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Alexa B Schrock,1 Russell Madison,1 Mark Rosenzweig,2 Justin M Allen,2 Rachel L Erlich,2 Siao-Yi Wang,3 Tarek Chidiac,4 Vodur Suresh Reddy,5 Jonathan W Riess,6 Ahmet Ersin Yassa,6 Abdur Shakir,7 Vincent A Miller,1 Brian M Alexander,1 Jeffrey Venstrom,1 Kimberly McGregor,1 Siraj M Ali1 1Foundation Medicine, Department of Clinical Development, Cambridge, MA, USA; 2Foundation Medicine, Department of Translational Oncology and Clinical Reporting, Cambridge, MA, USA; 3Loyola University Medical Cancer, Department of Hematology and Oncology, Maywood, IL, USA; 4Zangmeister Cancer Center, Department of Hematology and Oncology, Columbus, OH, USA; 5Cancer Care Specialists, Department of Hematology and Oncology, Reno, NV, USA; 6UC Davis Comprehensive Cancer Center, Department of Hematology and Oncology Sacramento, CA, USA; 7Sarah Bush Lincoln Health System, Department of Medical Oncology, Mattoon, IL, USACorrespondence: Alexa B SchrockFoundation Medicine, 150 Second Street, Cambridge, MA 02141, USATel +1617-418-2200Email aschrock@foundationmedicine.comBackground: ALK fusions are targetable drivers in non-small-cell lung cancer (NSCLC). However, patients with NSCLC harboring ALK rearrangements without a fusion partner identified in DNA have also been shown to respond to ALK inhibitors. We aimed to characterize complex ALK variants that may predict sensitivity to multiple approved ALK inhibitors.Methods: Comprehensive genomic profiling (CGP) of DNA isolated from formalin‐fixed paraffin‐embedded (FFPE) tumor tissue or blood-based circulating tumor DNA was performed for 39,159 NSCLC patients during routine clinical care. For a subset of cases, RNA sequencing was performed, and prior ALK test results and clinical treatment information were collected from treating physicians.Results: We queried the Foundation Medicine NSCLC database and identified ALK internal inversions, as well as internal deletions, as the sole ALK rearrangements in 6 (0.02%) and 3 (0.01%) of cases, respectively. In cases with ALK internal inversions, RNA testing identified an EML4-ALK fusion in 2/2 cases evaluated, and 3/3 patients treated with ALK inhibitors had durable responses. A single patient with an ALK internal deletion and clinical data available responded to multiple ALK inhibitors. RNA data available for a subset of non-NSCLC cases suggest that ALK internal deletions removing a portion of the N-terminus are drivers themselves and do not result in ALK fusions. Fluorescence in situ hybridization (FISH) results were inconsistent for both classes of DNA events.Conclusion: Rare internal inversions of ALK appear to be indicative of ALK fusions, which can be detected in RNA, and response to ALK inhibitors in patients with NSCLC. In contrast, ALK internal deletions are not associated with ALK fusions in RNA but likely represent targetable drivers themselves. These data suggest that CGP of DNA should be supplemented with immunohistochemistry or RNA-based testing to further resolve these events and match patients to effective therapies.Keywords: ALK rearrangement, inversion, deletion, genomic profiling, targeted therapy

Timothy D Becker,1 Henry C Lin,2 Victoria A Miller3 1Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; 2Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; 3Division of Adolescent Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA Background: Child participation in pediatric medical visits is low. In this pilot study, we sought to better understand relationships between observed communication and child-reported perceptions of communication in a clinical setting. Materials and methods: For this cross-sectional observational study, pediatric gastroenterology appointments (n=39) were videotaped and coded to quantify various adult affective (eg, chit-chat, empathy) and facilitative (eg, asking questions, encouraging responses) behaviors toward the child, interference with child participation (eg, interrupting or ignoring child), and child verbal participation. Post-visit surveys assessed child perceptions of having voice in the clinical encounter, ease of understanding, and satisfaction with communication. Results: Parent and provider chit-chat was associated with child-reported ease of understanding. Provider facilitation was positively associated with child participation, but affective communication strategies were not. Physician interference was negatively associated with ease of understanding but positively associated with perception of voice. Conclusion: Facilitative communication may improve outcomes by enhancing child participation and thus exchange of medical information, whereas chit-chat appears to positively impact children’s perceptions of communication. Keywords: physician–patient communication, partnership, child participation, pediatric patient experience, child satisfaction

Ankur R Parikh,1 Siraj M Ali,2 Alexa B Schrock,2 Lee A Albacker,2 Vincent A Miller,2 Phil J Stephens,2 Pamela Crilley,1 Maurie Markman1 1Eastern Regional Medical Center, Cancer Treatment Centers of America, Philadelphia, PA, USA; 2Foundation Medicine, Inc, Cambridge, MA, USA Abstract: In non-small-cell lung cancer (NSCLC) refractory to standard therapy and which lacks well-known oncogenic drivers, genomic profiling can still identify genomic alterations that may suggest potential sensitivity to targeted therapy. PTEN mutation in NSCLC may be sensitizing to analogs of rapamycin such as everolimus or temsirolimus, but more investigation is needed. We report the case of a patient with metastatic NSCLC harboring a PTEN mutation as well as high tumor mutational burden and PD-L1 positivity with a durable response to temsirolimus, but refractory to a checkpoint inhibitor. Even in the event of failure of treatment with checkpoint inhibitors in the background of a case with a higher tumor mutational burden and PD-L1 positivity, targeting specific genomic alterations may still result in patient benefit. Keywords: genomic profiling, temsirolimus, targeted therapy, immunotherapy

Casey B Williams,1,* Caitlin McMahon,2,* Siraj M Ali,2 Mark Abramovitz,1 Kirstin A Williams,1 Jessica Klein,1 Heidi McKean,1 Roman Yelensky,2 Thomas J George Jr,3 Julia A Elvin,2 Salil Soman,4 Doron Lipson,2 Juliann Chmielecki,2 Deborah Morosini,2 Vincent A Miller,2 Philip J Stephens,2 Jeffrey S Ross,2,5 Brian Leyland-Jones1 1Avera Cancer Institute, Sioux Falls, SD, USA; 2Foundation Medicine, Inc., Cambridge, MA, USA; 3University of Florida College of Medicine, Gainesville, FL, USA; 4Beth Israel Deaconess Medical Center, Boston, MA, USA; 5Albany Medical College, Albany, NY, USA *These authors contributed equally to this work Abstract: The subset of metastatic colorectal adenocarcinomas that harbor BRAF V600E mutations are aggressive tumors with significantly shortened survival and limited treatment options. Here we present a colorectal cancer patient whose disease progressed through standard chemotherapy and who developed liver metastasis. Comprehensive genomic profiling (FoundationOne®) identified a BRAF V600E mutation in the liver lesion, as well as other genomic alterations consistent with colorectal cancers. Combination therapy of dabrafenib and trametinib with standard cytotoxic chemotherapy resulted in a durable major ongoing response for the patient. This report illustrates the utility of comprehensive genomic profiling with personalized targeted therapy for aggressive metastatic colorectal adenocarcinomas. Keywords: oxaliplatin, colorectal adenocarcinoma, combination targeted therapy, BRAF mutations

Rachel M Squillace, Garrett M Frampton, Phil J Stephens, Jeffrey S Ross, Vincent A MillerFoundation Medicine Inc., Cambridge, MA, USAWe read with concern the paper “Evaluation and comparison of two commercially available targeted next-generation sequencing platforms to assist oncology decision- making”.1 The study directly compared results for the Paradigm Cancer Diagnostic test to the FoundationOne test for formalin-fixed, paraffin-embedded specimen pairs from 21 advanced cancer cases. We believe this study is fundamentally flawed, misleading, and potentially dangerous for patient care, for the reasons outlined herein.The paper neglected to address innumerable discordances between a rigorously analytically validated test (FoundationOne) and the experimental assay. It erroneously ascribes categorization of many genomic alterations detected on FoundationOne as “none”, when in fact available drugs have demonstrated activity or mechanism-based clinical trials exist, and it claims high levels of actionability based on the results of RNA-expression profiling of a single gene – TOPO2A.Read the original paper by Weiss et al.

James L Kreindler,1,2 Victoria A Miller1,31The Children’s Hospital of Philadelphia, 2Department of Pediatrics, 3Department of Anesthesiology and Critical Care Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USAAbstract: Survival for patients with cystic fibrosis (CF) increased to nearly 40 years in 2012 from the early childhood years in the 1940s. Therefore, patients are living long enough to require transition from pediatric CF centers to adult CF centers. The goal of transition is for the young adult to be engaged in the adult health care system in ways that optimize health, maximize potential, and increase quality of life. A successful transition promotes autonomy and responsibility with respect to one's own health. Currently, there is an information gap in the literature with respect to psychological models that can help guide informed transition processes. In this review, we establish the framework in which transition exists in CF; we review some of the published literature from the last 20 years of experience with transition in CF centers around the world; and we discuss psychological models of pediatric illness that can help to explain the current state of transition to adult-oriented care from pediatric-oriented care and help to formulate new models of ascertaining readiness for transition. Finally, we look at our current knowledge gaps and opportunities for future research endeavors.Keywords: cystic fibrosis, transition, adolescent, social-ecological model of AYA readiness for transition, SMART

BackgroundTo determine genomic alterations in head and neck squamous cell carcinoma (HNSCC) using formalin-fixed, paraffin-embedded (FFPE) tumors obtained through routine clinical practice, selected cancer-related genes were evaluated and compared with alterations seen in frozen tumors obtained through research studies.Patients and methodsDNA samples obtained from 252 FFPE HNSCC were analyzed using next-generation sequencing-based (NGS) clinical assay to determine sequence and copy number variations in 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. Human papillomavirus (HPV) status was determined by presence of the HPV DNA sequence in all samples and corroborated with high-risk HPV in situ hybridization (ISH) and p16 immunohistochemical (IHC) staining in a subset of tumors. Sequencing data from 399 frozen tumors in The Cancer Genome Atlas and University of Chicago public datasets were analyzed for comparison.ResultsAmong 252 FFPE HNSCC, 84 (33%) were HPV positive and 168 (67%) were HPV negative by sequencing. A subset of 40 tumors with HPV ISH and p16 IHC results showed complete concordance with NGS-derived HPV status. The most common genes with genomic alterations were PIK3CA and PTEN in HPV-positive tumors and TP53 and CDKN2A/B in HPV-negative tumors. In the pathway analysis, the PI3K pathway in HPV-positive tumors and DNA repair-p53 and cell cycle pathways in HPV-negative tumors were frequently altered. The HPV-positive oropharynx and HPV-positive nasal cavity/paranasal sinus carcinoma shared similar mutational profiles.ConclusionThe genomic profile of FFPE HNSCC tumors obtained through routine clinical practice is comparable with frozen tumors studied in research setting, demonstrating the feasibility of comprehensive genomic profiling in a clinical setting. However, the clinical significance of these genomic alterations requires further investigation through application of these genomic profiles as integral biomarkers in clinical trials.

Purpose: Paclitaxel is an effective therapy for patients with solid tumors. While the albumin-bound formulation eliminates the hypersensitivity reaction caused by the Cremaphor solvent, significant peripheral neuropathy persists when given over the standard 30-min infusion time. We sought to determine if the incidence and severity of peripheral neuropathy could be reduced when the infusion time is lengthened to 2-h.Methods: This was an open-label, single-arm, phase 2 study of albumin-bound paclitaxel given over 2 h. Twenty-five patients with advanced non-small-cell lung cancer were enrolled to determine whether the longer infusion reduced the severity of neuropathy compared to data from an earlier cohort of 40 similar patients treated over 30 min Patients received 125 mg/m(2) of albumin-bound paclitaxel IV over 2 h without premedication on days 1, 8, and 15 of a 28-day cycle. Radiologic assessment was performed every 8 weeks.Results: There was a significant 0.45 grade decrease in average peripheral neuropathy experienced by patients in the 2-h group versus the 30-min group (90% CI, 0.03-0.87). There was, in addition, a significant decrease in grade ≥2 peripheral neuropathy in patients treated over 2 h versus 30 min (28% vs. 55%, 2-sided P = 0.04). A decrease in grade ≥2 neutropenia (20% vs. 48%, 2-sided P = 0.07) was also observed. The median survival, 11 months, was the same for both groups.Conclusion: Increasing the infusion time of albumin-bound paclitaxel from 30 min to 2 h resulted in a significant reduction in both average and grade ≥2 peripheral neuropathy without affecting survival. [ABSTRACT FROM AUTHOR]

Tyrosine kinase inhibitors (TKIs) targeting the epidermal growth factor receptor (EGFR), such as erlotinib (Tarceva) and gefitinib (Iressa), have shown remarkable activity in a portion of patients with non-small-cell lung cancer (NSCLC). Based on a large randomized controlled trial showing a survival benefit compared with placebo, erlotinib gained US Food and Drug Administration approval for use in previously treated patients with NSCLC. However, its use in the first-line setting has been largely experimental. Recently, a large phase III randomized controlled trial demonstrated the superiority of first-line gefitinib therapy compared to combination chemotherapy in a clinically selected population consisting of Asian patients with adenocarcinoma and a light smoking history. This result was even more dramatic in the subset of patients whose tumors carried a mutation in the EGFR gene. Currently, randomized phase III trials of erlotinib as initial treatment of patients with EGFR mutant lung cancer are ongoing. III the setting of these recent developments, a review of the data regarding the use of erlotinib or gefitinib as initial therapy in the treatment of NSCLC is warranted. Currently active trials are referenced using their ClinicalTrials.gov identifier. [ABSTRACT FROM AUTHOR]

OBJECTIVES: To discuss selected molecular targets and new clinical variables that can serve as both predictive and prognostic markers for outcome in patients with non-small cell lung cancer (NSCLC) treated with EGFR-TKIs. DATA SOURCES: Research and journal articles. CONCLUSION: In the near future, treatment for NSCLC will rely ever increasingly on molecular targets rather than empirically chosen cytotoxic chemotherapy for some patients. This will improve outcomes for patients with NSCLC. IMPLICATIONS FOR NURSING PRACTICE: An understanding of the molecular targets and clinical variables that are predictive and prognostic of outcome in NSCLC will help nurses better care for these patients. Copyright © 2008 by Elsevier Inc. [ABSTRACT FROM AUTHOR]

This narrative review summarizes the empirical literature on children's competence for consent and assent in research and treatment settings. Studies varied widely regarding methodology, particularly in the areas of participant sampling, situational context studied (e.g., psychological versus medical settings), procedures used (e.g., lab-based vs. real-world approaches), and measurement of competence. This review also identifies several fundamental dilemmas underlying approaches to children's informed consent. These dilemmas, including autonomy versus best interest approaches, legal versus psychological or ethical approaches, child- versus family-based approaches, and approaches that emphasize consent versus those that emphasize assent, have implications for the measurement of children's competence and interpretation of findings. Recommendations for future research in the area of children's informed consent include the use of diverse samples and control groups, development of multidimensional and standardized measures of competence, utilization of multidimensional and standardized measures of competence, utilization of observational methods and longitudinal designs, examination of noncognitive aspects of children's competence and comparison of children's competence for treatment and research decisions. [ABSTRACT FROM AUTHOR]