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PURPOSE The routine use of large next-generation sequencing (NGS) pan-cancer panels is required to identify the increasing number of, but often uncommon, actionable alterations to guide therapy. Inconsistent coverage and variable payment is hindering NGS adoption into clinical practice. A review of test utilization, clinical utility, coverage, and reimbursement was conducted in a cohort of patients diagnosed with high-risk cancer who received pan-cancer panel testing as part of their clinical care. MATERIALS AND METHODS The Columbia Combined Cancer Panel (CCCP), a 467-gene panel designed to detect DNA variations in solid and liquid tumors, was performed in the Laboratory of Personalized Genomic Medicine at Columbia University Irving Medical Center. Utilization was characterized at test order. Results were reviewed by a molecular pathologist, followed by a multidisciplinary molecular tumor board where clinical utility was classified by consensus. Reimbursement was reviewed after payers provided final coverage decisions. RESULTS NGS was performed on 359 high-risk tumors from 349 patients. Reimbursement data were available for 246 cases. The most common reason providers ordered CCCP testing was for patients diagnosed with a treatment-resistant or recurrent tumor (n = 214; 61%). Findings were clinically impactful for 229 cases (64%). Molecular alterations that may inform future therapy in the event of progression or relapse were found in 42% of cases, and a targeted therapy was initiated in 23 cases (6.6%). The majority of tests were denied coverage by payers (n = 190; 77%). On average, insurers reimbursed 10.75% of the total NGS service charge. CONCLUSION CCCP testing identified clinically impactful alterations in 64% of cases. Limited coverage and low reimbursement remain barriers, and broader reimbursement policies are needed to adopt pan-cancer NGS testing that benefits patients into clinical practice.

COVID‐19 has upended medical practice and education, but has also catalyzed enhancements in the field. Early on, a local group of researchers united to investigate the impact of the pandemic on pediatric hematology oncology (PHO). From this group, a regional educational series was established, “virtual‐Symposium of Pediatric Hematology/Oncology of New York” (v‐SYMPHONY). The implementation of these endeavors while PHO fellowship applications are declining has highlighted our perceptions that education, mentoring, and career expectations are not keeping up with the needs of current trainees. We describe our regional experience joining together to further education and research, and reflect on the current landscape of PHO training and workforce.

Purpose The complexity of results generated from whole-genome sequencing (WGS) and whole-exome sequencing (WES) adds challenges to obtaining informed consent in pediatric oncology. Little is known about knowledge of WGS and WES in this population, and no validated tools exist in pediatric oncology. Methods We developed and psychometrically evaluated a novel WGS and WES knowledge questionnaire, the Precision in Pediatric Sequencing Knowledge Questionnaire (PIPseqKQ), to identify levels of understanding among parents and young adult cancer survivors (≥ 18 years old), off therapy for at least 1 year from a single-institution pediatric oncology outpatient clinic. Participants also completed health literacy and numeracy questionnaires. All participants provided written informed consent. Results One hundred eleven participants were enrolled: 76 were parents, and 35 were young adults. Of the total cohort, 77 (69%) were female, 63 (57%) self-identified as white, and 74 (67%) self-identified as non-Hispanic. Sixty-six (59%) had less than a college degree. Adequate health literacy (n = 87; 80%) and numeracy (n = 89; 80%) were demonstrated. Internal consistency was high (Cronbach’s α = .88), and test-retest reliability was greater than the 0.7 minimum requirement. Scores were highest for genetic concepts related to health and cancer and lowest for WGS and WES concepts. Health literacy and educational attainment were significantly associated with PIPseqKQ scores. Overall, participants felt the benefits of WGS and WES outweighed the potential risks. Conclusion Parents and young adult cancer survivors have some genetics knowledge, but they lack knowledge about WGS and WES. The PIPseqKQ is a reliable tool that can identify deficits in knowledge, identify perceptions of risks and benefits of WGS and WES, and help clinicians tailor their consent discussions to best fit families. The PIPseqKQ also may inform the development of educational tools to better facilitate the informed consent process in pediatric oncology.

Precision medicine is a dynamic area embracing a diverse and increasing type of approaches that allow the targeting of new medicines, screening programs or preventive healthcare strategies, which include the use of biologic markers or complex tests driven by algorithms also potentially taking account of patient preferences. The International Society for Pharmacoeconomics and Outcome Research expanded its current work around precision medicine to (1) describe the evolving paradigm of precision medicine with examples of current and evolving applications, (2) describe key stakeholders perspectives on the value of precision medicine in their respective domains, and (3) define the core factors that should be considered in a value assessment framework for precision medicine. With the ultimate goal of improving health of well-defined patient groups, precision medicine will affect all stakeholders in the healthcare system at multiple levels spanning the individual perspective to the societal perspective. For an efficient, timely and practical precision medicine value assessment framework, it will be important to address these multiple perspectives through building consensus among the stakeholders for robust procedures and measures of value aspects, including performance of precision mechanism; aligned reimbursement processes of precision mechanism and subsequent treatment; transparent expectations for evidence requirements and study designs adequately matched to the intended use of the precision mechanism and to the smaller target patient populations; recognizing the potential range of value-generation such as ruling-in and ruling-out decisions.

Whole-genome sequencing (WGS) provides the most compre-hensive view of the genome and is increasingly being explored forclinical use by pediatric oncology researchers across the country.WGS research conducted by a CLIA compliant lab to guideprecisioncancertherapyispredicatedonthenotionthatcomparisonoftumorandnormaltissuewillidentifytargetablesomaticvariantsleading to improved clinical outcomes through selection of moreeffective, less toxic treatments [1]. However, the technologypresents challenges related to identification, interpretation, andreturn of clinical- grade somatic and germline results. Specifically,somatic mutations currently include only a few medicallyactionable variants and a large number of variants of unknownsignificance [2]. Non-cancerous germline disease-causing muta-tions and germline cancer susceptibility mutations, referred to assecondary findings, may also be identified [3]. Furthermore,secondary findings may be present in other family members notinvolved in the research [4,5]. These aspects of genomic researchraise pragmatic and ethical dilemmas including defining essentialcomponents of the informed consent process, determining whattypes of results should be returned, whether patients should have aroleinmakingthisdetermination,andwhattypesofdatashouldbeincorporated into medical records [6-11].Obtaining consent for WGS research from parents of childrenwith newly diagnosed cancer poses additional challenges to thoseoutlined above. Given the high efficacy of standardized treatmentprotocols for the majority of pediatric cancer patients [12], there isonly a small chance that initial therapy will be altered by WGSresearch.Inaddition,tissueforsequencingshouldbeobtainedpriorto initiating therapy, a time when patients and parents often feeloverwhelmed with uncertainty and fear. With hopes for a cure,parental motivation to participate in WGS research may be highwithout fully understanding the range of results that may bereturned,includingvariantsofunknownsignificanceandsecondaryfindings.Conversely,parentsmayrejectparticipationinstudiesnotdirectly related to the immediate diagnosis or treatment of theirchild.These considerations suggest that parents of children newlydiagnosed with cancer will need to understand WGS and itsconsequences to make informed decisions before participating inresearch [13,14]. In anticipation of launching a pediatric precisionmedicine program, with an emphasis on WGS, for all newlydiagnosed cancer patients, we explored challenges to informed

INTRODUCTION: Whole exome sequencing (WES) of newly diagnosed pediatric central nervous system (CNS) tumors is quickly becoming part of routine care. Through the Precision in Pediatric Sequencing (PiPseq) program at Columbia University, we have found potentially actionable mutations in more than 40% of evaluable CNS cases at diagnosis. More recently, we have integrated this approach into the management of patients undergoing surgery for CNS tumor recurrence. METHOD: After obtaining informed consent, tumor-normal WES with transcriptome analysis was performed in a CLIA-certified laboratory on fresh frozen or paraffin embedded CNS tumor samples and peripheral blood. RESULTS: 7 cases (5 male, 2 female; median age 5 years) with adequate diagnostic and recurrent tumor tissue were tested. No case had a somatic mutation of established clinical utility (tier 1). Among 3 embryonal tumors, a splice site variant in TSC1 (tier 2 mutation of potential utility) was detected in a medulloblastoma, but only at recurrence and not at initial diagnosis. FOXR2 overexpression was detected at diagnosis and confirmed at early progression of a temporal lobe tumor, prompting revision of the initial diagnosis of high grade glioma to CNS neuroblastoma subtype of PNET, and treated accordingly. In a third patient initially diagnosed with medulloblastoma, overexpression of PDGFRA, MDM4, CDKN2A, EGFR, OLIG2, and GFAP supported a change in diagnosis to glioblastoma. Two gliomas had tier 2 mutations detected at initial diagnosis and progression: SETD2 p.R2040* (optic nerve lesion, called pseudotumor initially but glioma at progression), and H3F3A p.K28M (thalamic low grade glioma). In one patient with ependymoma, copy number gain of 1q25 (associated with poor prognosis) was seen only in the recurrence specimen. CONCLUSION: Our preliminary experience suggests that in pediatric CNS tumor patients referred for reoperation at recurrence, repeat WES may reveal a previously unrecognized treatment option, at least in embryonal tumors.

Malignant gliomas, the most common type of primary brain tumor in adults, remain highly proliferative, invasive tumors that are resistant to conventional treatment with surgery, radiation, and chemotherapy. Salvage therapies after disease progression have been ineffective; median survival ranges between 3 and 9 months,1,2 necessitating the development of alternative treatment strategies. Furthermore, recurrence is typically accompanied by progressive physical and cognitive debilitation.3 As a result, 2 secondary outcome measures have emerged in neuro-oncology trials: evaluations of neurocognitive function (NCF) and quality of life (QoL). NCF evaluation in neuro-oncology patients is an important area of study because malignant brain tumor infiltration of the brain parenchyma can result in a progressive neurodegenerative state.4 Moreover, the therapeutic options available—surgery, radiation therapy, and chemotherapy—all have potential neurotoxicity. While tumors can cause focal neurologic deficits, treatment can often result in damage to subcortical white matter, resulting in diffuse deficits.5 Cognitive impairment in brain tumor patients is a common disability that patients and their caregivers frequently cite as a significant concern.4 The importance of QoL is underscored in brain tumor patients, particularly those with recurrent or advanced disease because prognosis remains poor.6–9 Additionally, patients with brain tumors are generally more incapacitated than those with systemic disease, which can significantly affect QoL.10 The aggressive nature and toxicity of treatments undergone by brain-tumor patients make assessments of QoL especially important and may influence decision-making of both patients and physicians.6,11 Given the poor prognosis for this patient population, the development of surrogate treatment strategies is imperative. One such alternative is convection-enhanced delivery (CED) of chemotherapeutics. Developed by Bobo et al.,12 CED delivers drugs directly to a tumor and/or the surrounding interstitium via chronic positive-pressure infusion. This allows high local concentrations of drug while overcoming the limitations imposed by toxicity and the blood-brain barrier in systemic therapies that prevent the use of many potentially effective drugs. Although this delivery mechanism is promising, challenges to CED have been reported and require further investigation including inadequate catheter positioning that results in poor coverage and monitoring of drug distribution into the brain.13 Recurrent malignant gliomas are locally invasive but rarely metastatic, making them desirable tumors for local regional delivery approaches such as CED.14 In an effort to improve outcomes for these patients, a phase Ib dose escalation trial of topotecan by CED was conducted in participants with recurrent malignant gliomas refractory to conventional therapy. Topotecan, a topoisomerase-I inhibitor, is an ideal antiglioma drug for local delivery since it is cytotoxic to glioma cells and relatively nontoxic to normal brain tissue.15 As part of this dose escalation study, the effect of topotecan by CED on neurocognitive functioning and QoL was assessed as an exploratory endpoint.

Primary low-grade gliomas are common brain tumors of childhood, many of which require radiation therapy (RT) as definitive treatment. Increased conformality of RT could decrease the incidence and severity of late effects. We report our experience with 32 pediatric patients treated with proton RT.Thirty-two pediatric patients with low-grade gliomas of the brain or spinal cord were treated with proton RT from 1995 to 2007. Sixteen patients received at least 1 regimen of chemotherapy before definitive RT. The median radiation dose was 52.2 GyRBE (48.6-54 GyRBE).The median age at treatment was 11.0 years (range, 2.7-21.5 years), with a median follow-up time of 7.6 years (range, 3.2-18.2 years). The 6-year and 8-year rates of progression-free survival were 89.7% and 82.8%, respectively, with an 8-year overall survival of 100%. For the subset of patients who received serial neurocognitive testing, there were no significant declines in Full-Scale Intelligence Quotient (P=.80), with a median neurocognitive testing interval of 4.5 years (range, 1.2-8.1 years) from baseline to follow-up, but subgroup analysis indicated some significant decline in neurocognitive outcomes for young children (7 years) and those with significant dose to the left temporal lobe/hippocampus. The incidence of endocrinopathy correlated with a mean dose of ≥40 GyRBE to the hypothalamus, pituitary, or optic chiasm. Stabilization or improvement of visual acuity was achieved in 83.3% of patients at risk for radiation-induced injury to the optic pathways.This report of late effects in children with low-grade gliomas after proton RT is encouraging. Proton RT appears to be associated with good clinical outcome, especially when the tumor location allows for increased sparing of the left temporal lobe, hippocampus, and hypothalamic-pituitary axis.

Background Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. Methods The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient’s electronic medical record. Results NGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients. Conclusions Our results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0389-6) contains supplementary material, which is available to authorized users.

6593 Background: The routine use of large next generation sequencing (NGS) cancer panels is required to identify the increasing number of, but often uncommon actionable alterations present across multiple tumor histologies to guide therapy. Inconsistent coverage and variable payment is hindering adoption of these tests into clinical practice. A review of clinical utility, coverage and reimbursement was conducted in a cohort of adult oncology patients who received expanded genomic panel testing as part of their clinical care. Methods: The Columbia Combined Cancer Panel (CCCP), a 467 gene panel designed to detect single nucleotide variants, indels, and copy number variations in solid and liquid tumors was performed in a CLIA-certified laboratory at Columbia University Irving Medical Center. Clinical utility categories included: immediate change in management; informed future treatment options; provided diagnostic/prognostic information; and other impact. Claims were submitted between 1/1/17 and 4/30/18. Carriers were categorized into commercial, managed-government, and government plans. Results: 300 tumors underwent NGS. Reimbursement data were available for 258 cases. 57% of testing was performed for a treatment-resistant, recurrent, or high stage cancer, or for a cancer of rare/mixed histology (21%). Findings were clinically actionable in 183 cases (61%). Results led to an immediate change in management (n = 6, 2%), informed future treatment options (n = 140, 47%), and provided diagnostic/prognostic information (n = 29, 10%). Only 57 tests (22%) received coverage. In 59% of denials (118/201), a clinically-actionable result was found. Commercial plans reimbursed 29/119 tests (24%) and managed-government plans reimbursed 28/54 tests (52%). Government plans provided no coverage for 85 tests. On average, insurers reimbursed 10% of the total CCCP service charges: 12.5% for commercial and 22% for managed-government plans. Conclusions: Expanded genomic testing identified clinically-impactful alterations in 61% of cases. Limited coverage and low reimbursement remain a barrier and broader reimbursement policies are needed to adopt expanded genomic testing that benefits patients into clinical practice.

The incorporation of tumor-normal genomic testing into oncology can identify somatic mutations that inform therapeutic measures but also germline variants associated with unsuspected cancer predisposition. We describe a case in which a RET variant was identified in a 3-yr-old male with relapsed leukemia. Sanger sequencing revealed the patient's father and three siblings carried the same variant, associated with multiple endocrine neoplasia 2A (MEN2A). Evaluation of the father led to the diagnosis and treatment of metastatic medullary thyroid carcinoma. Detection of RET mutations in families with hereditary MTC allows for genetic risk stratification and disease surveillance to reduce morbidity and mortality.

Activated receptor tyrosine kinases recruit many signaling proteins to activate downstream cell proliferation and survival pathways, including phosphatidylinositol 3-kinase (PI3K) consisting of a p85 regulatory protein and a p110 catalytic protein. We have recently shown the p85alpha protein also has in vitro GTPase activating protein (GAP) activity towards Rab5 and Rab4, small GTPases that regulate vesicle trafficking events for activated receptors. Expression of a GAP-defective mutant, p85R274A, resulted in sustained levels of activated platelet-derived growth factor receptors (PDGFRs) and enhanced downstream signaling. In this report we have characterized Rab5- and Rab4-mediated PDGFR trafficking in cells expressing wild type p85 and GAP-defective mutant p85R274A. Wild type p85 overexpressing cells had slower PDGFR trafficking consistent with enhanced GAP activity deactivating Rab5 and Rab4 to block their vesicle trafficking functions. Mutant p85R274A expression increased the internalization rate of PDGFRs, a Rab5-dependent process, without preventing PDGFR ubiquitination. Immunofluorescence studies further demonstrated that p85R274A-expressing cells showed Rab5 accumulation at intracellular locations. Pull-down and FRAP (fluorescence recovery after photobleaching) experiments indicate this is likely membrane-associated Rab5-GTP, sustained due to decreased p85 GAP activity for the p85R274A mutant. These cells also had substantial amounts of activated PDGFRs in Rab4-positive recycling endosomes, a compartment that usually contains primarily deactivated/dephosphorylated receptors. Our results suggest that the PDGFR-associated GAP activity of p85 regulates both Rab5 and Rab4 functions in cells to influence the movement of activated PDGFR through endosomal compartments. Disruption of this regulation by p85R274A expression impacts PDGFR phosphorylation/dephosphorylation, degradation kinetics and downstream signaling by altering the time receptors spend in specific intracellular endosomal compartments. These results demonstrate that the p85alpha protein is an important regulator of Rab-mediated PDGFR trafficking, which significantly impacts receptor signaling and degradation.

Rab proteins regulate vesicle fusion events during the endocytosis, recycling, and degradation of activated receptor tyrosine kinases. The p85alpha subunit of phosphatidylinositol 3-kinase has GTPase-activating protein activity toward Rab5 and Rab4, an activity severely reduced by a single point mutation (p85-R274A). Expression of p85-R274A resulted in increased platelet-derived growth factor receptor (PDGFR) activation and downstream signaling (Akt and MAPK) and in decreased PDGFR degradation. We now report that the biological consequences of p85-R274A expression cause cellular transformation as determined by the following: aberrant morphological phenotype, loss of contact inhibition, growth in soft agar, and tumor formation in nude mice. Immunohistochemistry shows that the tumors contain activated PDGFR and high levels of activated Akt. Coexpression of a dominant negative Rab5-S34N mutant attenuated these transformed properties. Our results demonstrate that disruption of the RabGAP function of p85alpha due to a single point mutation (R274A) is sufficient to cause cellular transformation via a phosphatidylinositol 3-kinase-independent mechanism partially reversed by Rab5-S34N expression. This critical new role for p85 in the regulation of Rab function suggests a novel role for p85 in controlling receptor signaling and trafficking through its effects on Rab GTPases.

Introducing whole genome sequencing (WGS) into pediatric cancer research at diagnosis poses unique challenges related to informed consent. WGS requires tissue obtained prior to initiating treatment, when families may be overwhelmed with uncertainty and fear. Motivation to participate may be high without fully understanding the range of possible results, including secondary findings. Little is known about parental knowledge, attitudes, and beliefs about this type of research.A qualitative study was conducted to investigate parental knowledge about genetic concepts and WGS, thoughts about the informed consent process, and preferences for secondary findings. Focus groups were conducted with parents/guardians of children with cancer and semi-structured interviews were conducted in a control group without cancer. All transcripts were analyzed using content analysis.Four focus groups included 15 participants; eight semi-structured interviews included 10 participants. Basic knowledge about genetics was limited to heredity. Some knowledge of genomic analysis was present in 3/15 focus group participants. Major factors related to participation in WGS research were: (i) hope for their child and future children; (ii) no additional procedures; (iii) and protection of privacy. All favored a two-step consent process, first to store extra tissue from a diagnostic biopsy/resection, followed by consenting to WGS research, one-to-two months later. The desire to receive secondary findings was high among both groups, but there were individuals who did not want these results, fearing increased anxiety.Parents/guardians of children with cancer have limited knowledge about WGS. A two-step consent process may improve their ability to provide meaningful informed consent.

Background: Several landmark genomic profiling studies have dramatically advanced our understanding of the origin, progression and clonal evolution of adult acute myeloid leukemia (AML) and directly impacted clinical care. However, very little is known about the mutational landscape of pediatric AML, a distinct entity that shares few genetic and clinical characteristics with adult AML. To investigate potential drivers of high-risk pediatric AML, comprehensive genomic profiling was performed on high-risk AML samples as part of a prospective clinical next-generation sequencing program. Methods:Samples obtained from patients with known high-risk features at diagnosis or with refractory or relapsed AML were selected for molecular profiling. Comprehensive testing included whole-exome sequencing (WES) of matched tumor (bone marrow or chloroma tissue) and normal tissue (peripheral blood or buccal swab) samples and transcriptome analysis (RNAseq). Targeted sequencing of 467 cancer-associated genes was used when tumor tissue was limited. Sequencing was performed on Illumina's HiSeq 2500 with 150X and 500X average coverage for WES and targeted sequencing, respectively. Variants were filtered to select alterations in cancer-related genes or genes relevant for patient care. Results:Fifteen patients with AML (mean age 7.7 yrs; range 0.75-19 yrs) met high-risk criteria (high-risk features at diagnosis = 4, relapsed disease = 8, refractory disease = 3) and were selected for profiling. WES and RNAseq were performed on 11 samples, WES only on 3 samples and targeted DNA sequencing on 1 sample. The median number of variants was 60 (range 14- 5950) per case. After filtering, 54 mutations were identified in 35 genes with a mean of 3.6 mutated genes per patient sample (range 0-14); two samples only carried a fusion gene with no other genetic alterations. At least one driver genetic alteration was detected in each patient sample. Thirteen samples carried mutations in at least one gene known to be altered in AML (e.g. IDH1, WT1, TP53, NRAS) (mean, 2; range, 1-6) and 5 samples carried novel mutations in 15 genes not previously implicated in AML (e.g. CARD9, CHD9, Axin1). Mutations in 11 AML related genes were detected in more than one sample including NRAS in 4, TP53 in 3 and KRAS, PTPN11 PHF6, JAK3 in 2 samples each; genes not previously implicated in AML were only mutated in single patients. Of note, mutations in genes encoding members of the RAS pathway occurred in 60% of cases (9/15 samples). RNAseq identified gene fusions in 7/11 samples (63%). Four fusions involving KMT2A and core binding factor genes were also detected by FISH while three fusions were detected by RNAseq only: NUP98-NSD1 in two patients and CBFA2T3-GLIS2 in one patient. Samples carrying driver gene fusions had the lowest number of mutated genes (0-1) compared to samples lacking a gene fusion (1-5 mutated genes), with one exception of a patient with history of infant ALL who later developed KMT2A-AFF1AML with the highest number of mutated genes (n=14). There was no correlation between the number of mutated genes and age, clinical characteristics, initial risk classification at diagnosis or intensity of therapy prior to sequencing. Conclusion:Our study provides an initial overview of the genetic alterations that characterize high-risk, chemo-resistant pediatric AML. Analysis of the data highlights the overall low genetic complexity of high-risk AML despite the aggressive clinical behavior and exposure to intense chemotherapy, including stem cell transplant. Of interest, similar to adult AML, we found that mutations leading to aberrant activation of the RAS pathway were also very frequent in our cohort of pediatric high-risk AML, while genes typically mutated early in the process of leukemogenesis in adult AML, such as NPM1, DNMT3A, FLT3, IDH1, IDH2 were not affected. Such findings suggest that distinct, age-specific mechanisms of leukemogenesis might exist. Furthermore, our data also highlights the important role of RNA sequencing in complementing current standard diagnostic tools, allowing the identification of driver fusion genes in samples for which no other driver event is detected. Larger studies, preferably including diagnostic samples and utilizing broader approaches, are needed to better understand the mechanisms responsible for the initiation and progression of childhood AML. Disclosures No relevant conflicts of interest to declare.

The objective of this study was prospectively to investigate the health-related quality of life (HRQOL) of 80 pediatric recipients of allo-SCT for malignant and non-malignant diseases. The PedsQL 4.0 was used to assess self-reported physical, emotional and social functioning of children ⩾5 years old once, pre-allo-SCT and on days +100, +180, +365 and +730. Emotional and social functioning was stable pre-to-post-allo-SCT and comparable to the normative sample (P>0.05), and physical functioning was 17 points lower pre-allo-SCT (P⩽0.01) with improved scores equivalent to the norms by day +730. Lower physical scores were reflected by 50–54% of children reporting difficulties with movement, strength, pain and fatigue. At baseline, children ages 5–7 reported lower social functioning (P

1579Background: Increasing utilization of clinical comprehensive sequencing (CS) in pediatric oncology suggests that patients and/or their caregivers will need to understand the value and limitatio...

Background: Molecular characterization of tumor and/or host has the potential to advance the management of pediatric cancer and high risk hematologic disease, but the clinical utility of integrating genomic profiling into standard clinical practice has been limited. The PIPseq Program at Columbia University has instituted prospective CLIA-compliant genomic sequencing for newly diagnosed, high risk, relapsed or refractory pediatric cancer patients and patients referred for bone marrow transplantation. Methods: Families are consented for clinical cancer whole-exome sequencing (cWES) or constitutional whole-exome sequencing (WES) with opt out options for return of results, exclusion of results from medical records, receipt of American College of Medical Genetics (ACMG) recommended secondary germline variants, and data/ sample use in research. Molecular characterization utilizes next generation cWES, WES, RNAseq (transcriptome), or targeted sequencing of select cancer genes. Clinical cancer reports include: known tumor type-specific actionable somatic mutations (Tier 1); somatic mutations actionable in other tumor types, in targetable pathways, or in well-established cancer genes (Tier 2); other somatic mutations in cancer genes (Tier 3); and somatic variants of uncertain significance (VUS; Tier 4). Reports for cWES testing also note translocations, significantly over expressed genes, segmental copy number variation, and germline variants. Institutional Review Board approval was obtained to conduct a retrospective review of results to date. Five categories were developed to assess clinical utility and describe significance: 1) diagnostic, 2) prognostic, 3) potentially actionable target, 4) other critical role in decision making, and 5) implications for health maintenance and genetic counseling. Results: Since January 2014, adequate tissue samples were available for 47 patients, including 31 (66%) with solid tumors and 16 (34%) with hematologic conditions. Testing included cWES (n=8), cWES with transcriptome (n=15), transcriptome only (n=1), targeted somatic panel (n=8), constitutional WES only (n=6), and multiple sequencing platforms (n=7). Normal tissue was obtained from buccal swab (n=8), blood (n=18), and unaffected tissue (n=1). Three families opted out of receiving secondary findings. Genomic aberrations were reported in 41/47 patients. Of the 127 cancer alterations found, 70 (55%) were in 15 patients with hematologic disease (median 2, range 1-11) and 57 (45%), were in 26 patients with solid tumors (median 1, range 1-6). Among the hematologic cases, alterations of known or potential clinical relevance were categorized as Tier 1 (n=0), Tier 2 (n=27), Tier 3 (n=2) mutation, or translocation (n=4); whereas in solid tumors these were categorized as Tier 1 (n=1), Tier 2 (n=14), Tier 3 (n=3) mutation, or translocation (n=9). Twenty-four Tier 4 somatic VUS were identified in hematologic specimens and 26 in solid tumor specimens. Genomic interrogation informed diagnosis in 10 patients (3 previously unknown); provided new prognostic information in 4; identified potentially actionable targets in 15; influenced clinical decision making regarding bone marrow transplant in 2; and revealed cancer or other disease predisposition in 7. Secondary germline ACMG findings in BRCA1 and PMS2 were found. Germline APC mutation was confirmed in one patient and germline VUS in SDHC was seen in another. Novel germline findings were also observed in RUNX1, MLL2 and DICER1. Overall, the PIPseq platform provided clinically impactful results in 30/47 cases (64%). Conclusions: Utilizing a CLIA-compliant prospective WES-based platform, more than half of selected patients derived clinically impactful information. The potential clinical utility of genomic sequencing in pediatric hematology-oncology has likely been underestimated. This abstract is also presented as Poster 50. Citation Format: Julia L. Glade Bender, Jennifer A. Oberg, Maria Luisa Sulis, Filamon Dela Cruz, Anthony N. Sireci, Susan J. Hsiao, Darrell J. Yamashiro, Carrie Koval, Wendy K. Chung, Stephen G. Emerson, Rebecca Zylber, Samantha Cano, Danielle P. Denney, Stuart Andrews, Peter L. Nagy, Mahesh M. Mansukhani, Andrew L. Kung. Precision in Pediatric Sequencing (PIPseq): Clinical implementation of genomic sequencing into pediatric hematology-oncology practice. [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 PR01.

Background To evaluate the neuropsychological late effects amongst survivors treated on the Head Start II protocol between 1997 and 2003. Procedures Forty-nine patients (mean age 2.9 years) diagnosed with a malignant brain tumor underwent baseline neuropsychological assessment prior to autologous hematopoietic cell transplantation (AuHCT). Twenty-six survivors were retested after 3 years of follow-up as 20 patients did not survive. Patients were evaluated for intelligence, academic achievement, receptive language, visual-motor integration (VMI), learning/memory, social-emotional and behavioral functioning based upon age at testing. Results Overall intelligence and VMI at baseline were low average while verbal and non-verbal intelligence, academic achievement, and receptive vocabulary were in average range. Parents reported social-emotional and behavioral functioning within normal limits. Serial testing revealed Full Scale (FSIQ)/Mental Development Index (MDI), Verbal (VIQ), and Performance (PIQ) Intelligence to be generally stable over 3-year follow-up. Group-average analysis at follow-up demonstrated low average intelligence, academic achievement, receptive language, and VMI. Age at diagnosis was positively correlated with internalizing symptoms and visual immediate memory, while time since diagnosis was inversely correlated with FSIQ, VIQ, PIQ, reading and delayed verbal memory. Craniospinal irradiation (CSI) was avoided in two-thirds of patients. Conclusion Induction, with or without intensification using intravenous methotrexate, followed by myeloablative consolidation chemotherapy with AuHCT, may avoid or delay CSI, with possible stabilization of neuropsychological functioning, including those younger at diagnosis. Continued follow-up is necessary to determine the preservation of neuropsychological, academic, social-emotional and behavioral functioning. Pediatr Blood Cancer 2010;54:429–436. © 2010 Wiley-Liss, Inc.

10090 Background: Introducing whole genome sequencing (WGS) in pediatric cancer patients at diagnosis poses a unique set of issues. We investigated parental knowledge, attitudes and beliefs about t...

Abstract 2069 Over the past decade there has been a shift in treating pediatric patients with RTC followed by allogeneic stem cell transplantation (alloSCT) for malignant and non-malignant diseases (Satwani/Cairo et al, BBMT 2005). Advantages of RTC over MAC include reduced acute short- and long-term late complications, reduced risk of infections, and improved survival. However, relatively little is known about the impact of RTC on the longitudinal quality of life (QOL) of these patients following alloSCT. The objective of this study was to compare the physical, emotional, and social functioning of children who received RTC versus MAC regimens prior to and after alloSCT. Hierarchical linear modeling (HLM) was used to explore trends in the PedsQL 4.0 physical, emotional, and social functioning and select individual items of 80 children ≥ 5 years of age undergoing alloSCT between Nov. 2002 and Dec. 2008. QOL was assessed once pre-alloSCT and on days 100, 180, 365, and 730, post-alloSCT. In addition, post hoc exploratory analyses were performed to further evaluate the effect of RTC and MAC regimens on QOL outcomes. If significant between- or within-group differences were observed for any of the three sub-scales, HLM procedures were performed for each sub-scale item to identify the item(s) affected by treatment. Since post hoc analyses were exploratory no adjustments were made in the alpha level. This secondary data analysis was not powered to detect statistically significant differences. Effect size (ES) calculations were included to describe the magnitude of change in scores from baseline and were calculated using the within patient standard deviation (SD), whereas the magnitude of the difference in scores between RTC and MAC regimens were calculated using the between group SD and interpreted according to Cohen's thresholds. Mean age: 12.67 years; malignant/non-malignant 59%/41%; RTC/MAC 54%/46%. There was no significant difference (p = 0.87) between the baseline mean emotional functioning scores of patients treated with RTC (M = 75.90) or MAC (M = 75.30). In addition, there was no appreciable difference (p = 0.08) in the slope function between these two groups. Similarly, the baseline mean social functioning scores did not differ (p = 0.51) between groups with the RTC patients (M = 81.62) having equivalent function to MAC patients (M = 83.73). Furthermore, the rate of change over time between the two groups was not significantly different (p = 0.96). However, a significant change from baseline in overall physical functioning was estimated for RTC (M = 66.84) compared to MAC (M = 68.05) with RTC improving at a rate of 0.48 points per month (ppm)/ 5.82 points per year (ppy) and MAC improving by 0.04ppm/ 0.52ppy (t = 2.34; p = 0.02) (Figure 1). At 2-years post-alloSCT a moderate difference was estimated (ES = 0.71 SD) with RTC scoring 9.35 points higher than MAC. Post hoc analyses of physical functioning items revealed baseline impairments in lifting something heavy for both RTC (M = 55.55) and MAC (M = 56.06). However, the RTC group rapidly improved by 7.12ppm (t = 2.07; p = 0.03) with no lifting problems estimated by 6-months post-alloSCT. MAC improved by 1.27ppm, with some lifting difficulties predicted throughout the follow-up period. A large effect size difference in lifting scores was estimated at 2-years post-alloSCT with MAC scoring 6.74 SD lower than RTC. Greater improvements in fatigue scores were predicted for RTC (M = 60.11; 3.39ppm) compared with MAC (M = 65.19; 2.46ppm) (p > 0.05) with no fatigue estimated by 1-year post-alloSCT for both groups. RTC pain scores improved from baseline by 2.82ppm (M = 66.02) and 5.35ppm for MAC (M = 66.95). No difficulties with pain were estimated by 1-year for RTC and by 6-months for MAC. Emotional and social functioning were not influenced by the intensity of conditioning regimen received. Deficits in physical functioning appeared transient with most perturbations expressed in the acute post-alloSCT period. RTC versus MAC prior to AlloSCT in pediatric recipients was associated with significantly fewer deficits and faster recovery in overall physical functioning, strength, and fatigue. This study highlights the importance of including QOL as part of the treatment investigations to further define outcomes that are related to the intensity of conditioning regimens used in pediatric alloSCT.Figure 1:Estimated change in physical functioning between RTC vs. MAC in pediatric alloSCT recipientsFigure 1:. Estimated change in physical functioning between RTC vs. MAC in pediatric alloSCT recipients Disclosures: No relevant conflicts of interest to declare.