitial cystitis is a painful disease that primarily affects women. It involves a chronic bladder inflammation of unknown etiology and unpredictable course. There is no consensus about treatment. Women with interstitial cystitis report using multiple strategies and interventions to prevent and manage urinary urgency, frequency, and suprapubic pain. A survey questionnaire on self-care strategies was completed by 138 members of the Interstitial Cystitis Association. Subjects indicated how often they used more than 300 self-care strategies and the effectiveness of these strategies. This article reports findings from five physical subdomains (medications, treatments, hygiene, diet, and body comfort). Among those who report actually using the methods the effectiveness ratings for many body comfort strategies are comparable to the reported effectiveness of medications (including narcotics) for managing mild to moderate symptoms.

Evidence from case-control studies, but less so from cohort studies, suggests a positive association between meat intake and risk of lung cancer. Therefore, this association was evaluated in the frame of the European Prospective Investigation into Cancer and Nutrition, EPIC. Data from 478,021 participants, recruited from 10 European countries, who completed a dietary questionnaire in 1992-2000 were evaluated; 1,822 incident primary lung cancer cases were included in the present evaluation. Relative risk estimates were calculated for categories of meat intake using multi-variably adjusted Cox proportional hazard models. In addition, the continuous intake variables were calibrated by means of 24-h diet recall data to account for part of the measurement error. There were no consistent associations between meat consumption and the risk of lung cancer. Neither red meat (RR = 1.06, 95% CI 0.89-1.27 per 50 g intake/day; calibrated model) nor processed meat (RR = 1.13, 95% CI 0.95-1.34 per 50 g/day; calibrated model) was significantly related to an increased risk of lung cancer. Also, consumption of white meat and fish was not associated with the risk of lung cancer. These findings do not support the hypothesis that a high intake of red and processed meat is a risk factor for lung cancer.

In this chapter, the authors explore Area under Curve (AUC) as an error-metric suitable for imbalanced data, as well as survey methods of optimizing this metric directly. We also address the issue of cut-point thresholds for practical decision-making. The techniques will be illustrated by a study that examines predictive rule development and validation procedures for establishing risk levels for violent felony crimes committed when criminal offenders are released from prison in the USA. The “violent felony” category was selected as the key outcome since these crimes are a major public safety concern, have a low base-rate (around 7%), and represent the most extreme forms of violence. The authors compare the performance of different algorithms on the dataset and validate using survival analysis whether the risk scores produced by these techniques are computing reasonable estimates of the true risk.

Using rockets to launch communications satellites and other spacecraft poses risks to the uninvolved public, including persons and property under the flight path of the launch vehicle. The federal government plays a pivotal technical role during the actual launch by carrying out certain risk-related procedures, thus causing third-party risk to be jointly produced by the company and the government. In addition, under the Commercial Space Launch Act, the government partially indemnifies commercial launch companies for third-party damages. We compare the indemnification policy to optimal liability rules under public-private co-production of risk. Under modest assumptions, shared liability created by the indemnification rules decreases the incentive of both parties to take care relative to the optimum. If care were observable, it would be preferable for the government to fully indemnify companies that take due care. The role of the government as an agent for third parties may qualify these findings.

The move from regulation to competition in different parts of the economy is one of the great success stories of the past 30 years. And more competition in the electricity sector could offer lower consumer prices and improved stability of supply. So why has market deregulation in electricity been difficult to achieve?

Amplification and point mutation in MET are well-characterized oncogenic drivers that confer susceptibility to MET inhibitors, such as crizotinib, particularly in non-small cell lung cancer. Splice site alterations at exon 14 of the MET (METex14) gene result in exon skipping and MET activation through loss of a DpYR motif (Y1003) that recruits the ubiquitin ligase CBL, targeting MET for degradation. METex14 skipping mutations have primarily been detected in lung adenocarcinoma, occurring in ∼3% of cases, but also in neuroblastoma and gastric cancer cell lines. 17 distinct variants have been characterized, however, their full diversity and prevalence across tumor types is unknown. Most importantly, it is unknown whether these mutations confer clinical susceptibility to targeted therapy with multiple MET inhibitors. We report here analysis of 29,714 cancer genomes to identify 168 harboring METex14 splicing mutations, including 101 distinct genomic variants. They are detected most frequently in lung adenocarcinoma (3.1%, 104/3360), but also in other lung neoplasms (2.0%, 40/2022), brain glioma (0.5%, 6/1312), tumors of unknown primary origin (0.4%, 11/2516), and other tumor types (0.03% 7/20504). Lung malignancies with these mutations do not have other characteristic driver mutations, and have a distinct profile of co-occurring mutations, supporting the role of METex14 skipping as the primary drivers of oncogenesis in these specimens. Most importantly, patients with tumors harboring these mutations demonstrate durable response to anti-MET targeted therapy, in several tumor types. These data demonstrate that METex14 splicing mutations define a distinct class of tumors that are responsive to targeted therapy. The diversity of these variants indicates that diagnostic testing via massively parallel sequencing is necessary for detection in a clinical setting. The data also suggest that thousands of cancer genome profiles will be required to discover non-coding cancer drivers with degenerate genomic signatures. Citation Format: Garrett M. Frampton, Siraj Ali, Juliann Chmielecki, Mark Rosenzweig, Timothy Brennan, Zachary Chalmers, Julia Elvin, Alex Fichtenholtz, Kyle Gowan, Joel Greenbowe, Adrienne Johnson, Lily Khaira, Doron Lipson, Caitlin McMahon, Steven Roels, Roman Yelensky, Deborah Morosini, Philip Stephens, Vincent Miller. Activation of MET via diverse exon 14 skipping mutations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. [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 1118. doi:10.1158/1538-7445.AM2015-1118

Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA The PARP inhibitor olaparib (LynparzaTM) elicits responses in ovarian cancer patients with inherited (germline) loss of function mutations in the BRCA1 or BRCA2 genes (gBRCAm). In the tumors of such patients the unmutated (wt) copy of the relevant BRCA gene is usually lost. Many patients are aware of their BRCA mutation status due to the wide availability of blood testing. However, in around a third of ovarian tumors with BRCA mutations the mutation has not been inherited but is tumor-specific (sBRCAm). Given the difference in origin of mutation, it is important to determine whether there are genotypic and phenotypic differences between sBRCAm and gBRCAm ovarian tumors. In a randomized, Phase II trial of 265 patients with platinum-sensitive relapsed serous ovarian cancer ([NCT00753545][1]; Study 19), maintenance treatment with olaparib (400 mg bid; capsules) led to a significant increase in progression-free survival (PFS) vs placebo in patients with a BRCA mutation (HR 0.18; 95% CI 0.10-0.31; P

Background: Cisplatin based NAC prior to cystectomy is standard of care for MIBC, with 40-50% expected to respond with ≤pT1N0M0. Biomarkers predictive of response are lacking. Methods: MIBC pts who received 3 cycles of cisplatin based NAC on 1 of 2 prospective multicenter clinical trials were included. Pts treated with accelerated methotrexate, vinblastine, doxorubicin + cisplatin (AMVAC) provided the discovery set [n = 34, 15/34 (44%) ≤pT1N0M0]. Pts treated with dose dense gemcitabine + cisplatin (DDGC) provided the validation set [n = 24, 11/24 (46%) ≤pT1N0M0]. DNA from pre-treatment tumor tissue underwent sequencing for all coding exons of 287 cancer related genes and was analyzed for presence of base substitutions, indels, copy number alterations, and selected re-arrangements. The mean number of variants and variant status for each gene were correlated with response using two-sample t-test and Fisher's exact tests. Variant data were used to create a classification tree to discriminate responders vs. non-responders in the AMVAC discovery cohort. The resulting decision rule was then tested in the independent DDGC validation set. Overall survival analysis was performed using Kaplan-Meier. Results: Pts with pT0 had significantly more alterations than those with residual tumor in both the AMVAC discovery (p = .024) and DDGC validation (p = 0.018) set. In the AMVAC discovery set, alteration in ≥1 of the three DNA repair genes ATM, RB1 or FANCC predicted for ≤pT1N0M0 (p Conclusions: Alterations in ≥1 of ATM, RB1 and FANCC predict response to cisplatin based chemotherapy defined as ≤pT1N0M0 in both our AMVAC discovery and DDGC validation sets. We hypothesize that defects in these genes, which are important for maintenance of chromatin structure and DNA repair, confer sensitivity to DNA damaging chemotherapy and explain the accumulation of alterations seen among pts with pT0. External validation in collaboration with the cooperative groups is planned. Citation Format: Elizabeth R. Plimack, Roland L. Dunbrack, Timothy A. Brennan, Mark D. Andrake, Yan Zhou, Ilya Serebriiskii, Essel Dulaimi Al-Saleem, Jean Hoffman-Censits, Marijo Bilusic, Yu-Ning Wong, Alexander Kutikov, Rosalia Viterbo, Richard Greenberg, David Chen, Costas D. Lallas, Edouard J. Trabulsi, Roman Yelensky, Vincent A. Miller, Erica Golemis, Eric Ross. Defects in DNA repair genes and sensitivity to cisplatin based neoadjuvant chemotherapy (NAC) for bladder cancer. [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 4298. doi:10.1158/1538-7445.AM2015-4298

1558 Background: Intratumoral heterogeneity (ITH) or variations in genomic alterations (GA) between different areas of primary tumors or in their metastases has been an area of intense investigatio...

320 Background: Cisplatin based NAC prior to cystectomy is standard of care for MIBC, with 40-50% expected to respond with ≤pT1N0M0. Biomarkers predictive of response are lacking. Methods: MIBC pts who received 3 cycles of cisplatin based NAC on 1 of 2 prospective multicenter clinical trials were included. Pts treated with accelerated methotrexate, vinblastine, doxorubicin + cisplatin (AMVAC) provided the discovery set [n=34, 15/34 (44%) ≤pT1N0M0]. Pts treated with dose dense gemcitabine + cisplatin (DDGC) provided the validation set [n=24, 11/24 (46%) ≤pT1N0M0]. DNA from pre-treatment tumor tissue underwent sequencing for all coding exons of 287 cancer related genes and was analyzed for presence of base substitutions, indels, copy number alterations, and selected re-arrangements. The mean number of variants and variant status for each gene were correlated with response using two-sample t-test and Fisher’s exact tests. Variant data were used to create a classification tree to discriminate responders vs. non-responders in the AMVAC discovery cohort. The resulting decision rule was then tested in the independent DDGC validation set. Overall survival analysis was performed using Kaplan-Meier. Results: Pts with pT0 had significantly more alterations than those with residual tumor in both the AMVAC discovery (p=.024) and DDGC validation (p=0.018) set. In the AMVAC discovery set, alteration in ≥1 of the three DNA repair genes ATM, RB1 or FANCC predicted for ≤pT1N0M0 (p

Xenotransplantation of primary AML samples into immunodeficient mice (PDX models) represents a unique opportunity for pre-clinical testing on a group of primary human samples that possess defined genomic lesions. However, given recent recognition that multiple genomically distinct sub-clones can exist in AML, there is a risk that there may be selection for sub-clones from the transplanted sample that might not fully represent the patient’s disease. We transplanted 160 (70 T-ALL 56 AML, 32 B-ALL, 2 MLL) patient samples of which 120 engrafted into at least 1 irradiated NSG mouse. 45 AML samples engrafted with a median latency 107+/-41 days. Transplantation of 6 PDX AML samples resulted in immunophenotypically identical disease within 87+/-35 days. 2 MLL samples engrafted in 100% of mice with a median latency of 103+/-13 days. 25 B-ALL samples engrafted with a median latency of 95+/-44 days. Secondary transplantation of 3 PDX B-ALL samples resulted in engraftment of leukemia cells with an identical immunophenotype in 100% of transplanted mice within 52+/-3 days. 48 T-ALL samples engrafted in at least one mouse within 50 days. Secondary transplantation of a single T-ALL PDX sample resulted in 100% engraftment within 31+/-10 days. Genomic DNA and total RNA were isolated from 150 (AML: 16Pt+33PDX; MLL 2Pt+6PDX; B-ALL 17Pt+38PDX; T-ALL 19Pt+19PDX) samples. Adaptor ligated sequencing libraries were captured by solution hybridization using baitsets for 405 cancer-related genes and selected introns for 31 genes frequently rearranged for DNA-seq, and 405 cancer-related and 265 genes frequently rearranged for RNA-seq. All libraries were sequenced averaging >500x for DNA and >6M total pairs for RNA (HiSeq). We detected on average 23+/-12 including a mean 5+/-4 known pathogenic variants such as CDKN2A/B deletion (20/13); FLT3 (SNV & -ITD) and NOTCH (11 ea); WT1 and TP53 (10 ea); NRAS (9); PTPN11 (7); NPM1c, PTEN, and KRAS (6) DNMT3A, IDH1/2, and ASXL1 (5 ea); FBXW7, CEBPA, and TET2 (4 ea); PHF6 and NF1 (3 ea); IKZF1, ATM, and JAK2 (2 ea). Analyses of fusion RNA molecules detected known fusions: MLL-AF4 (4); MLL-AF9 (2), CRLF2-P2RY8, ETV6-RUNX1 or TEL-AML1, PBX1-TCF3 (2 ea); MLL-AF10, MLL-ELL, MLL-EP300, MLL-PTD, BCR-ABL, BCL2-IGK, MYH11-CBFB, along with novel fusions: TCF3-OAZ1, RB1-RCBTB2, PAX5-FLI1, and PAX5-MSI2. The mutations found in the 54 patient samples were consistently identified in the 96 PDX, however some cases showing variation in allele frequency between diagnostic and engrafted samples. Collectively, all 1420 and 288 disease relevant variant allele frequency (VAF) correlated significantly between patient and PDX samples (R2=0.55, R2=0.43), respectively. We then assessed VAF changes from diagnostic to PDX sample as a measure of clonal concordance. Diagnostic and PDX sample were considered discordant if at least one disease relevant VAF demonstrated significant variation between these samples, accounted for small variability of infrequent variances considering SD of sequencing detection. 31 samples were scored as concordant and 23 as discordant which were similarly distributed between disease lineages and did not correlate with diseases status, future relapse or overall survival. Using the same rules we further accessed concordance only between PDX samples in 23 cases when patient samples were transplanted into multiple mice. All 10 groups of PDX samples that were concordant with patient samples were also concordant within the groups. 5 groups of PDX samples that were discordant with patient samples were concordant within groups. 8 groups of PDX samples that were discordant with patient samples were also discordant within their groups. Overall 15 samples produced concordant engraftment in mice and 8 samples produced discordant engraftment. We hypothesized that specific genomic lesions in the 8 groups might underline this discordance. Mutations of FLT3, RAS, TP53, PTPN11 and NOTCH1 correlated with clonal discordance. These findings show that the leukemias that are engrafted in mice mirror the genomic diversity of primary leukemia samples, and that the majority of PDX samples have a genotype similar to that observed in the clinical isolate. More importantly, our data demonstrate the feasibility of developing a large, genetically annotated bank of PDX leukemia models that can be used to test and credential novel therapeutics that target driver mutations in different leukemia subsets. Disclosures Stein: Seattle Genetics, Inc.: Research Funding; Janssen Pharmaceuticals: Consultancy. Wang:Foundation Medicine Inc: Employment. Miller:Foundation Medicine: Employment. Armstrong:Epizyme: Consultancy.