Uma Ramamurthy

Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors.

Importance Whole-exome sequencing (WES) has the potential to reveal tumor and germline mutations of clinical relevance, but the diagnostic yield for pediatric patients with solid tumors is unknown. Objective To characterize the diagnostic yield of combined tumor and germline WES for children with solid tumors. Design Unselected children with newly diagnosed and previously untreated central nervous system (CNS) and non-CNS solid tumors were prospectively enrolled in the BASIC3 study at a large academic childrens hospital during a 23-month period from August 2012 through June 2014. Blood and tumor samples underwent WES in a certified clinical laboratory with genetic results categorized on the basis of perceived clinical relevance and entered in the electronic health record. Main Outcomes and Measures Clinical categorization of somatic mutations; frequencies of deleterious germline mutations related to patient phenotype and incidental medically-actionable mutations. Results Of the first 150 participants (80 boys and 70 girls, mean age, 7.4 years), tumor samples adequate for WES were available from 121 patients (81%). Somatic mutations of established clinical utility (category I) were reported in 4 (3%) of 121 patients, with mutations of potential utility (category II) detected in an additional 29 (24%) of 121 patients. CTNNB1 was the gene most frequently mutated, with recurrent mutations in KIT, TSC2, and MAPK pathway genes (BRAF, KRAS, and NRAS) also identified. Mutations in consensus cancer genes (category III) were found in an additional 24 (20%) of 121 tumors. Fewer than half of somatic mutations identified were in genes known to be recurrently mutated in the tumor type tested. Diagnostic germline findings related to patient phenotype were discovered in 15 (10%) of 150 cases: 13 pathogenic or likely pathogenic dominant mutations in adult and pediatric cancer susceptibility genes (including 2 each in TP53, VHL, and BRCA1), 1 recessive liver disorder with hepatocellular carcinoma (TJP2), and 1 renal diagnosis (CLCN5). Incidental findings were reported in 8 (5%) of 150 patients. Most patients harbored germline uncertain variants in cancer genes (98%), pharmacogenetic variants (89%), and recessive carrier mutations (85%). Conclusions and Relevance Tumor and germline WES revealed mutations in a broad spectrum of genes previously implicated in both adult and pediatric cancers. Combined reporting of tumor and germline WES identified diagnostic and/or potentially actionable findings in nearly 40% of newly diagnosed pediatric patients with solid tumors.

A prospective newborn screening and treatment program for sickle cell anemia in Luanda Angola.

Over 300,000 infants are born annually with sickle cell anemia (SCA) in sub‐Saharan Africa, and >50% die young from infection or anemia, usually without diagnosis of SCA. Early identification by newborn screening (NBS), followed by simple interventions dramatically reduced the mortality of SCA in the United States, but this strategy is not yet established in Africa. We designed and implemented a proof‐of‐principle NBS and treatment program for SCA in Angola, with focus on capacity building and local ownership. Dried bloodspots from newborns were collected from five birthing centers. Hemoglobin identification was performed using isoelectric focusing; samples with abnormal hemoglobin patterns were analyzed by capillary electrophoresis. Infants with abnormal FS or FSC patterns were enrolled in a newborn clinic to initiate penicillin prophylaxis and receive education, pneumococcal immunization, and insecticide‐treated bed nets. A total of 36,453 infants were screened with 77.31% FA, 21.03% FAS, 1.51% FS, and 0.019% FSC. A majority (54.3%) of affected infants were successfully contacted and brought to clinical care. Compliance in the newborn clinic was excellent (96.6%). Calculated first‐year mortality rate for babies with SCA compares favorably to the national infant mortality rate (6.8 vs. 9.8%). The SCA burden is extremely high in Angola, but NBS is feasible. Capacity building and training provide local healthcare workers with skills needed for a functional screening program and clinic. Contact and retrieval of all affected SCA infants remains a challenge, but families are compliant with clinic appointments and treatment. Early mortality data suggest screening and early preventive care saves lives. Am. J. Hematol. 88:984–989, 2013.

Obtaining informed consent for clinical tumor and germline exome sequencing of newly diagnosed childhood cancer patients

BackgroundEffectively educating families about the risks and benefits of genomic tests such as whole exome sequencing (WES) offers numerous challenges, including the complexity of test results and potential loss of privacy. Research on best practices for obtaining informed consent (IC) in a variety of clinical settings is needed. The BASIC3 study of clinical tumor and germline WES in an ethnically diverse cohort of newly diagnosed pediatric cancer patients offers the opportunity to study the IC process in the setting of critical illness. We report on our experience for the first 100 families enrolled, including study participation rates, reasons for declining enrollment, assessment of clinical and demographic factors that might impact study enrollment, and preferences of parents for participation in optional genomics study procedures.MethodsA specifically trained IC team offered study enrollment to parents of eligible children for procedures including clinical tumor and germline WES with results deposited in the medical record and disclosure of both diagnostic and incidental results to the family. Optional study procedures were also offered, such as receiving recessive carrier status and deposition of data into research databases. Stated reasons for declining participation were recorded. Clinical and demographic data were collected and comparisons made between enrolled and non-enrolled patients.ResultsOver 15 months, 100 of 121 (83%) eligible families elected to enroll in the study. No significant differences in enrollment were detected based on factors such as race, ethnicity, use of Spanish interpreters and Spanish consent forms, and tumor features (central nervous system versus non-central nervous system, availability of tumor for WES). The most common reason provided for declining enrollment (10% of families) was being overwhelmed by the new cancer diagnosis. Risks specific to clinical genomics, such as privacy concerns, were less commonly reported (5.5%). More than 85% of parents consented to each of the optional study procedures.ConclusionsAn IC process was developed that utilizes a specialized IC team, active communication with the oncology team, and an emphasis on scheduling flexibility. Most parents were willing to participate in a clinical germline and tumor WES study as well as optional procedures such as genomic data sharing independent of race, ethnicity or language spoken.

Establishment and Results of a Magnetic Resonance Quality Assurance Program for the Pediatric Brain Tumor Consortium

RATIONALE AND OBJECTIVES Magnetic resonance (MR) imaging is used to assess brain tumor response to therapies, and a MR quality assurance (QA) program is necessary for multicenter clinical trials employing imaging. This study was performed to determine overall variability of quantitative imaging metrics measured with the American College of Radiology (ACR) phantom among 11 sites participating in the Pediatric Brain Tumor Consortium (PBTC) Neuroimaging Center (NIC) MR QA program. MATERIALS AND METHODS An MR QA program was implemented among 11 participating PBTC sites and quarterly evaluations of scanner performance for seven imaging metrics defined by the ACR were sought and subject to statistical evaluation over a 4.5-year period. Overall compliance with the QA program, means, standard deviations, and coefficients of variation (CV) for the quantitative imaging metrics were evaluated. RESULTS Quantitative measures of the seven imaging metrics were generally within ACR recommended guidelines for all sites. Compliance improved as the study progressed. Intersite variabilities, as gauged by CV for slice thickness and geometric accuracy, imaging parameters that influence size or positioning measurements in tumor studies, were on the order of 10% and 1%, respectively. CONCLUSIONS Although challenging to establish, MR QA programs within the context of PBTC multisite clinical trials when based on the ACR MR phantom program can indicate sites performing below acceptable image quality levels and establish levels of precision through instrumental variabilities that are relevant to quantitative image analyses (eg, tumor volume changes).

RESILIENT ARCHITECTURES TO FACILITATE BOTH FUNCTIONAL CONSCIOUSNESS AND PHENOMENAL CONSCIOUSNESS IN MACHINES

Cognitive theories of consciousness should provide effective frameworks to implement machine consciousness. The Global Workspace Theory is a leading theory of consciousness which postulates that the primary function of consciousness is a global broadcast that facilitates recruitment of internal resources to deal with the current situation as well as modulate several types of learning. In this paper, we look at architectures for machine consciousness that have the Global Workspace Theory as their basis and discuss the requirements in such architectures to bring about both functional and phenomenal aspects of consciousness in machines.

An Operational Perspective of Challenging Statistical Dogma While Establishing a Modern, Secure Distributed Data Management and Imaging Transport System: The Pediatric Brain Tumor Consortium Phase I Experience

The Pediatric Brain Tumor Consortium (PBTC) is a multidisciplinary cooperative research organization devoted to the study of correlative tumor biology and new therapies for primary central nervous system (CNS) tumors of childhood. The PBTC was created in 1999 to conduct early‐phase studies in a rapid fashion in order to provide sound scientific foundation for the Childrens Oncology Group to conduct definitive trials. The Operations and Biostatistics Center (OBC) of the PBTC is responsible for centrally administering study design and trial development, study conduct and monitoring, data collection and management as well as various regulatory and compliance processes. The phase I designs utilized for the consortium trials have accommodated challenges unique to pediatric trials such as body surface area (BSA)‐based dosing in the absence of pediatric formulations of oral agents. Further during the past decade, the OBC has developed and implemented a state‐of‐the‐art secure and efficient internet‐based paperless distributed data management system. Additional web‐based systems are also in place for tracking and distributing correlative study data as well as neuroimaging files. These systems enable effective communications among the members of the consortium and facilitate the conduct and timely reporting of multi‐institutional early‐phase clinical trials.

Abstract IA16: Evaluating the implementation and utility of clinical tumor exome sequencing in the pediatric oncology clinic: Early results of the BASIC3 study

Advances in sequencing technologies allow for provision of genome-scale data to oncologists and geneticists caring for pediatric cancer patients but current experience with the clinical application of genomic sequencing is limited. The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating CLIA-certified tumor and constitutional whole exome sequencing (WES) into the care of children with newly diagnosed solid tumors. This study follows pediatric patients with newly diagnosed CNS and non-CNS solid tumors (target enrollment n=280) at Texas Children9s Cancer Center for two years after performing CLIA-certified whole exome sequencing (WES) of blood and frozen tumor samples. Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. The potential impact of tumor exome findings on clinical decision-making is assessed through review of the medical record over the two year follow-up period as well as through surveys of the oncologists regarding prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Preferences of patient families and oncologists for reporting this complex information are obtained by interviews and audiorecording of the exome result disclosure visits. Since the study opened in August 2012, ∼85% of potentially eligible families have consented to enrollment. The first 100 patients comprise a diverse representation of diagnoses, including 32 with CNS tumors (32%) and 68 with non-CNS tumors (68%). Despite limited diagnostic biopsies in many patents, snap-frozen tumor samples adequate for WES were obtained from 84 subjects (84%), including 62/68 non-CNS solid tumors (91%) and 22/32 (69%) CNS solid tumors. Tumor WES results have been reported for the first 55 patients, revealing a median of 9 (range of 0 to 78) protein-altering mutations per tumor and alterations of known cancer genes such as ALK, BRAF, DICER1, KIT, KRAS, NRAS, MET, JAK2, FGFR3, ARID1A, CTNNB1, and TP53. Fourteen of 55 tumors (25%) contained mutations classified as having proven or potential clinical utility. These results demonstrate the feasibility of routine tumor WES in the pediatric oncology clinic and a significant level of parental interest in receiving WES results. Potentially clinically-relevant mutations can be identified in a substantial minority of pediatric solid tumor patients but distinct from the medically actionable mutations seen in adult cancer patients. Data further assessing the clinical utility of the tumor exomes and the preferences of oncologists and parents for reporting of these results are under study. Supported by NHGRI/NCI 1U01HG006485. Citation Format: D. Williams Parsons, Angshumoy Roy, Federico A. Monzon, Dolores H. Lopez-Terrada, Murali M. Chintagumpala, Stacey L. Berg, Susan G. Hilsenbeck, Tao Wang, Robin A. Kerstein, Sarah Scollon, Katie Bergstrom, Richard L. Street, Jr., Laurence B. McCullough, Amy L. McGuire, Uma Ramamurthy, David A. Wheeler, Christine M. Eng, Yaping Yang, Jeff G. Reid, Donna M. Muzny, Richard A. Gibbs, Sharon E. Plon. Evaluating the implementation and utility of clinical tumor exome sequencing in the pediatric oncology clinic: Early results of the BASIC3 study. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr IA16.

Development of a Queriable Database for Oncology Outcome Analysis

Clinical trials and oncology data management have undergone considerable change in the past decade. Imaging has become a key tool for clinical trials management and a biomarker for clinical trial validation as imaging technologies improve and become more precise. Images have become extremely helpful in determining staging/eligibility, treatment response, and outcome determination including disease recurrence and progression. In modern protocols, images are often reviewed in real time to validate these points in order to improve compliance to study requirements and create uniform patient populations for clinical trials analysis. Data acquisition and management systems are currently in use to acquire and display images in electronic digital formats for view by both on site and off site radiology reviewers. As clinical trials become more global in focus, the ability for databases to accommodate diverse imaging acquisition strategies will become increasingly important for information review.

Individualized growth assessment: conceptual framework and practical implementation for the evaluation of fetal growth and neonatal growth outcome

&NA; Fetal growth abnormalities can pose significant consequences on perinatal morbidity and mortality of nonanomalous fetuses. The most widely accepted definition of fetal growth restriction is an estimated fetal weight less than the 10th percentile for gestational age according to population‐based criteria. However, these criteria do not account for the growth potential of an individual fetus, nor do they effectively separate constitutionally small fetuses from ones that are malnourished. Furthermore, conventional approaches typically evaluate estimated fetal weight at a single time point, rather than using serial scans, to evaluate growth. This article provides a conceptual framework for the individualized growth assessment of a fetus/neonate based on measuring second‐trimester growth velocity of fetal size parameters to estimate growth potential. These estimates specify size models that generate individualized third‐trimester size trajectories and predict birth characteristics. Comparisons of measured and predicted values are used to separate normally growing fetuses from those with growth abnormalities. This can be accomplished with individual anatomical parameters or sets of parameters. A practical and freely available software (Individualized Growth Assessment Program) has been developed to allow implementation of this approach for clinical and research purposes.

Abstract IA16: Clinical genomics for children with solid tumors: Current realities and future opportunities

Genome-scale sequencing methods such as whole exome sequencing (WES) have provided significant insight into the pathogenesis of cancer. However, experience with the use of these tests in the clinical care of cancer patients remains limited. Sequencing of tumor and matched normal samples can reveal multiple types of results with implications for clinical practice. The identification of somatic (tumor-specific) mutations has the potential to offer diagnostic and prognostic information and inform selection of therapies. Detection of germline mutations in cancer susceptibility genes may prompt further genetic testing and guide cancer surveillance strategies for both the patient and family members. Germline mutations may also explain non-cancer phenotypes, predict drug responses, or provide reproductive counseling information for parents. The goal of the BASIC3 (Baylor College of Medicine Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating clinical tumor and constitutional WES into the care of children with newly diagnosed solid tumors. This study follows pediatric patients with newly diagnosed CNS and non-CNS solid tumors at Texas Children9s Cancer Center for two years after performing CLIA-certified WES of blood and frozen tumor samples. Results are deposited into the electronic health record and disclosed to families by their oncologist and a genetic counselor. The potential impact of tumor exome findings on clinical decision-making is assessed through review of the medical record over the two year follow-up period as well as through surveys of the oncologists regarding prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Preferences of patient families and oncologists for reporting this complex information are obtained by interviews and audio recording of the WES result disclosure visits. Since the study opened in August 2012, more than 210 subjects have been enrolled (~80% of potentially eligible patients), representing the expected distribution of both CNS and non-CNS tumors. WES results have been reported for 170 subjects, revealing potentially-clinically relevant germline and somatic mutations in cancer genes known to be related to pediatric solid tumors as well as others known to be mutated primarily in adult cancer patients. Data will be presented regarding the diagnostic yield of combined tumor and germline WES for children with newly-diagnosed solid tumors. These results demonstrate the feasibility of routine tumor WES in the pediatric oncology clinic and a significant level of parental interest in receiving WES results and have significant implications for the treatment of children with relapsed and refractory solid tumors and the design of clinical trials using precision oncology approaches for these patients. Further analyses of the clinical utility of the WES data and the preferences of oncologists and parents for reporting of these results are under study. The BASIC3 study is a Clinical Sequencing Exploratory Research (CSER) program project supported by NHGRI/NCI 1U01HG006485. Citation Format: D. William Parsons, Angshumoy Roy, Yaping Yang, Tao Wang, Sarah Scollon, Katie Bergstrom, Robin A. Kerstein, Stephanie Gutierrez, Abhishek Bavle, Frank Y. Lin, Dolores H. Lopez-Terrada, Federico A. Monzon, Jed G. Nuchtern, Uma Ramamurthy, Amy L. McGuire, Susan G. Hilsenbeck, Jeffrey G. Reid, Donna M. Muzny, David A. Wheeler, Stacey L. Berg, Murali M. Chintagumpala, Christine M. Eng, Richard A. Gibbs, Sharon E. Plon. Clinical genomics for children with solid tumors: Current realities and future opportunities. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr IA16.