%0 Journal Article %J Pediatr Hematol Oncol %D 2023 %T Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study. %A Mangum, Ross %A Reuther, Jacquelyn %A Sen Baksi, Koel %A Gandhi, Ilavarasi %A Zabriskie, Ryan C %A Recinos, Alva %A Raesz-Martinez, Robin %A Lin, Frank Y %A Potter, Samara L %A Sher, Andrew C %A Kralik, Stephen F %A Mohila, Carrie A %A Chintagumpala, Murali M %A Donna M Muzny %A Jianhong Hu %A Richard A Gibbs %A Fisher, Kevin E %A Bernini, Juan Carlos %A Gill, Jonathan %A Griffin, Timothy C %A Tomlinson, Gail E %A Vallance, Kelly L %A Plon, Sharon E %A Roy, Angshumoy %A Parsons, D Williams %K Biomarkers, Tumor %K Brain Neoplasms %K Child %K Circulating Tumor DNA %K Feasibility Studies %K High-Throughput Nucleotide Sequencing %K Humans %K Mutation %X

The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time "liquid biopsy" for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.

%B Pediatr Hematol Oncol %V 40 %P 719-738 %8 2023 %G eng %N 8 %1 https://www.ncbi.nlm.nih.gov/pubmed/37366551?dopt=Abstract %R 10.1080/08880018.2023.2228837 %0 Journal Article %J Pediatr Blood Cancer %D 2022 %T Clinical and molecular features of pediatric cancer patients with Lynch syndrome. %A Scollon, Sarah %A Eldomery, Mohammad K %A Reuther, Jacquelyn %A Lin, Frank Y %A Potter, Samara L %A Desrosiers, Lauren %A McClain, Kenneth L %A Smith, Valeria %A Su, Jack Meng-Fen %A Venkatramani, Rajkumar %A Jianhong Hu %A Korchina, Viktoriya %A Zarrin-Khameh, Neda %A Richard A Gibbs %A Donna M Muzny %A Eng, Christine %A Roy, Angshumoy %A Parsons, D Williams %A Plon, Sharon E %K Brain Neoplasms %K Child %K Colorectal Neoplasms %K Colorectal Neoplasms, Hereditary Nonpolyposis %K DNA Mismatch Repair %K DNA-Binding Proteins %K Germ-Line Mutation %K Humans %K MutL Protein Homolog 1 %K MutS Homolog 2 Protein %K Neoplastic Syndromes, Hereditary %X

BACKGROUND: The association of childhood cancer with Lynch syndrome is not established compared with the significant pediatric cancer risk in recessive constitutional mismatch repair deficiency syndrome (CMMRD).

PROCEDURE: We describe the clinical features, germline analysis, and tumor genomic profiling of patients with Lynch syndrome among patients enrolled in pediatric cancer genomic studies.

RESULTS: There were six of 773 (0.8%) pediatric patients with solid tumors identified with Lynch syndrome, defined as a germline heterozygous pathogenic variant in one of the mismatch repair (MMR) genes (three with MSH6, two with MLH1, and one with MSH2). Tumor analysis demonstrated evidence for somatic second hits and/or increased tumor mutation burden in three of four patients with available tumor with potential implications for therapy and identification of at-risk family members. Only one patient met current guidelines for pediatric cancer genetics evaluation at the time of tumor diagnosis.

CONCLUSION: Approximately 1% of children with cancer have Lynch syndrome, which is missed with current referral guidelines, suggesting the importance of adding MMR genes to tumor and hereditary pediatric cancer panels. Tumor analysis may provide the first suggestion of an underlying cancer predisposition syndrome and is useful in distinguishing between Lynch syndrome and CMMRD.

%B Pediatr Blood Cancer %V 69 %P e29859 %8 2022 Nov %G eng %N 11 %1 https://www.ncbi.nlm.nih.gov/pubmed/35713195?dopt=Abstract %R 10.1002/pbc.29859 %0 Journal Article %J Cancer Genet %D 2022 %T Distinct somatic DICER1 hotspot mutations in three metachronous ovarian Sertoli-Leydig cell tumors in a patient with DICER1 syndrome. %A Garcia, Annie %A Desrosiers, Lauren %A Scollon, Sarah %A Gruner, Stephanie %A Reuther, Jacquelyn %A Gandhi, Ilavarasi %A Patil, Ninad %A Fuller, Maren Y %A Dai, Hongzheng %A Donna M Muzny %A Richard A Gibbs %A Bercaw-Pratt, Jennifer L %A Rao, Seema L %A Rainusso, Nino %A Fisher, Kevin E %A Lin, Frank Y %A Plon, Sharon E %A Parsons, D Williams %A Roy, Angshumoy %K DEAD-box RNA Helicases %K Female %K Humans %K Mutation %K Ovarian Neoplasms %K Ribonuclease III %K Sertoli-Leydig Cell Tumor %B Cancer Genet %V 262-263 %P 53-56 %8 2022 Apr %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/35026696?dopt=Abstract %R 10.1016/j.cancergen.2022.01.001 %0 Journal Article %J J Mol Diagn %D 2022 %T A Validation Framework for Somatic Copy Number Detection in Targeted Sequencing Panels. %A Chandramohan, Raghu %A Reuther, Jacquelyn %A Gandhi, Ilavarasi %A Voicu, Horatiu %A Alvarez, Karla R %A Plon, Sharon E %A López-Terrada, Dolores H %A Fisher, Kevin E %A Parsons, D Williams %A Roy, Angshumoy %K Algorithms %K Child %K DNA Copy Number Variations %K High-Throughput Nucleotide Sequencing %K Humans %K Neoplasms %K Sequence Analysis, DNA %X

Somatic copy number alterations (SCNAs) in tumors are clinically significant diagnostic, prognostic, and predictive biomarkers. SCNA detection from targeted next-generation sequencing panels is increasingly common in clinical practice; however, detailed descriptions of optimization and validation of SCNA pipelines for small targeted panels are limited. This study describes the validation and implementation of a tumor-only SCNA pipeline using CNVkit, augmented with custom modules and optimized for clinical implementation by testing reference materials and clinical tumor samples with different classes of copy number variation (CNV; amplification, single copy loss, and biallelic loss). Using wet-bench and in silico methods, various parameters impacting CNV calling, including assay-intrinsic variables (establishment of normal reference and sequencing coverage), sample-intrinsic variables (tumor purity and sample quality), and CNV algorithm-intrinsic variables (bin size), were optimized. The pipeline was trained and tested on an optimization cohort and validated using an independent cohort with a sensitivity and specificity of 100% and 93%, respectively. Using custom modules, intragenic CNVs with breakpoints within tumor suppressor genes were uncovered. Using the validated pipeline, re-analysis of 28 pediatric solid tumors that had been previously profiled for mutations identified SCNAs in 86% (24/28) samples, with 46% (13/28) samples harboring findings of potential clinical relevance. Our report highlights the importance of rigorous establishment of performance characteristics of SCNA pipelines and presents a detailed validation framework for optimal SCNA detection in targeted sequencing panels.

%B J Mol Diagn %V 24 %P 760-774 %8 2022 Jul %G eng %N 7 %1 https://www.ncbi.nlm.nih.gov/pubmed/35487348?dopt=Abstract %R 10.1016/j.jmoldx.2022.03.011 %0 Journal Article %J JCO Precis Oncol %D 2021 %T Durable Response to Larotrectinib in a Child With Histologic Diagnosis of Recurrent Disseminated Ependymoma Discovered to Harbor an Fusion: The Impact of Integrated Genomic Profiling. %A Mangum, Ross %A Reuther, Jacquelyn %A Bertrand, Kelsey C %A Chandramohan, Raghu %A Kukreja, Marcia K %A Paulino, Arnold C %A Donna M Muzny %A Jianhong Hu %A Richard A Gibbs %A Curry, Daniel J %A Malbari, Fatema %A Chintagumpala, Murali M %A Adesina, Adekunle M %A Fisher, Kevin E %A Mack, Stephen C %A Plon, Sharon E %A Roy, Angshumoy %A Parsons, D Williams %A Lin, Frank Y %K Brain Neoplasms %K Child %K Ependymoma %K Gene Expression Profiling %K Humans %K Male %K Membrane Glycoproteins %K Neoplasm Recurrence, Local %K Pyrazoles %K Pyrimidines %K Receptor, trkB %B JCO Precis Oncol %V 5 %8 2021 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/34651095?dopt=Abstract %R 10.1200/PO.20.00375 %0 Journal Article %J J Pathol %D 2021 %T Genomic analysis and preclinical xenograft model development identify potential therapeutic targets for MYOD1-mutant soft-tissue sarcoma of childhood. %A Ting, Michelle A %A Reuther, Jacquelyn %A Chandramohan, Raghu %A Voicu, Horatiu %A Gandhi, Ilavarasi %A Liu, Meng %A Cortes-Santiago, Nahir %A Foster, Jennifer H %A Hicks, John %A Nuchtern, Jed %A Scollon, Sarah %A Plon, Sharon E %A Chintagumpala, Murali %A Rainusso, Nino %A Roy, Angshumoy %A Parsons, D Williams %K Adolescent %K Animals %K Antineoplastic Agents %K Child %K Female %K Genomics %K Humans %K Imidazoles %K Male %K Mice %K Mutation %K MyoD Protein %K Quinolines %K Rhabdomyosarcoma %K Soft Tissue Neoplasms %K Xenograft Model Antitumor Assays %K Young Adult %X

The myogenic differentiation 1 gene (MYOD1) p.L122R somatic mutation was first discovered in a subset of clinically aggressive embryonal rhabdomyosarcomas and has since been described in both pediatric and adult spindle cell/sclerosing rhabdomyosarcomas. Relatively little is known about the clinical, molecular, and histopathological features of these tumors in children. In order to further characterize the genomic and clinical features of pediatric MYOD1-mutant sarcomas, we evaluated a cohort of soft-tissue sarcoma patients treated at Texas Children's Hospital. Tumor DNA was subjected to next-generation panel sequencing and/or Sanger sequencing of the MYOD1 hotspot mutation. The MYOD1 p.L122R mutation was identified in six tumors, with a variant allele fraction greater than 0.8 in three cases, suggestive of loss of heterozygosity. One sclerosing rhabdomyosarcoma lacking the MYOD1 hotspot mutation was observed to have a MYOD1 copy number gain, also with evidence of loss of heterozygosity. Cancer gene panel sequencing revealed potentially targetable alterations in six of seven (86%) patients with MYOD1 alterations, including four patients with an alteration in the PI3K-AKT pathway: two hotspot PIK3CA mutations and deletions in PTEN and TSC2. On histopathologic review, MYOD1-altered tumors exhibited spindle and/or round cells and varying degrees of hyaline sclerosis. At last follow-up, six patients had died of disease and the seventh progressed early and was subsequently lost to follow-up. Both pre- and post-therapy patient-derived xenograft models were generated from one patient's tumor. These models were confirmed to harbor the MYOD1 and PIK3CA mutations seen in the primary tumor and were shown to be sensitive to PI3K/mTOR inhibition in vitro and in vivo. In conclusion, this study adds to recent reports describing the clinicopathologic and genomic features of MYOD1-altered soft-tissue sarcomas in children, including dismal prognosis and potential molecular targets for therapy. The novel preclinical models developed will facilitate further biological and preclinical study of this rare and aggressive tumor. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

%B J Pathol %V 255 %P 52-61 %8 2021 Sep %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/34086347?dopt=Abstract %R 10.1002/path.5736 %0 Journal Article %J Hepatology %D 2017 %T Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups. %A Sumazin, Pavel %A Chen, Yidong %A Treviño, Lisa R %A Sarabia, Stephen F %A Hampton, Oliver A %A Patel, Kayuri %A Mistretta, Toni-Ann %A Zorman, Barry %A Thompson, Patrick %A Heczey, Andras %A Comerford, Sarah %A Wheeler, David A %A Chintagumpala, Murali %A Meyers, Rebecka %A Rakheja, Dinesh %A Finegold, Milton J %A Tomlinson, Gail %A Parsons, D Williams %A López-Terrada, Dolores %K Gene Expression Regulation, Neoplastic %K Genomics %K Hepatoblastoma %K Humans %K Liver Neoplasms %K Prognosis %X

UNLABELLED: Despite being the most common liver cancer in children, hepatoblastoma (HB) is a rare neoplasm. Consequently, few pretreatment tumors have been molecularly profiled, and there are no validated prognostic or therapeutic biomarkers for HB patients. We report on the first large-scale effort to profile pretreatment HBs at diagnosis. Our analysis of 88 clinically annotated HBs revealed three risk-stratifying molecular subtypes that are characterized by differential activation of hepatic progenitor cell markers and metabolic pathways: high-risk tumors were characterized by up-regulated nuclear factor, erythroid 2-like 2 activity; high lin-28 homolog B, high mobility group AT-hook 2, spalt-like transcription factor 4, and alpha-fetoprotein expression; and high coordinated expression of oncofetal proteins and stem-cell markers, while low-risk tumors had low lin-28 homolog B and lethal-7 expression and high hepatic nuclear factor 1 alpha activity.

CONCLUSION: Analysis of immunohistochemical assays using antibodies targeting these genes in a prospective study of 35 HBs suggested that these candidate biomarkers have the potential to improve risk stratification and guide treatment decisions for HB patients at diagnosis; our results pave the way for clinical collaborative studies to validate candidate biomarkers and test their potential to improve outcome for HB patients. (Hepatology 2017;65:104-121).

%B Hepatology %V 65 %P 104-121 %8 2017 Jan %G eng %N 1 %1 https://www.ncbi.nlm.nih.gov/pubmed/27775819?dopt=Abstract %R 10.1002/hep.28888 %0 Journal Article %J Pediatr Blood Cancer %D 2017 %T Renal cell carcinoma harboring somatic TSC2 mutations in a child with methylmalonic acidemia. %A Potter, Samara L %A Venkatramani, Rajkumar %A Wenderfer, Scott %A Graham, Brett H %A Vasudevan, Sanjeev A %A Sher, Andrew %A Wu, Hao %A Wheeler, David A %A Yang, Yaping %A Eng, Christine M %A Gibbs, Richard A %A Roy, Angshumoy %A Plon, Sharon E %A Parsons, D Williams %K Amino Acid Metabolism, Inborn Errors %K Antineoplastic Agents %K Carcinoma, Renal Cell %K Child %K Everolimus %K Female %K Humans %K Kidney Neoplasms %K Sirolimus %K TOR Serine-Threonine Kinases %K Tuberous Sclerosis Complex 2 Protein %K Tumor Suppressor Proteins %X

Pediatric renal cell carcinoma (RCC) is a rare cancer that can be associated with inherited diseases including tuberous sclerosis complex (TSC) caused by germline mutations in TSC1 or TSC2. Somatic mutations in TSC1 and TSC2 have also been reported in adult RCC, which predict response to mTOR inhibitors. Here, we present the first case of RCC in a child with methylmalonic acidemia (MMA). Clinical whole exome sequencing of blood and tumor samples confirmed the diagnosis of MMA and revealed two somatic inactivating mutations in TSC2, suggesting the potential consideration of an mTOR inhibitor in the event of tumor recurrence.

%B Pediatr Blood Cancer %V 64 %8 2017 May %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27748010?dopt=Abstract %R 10.1002/pbc.26286 %0 Journal Article %J J Natl Cancer Inst %D 2017 %T Target and Agent Prioritization for the Children's Oncology Group-National Cancer Institute Pediatric MATCH Trial. %A Allen, Carl E %A Laetsch, Theodore W %A Mody, Rajen %A Irwin, Meredith S %A Lim, Megan S %A Adamson, Peter C %A Seibel, Nita L %A Parsons, D Williams %A Cho, Y Jae %A Janeway, Katherine %K Anaplastic Lymphoma Kinase %K Antineoplastic Agents %K Child %K Cyclin-Dependent Kinase 4 %K Cyclin-Dependent Kinase 6 %K Humans %K MAP Kinase Kinase Kinases %K Molecular Targeted Therapy %K Neoplasms %K Oncogene Proteins %K Phosphoinositide-3 Kinase Inhibitors %K Protein Kinase Inhibitors %K Receptor Protein-Tyrosine Kinases %K Receptors, Fibroblast Growth Factor %K Receptors, Platelet-Derived Growth Factor %K Research Design %K TOR Serine-Threonine Kinases %X

Over the past decades, outcomes for children with cancer have improved dramatically through serial clinical trials based in large measure on dose intensification of cytotoxic chemotherapy for children with high-risk malignancies. Progress made through such dose intensification, in general, is no longer yielding further improvements in outcome. With the revolution in sequencing technologies and rapid development of drugs that block specific proteins and pathways, there is now an opportunity to improve outcomes for pediatric cancer patients through mutation-based targeted therapeutic strategies. The Children's Oncology Group (COG), in partnership with the National Cancer Institute (NCI), is planning a trial entitled the COG-NCI Pediatric Molecular Analysis for Therapeutic Choice (Pediatric MATCH) protocol utilizing an umbrella design. This protocol will have centralized infrastructure and will consist of a biomarker profiling protocol and multiple single-arm phase II trials of targeted therapies. Pediatric patients with recurrent or refractory solid tumors, lymphomas, or histiocytoses with measurable disease will be eligible. The Pediatric MATCH Target and Agent Prioritization (TAP) committee includes membership representing COG disease committees, the Food and Drug Administration, and the NCI. The TAP Committee systematically reviewed target and agent pairs for inclusion in the Pediatric MATCH trial. Fifteen drug-target pairs were reviewed by the TAP Committee, with seven recommended for further development as initial arms of the Pediatric MATCH trial. The current evidence for availability, efficacy, and safety of targeted agents in children for each class of mutation considered for inclusion in the Pediatric MATCH trial is discussed in this review.

%B J Natl Cancer Inst %V 109 %8 2017 May 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/28376230?dopt=Abstract %R 10.1093/jnci/djw274 %0 Journal Article %J Blood %D 2016 %T Alternative genetic mechanisms of BRAF activation in Langerhans cell histiocytosis. %A Chakraborty, Rikhia %A Burke, Thomas M %A Hampton, Oliver A %A Zinn, Daniel J %A Lim, Karen Phaik Har %A Abhyankar, Harshal %A Scull, Brooks %A Kumar, Vijetha %A Kakkar, Nipun %A Wheeler, David A %A Roy, Angshumoy %A Poulikakos, Poulikos I %A Merad, Miriam %A McClain, Kenneth L %A Parsons, D Williams %A Allen, Carl E %K Adolescent %K Adult %K Aged %K Child %K Child, Preschool %K Enzyme Activation %K Female %K Histiocytosis, Langerhans-Cell %K Humans %K Infant %K Male %K Mutation %K Oncogene Proteins, Fusion %K Protein Domains %K Proto-Oncogene Proteins B-raf %X

Langerhans cell histiocytosis (LCH) is characterized by inflammatory lesions containing pathologic CD207 dendritic cells with constitutively activated ERK. Mutually exclusive somatic mutations in MAPK pathway genes have been identified in ∼75% of LCH cases, including recurrent BRAF-V600E and MAP2K1 mutations. To elucidate mechanisms of ERK activation in the remaining 25% of patients, we performed whole-exome sequencing (WES, n = 6), targeted BRAF sequencing (n = 19), and/or whole-transcriptome sequencing (RNA-seq, n = 6) on 24 LCH patient samples lacking BRAF-V600E or MAP2K1 mutations. WES and BRAF sequencing identified in-frame BRAF deletions in the β3-αC loop in 6 lesions. RNA-seq revealed one case with an in-frame FAM73A-BRAF fusion lacking the BRAF autoinhibitory regulatory domain but retaining an intact kinase domain. High levels of phospho-ERK were detected in vitro in cells overexpressing either BRAF fusion or deletion constructs and ex vivo in CD207 cells from lesions. ERK activation was resistant to BRAF-V600E inhibition, but responsive to both a second-generation BRAF inhibitor and a MEK inhibitor. These results support an emerging model of universal ERK-activating genetic alterations driving pathogenesis in LCH. A personalized approach in which patient-specific alterations are identified may be necessary to maximize benefit from targeted therapies for patients with LCH.

%B Blood %V 128 %P 2533-2537 %8 2016 Nov 24 %G eng %N 21 %1 https://www.ncbi.nlm.nih.gov/pubmed/27729324?dopt=Abstract %R 10.1182/blood-2016-08-733790 %0 Journal Article %J JAMA Oncol %D 2016 %T Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors. %A Parsons, D Williams %A Roy, Angshumoy %A Yang, Yaping %A Wang, Tao %A Scollon, Sarah %A Bergstrom, Katie %A Kerstein, Robin A %A Gutierrez, Stephanie %A Petersen, Andrea K %A Bavle, Abhishek %A Lin, Frank Y %A López-Terrada, Dolores H %A Monzon, Federico A %A Hicks, M John %A Eldin, Karen W %A Quintanilla, Norma M %A Adesina, Adekunle M %A Mohila, Carrie A %A Whitehead, William %A Jea, Andrew %A Vasudevan, Sanjeev A %A Nuchtern, Jed G %A Ramamurthy, Uma %A McGuire, Amy L %A Hilsenbeck, Susan G %A Reid, Jeffrey G %A Muzny, Donna M %A Wheeler, David A %A Berg, Stacey L %A Chintagumpala, Murali M %A Eng, Christine M %A Gibbs, Richard A %A Plon, Sharon E %X

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 children's 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.

%B JAMA Oncol %V 2 %P 616-624 %8 2016 May 01 %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/26822237?dopt=Abstract %R 10.1001/jamaoncol.2015.5699 %0 Journal Article %J Cold Spring Harb Mol Case Stud %D 2016 %T Integrated tumor and germline whole-exome sequencing identifies mutations in MAPK and PI3K pathway genes in an adolescent with rosette-forming glioneuronal tumor of the fourth ventricle. %A Lin, Frank Y %A Bergstrom, Katie %A Person, Richard %A Bavle, Abhishek %A Ballester, Leomar Y %A Scollon, Sarah %A Raesz-Martinez, Robin %A Jea, Andrew %A Birchansky, Sherri %A Wheeler, David A %A Berg, Stacey L %A Chintagumpala, Murali M %A Adesina, Adekunle M %A Eng, Christine %A Roy, Angshumoy %A Plon, Sharon E %A Parsons, D Williams %X

The integration of genome-scale studies such as whole-exome sequencing (WES) into the clinical care of children with cancer has the potential to provide insight into the genetic basis of an individual's cancer with implications for clinical management. This report describes the results of clinical tumor and germline WES for a patient with a rare tumor diagnosis, rosette-forming glioneuronal tumor of the fourth ventricle (RGNT). Three pathogenic gene alterations with implications for clinical care were identified: somatic activating hotspot mutations in FGFR1 (p.N546K) and PIK3CA (p.H1047R) and a germline pathogenic variant in PTPN11 (p.N308S) diagnostic for Noonan syndrome. The molecular landscape of RGNT is not well-described, but these data are consistent with prior observations regarding the importance of the interconnected MAPK and PI3K/AKT/mTOR signaling pathways in this rare tumor. The co-occurrence of FGFR1, PIK3CA, and PTPN11 alterations provides further evidence for consideration of RGNT as a distinct molecular entity from pediatric low-grade gliomas and suggests potential therapeutic strategies for this patient in the event of tumor recurrence as novel agents targeting these pathways enter pediatric clinical trials. Although RGNT has not been definitively linked with cancer predisposition syndromes, two prior cases have been reported in patients with RASopathies (Noonan syndrome and neurofibromatosis type 1 [NF1]), providing an additional link between these tumors and the mitogen-activated protein kinase (MAPK) signaling pathway. In summary, this case provides an example of the potential for genome-scale sequencing technologies to provide insight into the biology of rare tumors and yield both tumor and germline results of potential relevance to patient care.

%B Cold Spring Harb Mol Case Stud %V 2 %P a001057 %8 2016 Sep %G eng %N 5 %1 https://www.ncbi.nlm.nih.gov/pubmed/27626068?dopt=Abstract %R 10.1101/mcs.a001057 %0 Journal Article %J J Hepatol %D 2016 %T Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer. %A Bissig-Choisat, Beatrice %A Kettlun-Leyton, Claudia %A Legras, Xavier D %A Zorman, Barry %A Barzi, Mercedes %A Chen, Leon L %A Amin, Mansi D %A Huang, Yung-Hsin %A Pautler, Robia G %A Hampton, Oliver A %A Prakash, Masand M %A Yang, Diane %A Borowiak, Malgorzata %A Muzny, Donna %A Doddapaneni, Harsha Vardhan %A Hu, Jianhong %A Shi, Yan %A Gaber, M Waleed %A Hicks, M John %A Thompson, Patrick A %A Lu, Yiling %A Mills, Gordon B %A Finegold, Milton %A Goss, John A %A Parsons, D Williams %A Vasudevan, Sanjeev A %A Sumazin, Pavel %A López-Terrada, Dolores %A Bissig, Karl-Dimiter %K Animals %K Carcinoma, Hepatocellular %K Cell Line, Tumor %K Child %K Disease Models, Animal %K Heterografts %K Humans %K Liver Neoplasms %K Mice %K Neoplasm Transplantation %K Xenograft Model Antitumor Assays %X

BACKGROUND & AIMS: Pediatric liver cancer is a rare but serious disease whose incidence is rising, and for which the therapeutic options are limited. Development of more targeted, less toxic therapies is hindered by the lack of an experimental animal model that captures the heterogeneity and metastatic capability of these tumors.

METHODS: Here we established an orthotopic engraftment technique to model a series of patient-derived tumor xenograft (PDTX) from pediatric liver cancers of all major histologic subtypes: hepatoblastoma, hepatocellular cancer and hepatocellular malignant neoplasm. We utilized standard (immuno) staining methods for histological characterization, RNA sequencing for gene expression profiling and genome sequencing for identification of druggable targets. We also adapted stem cell culturing techniques to derive two new pediatric cancer cell lines from the xenografted mice.

RESULTS: The patient-derived tumor xenografts recapitulated the histologic, genetic, and biological characteristics-including the metastatic behavior-of the corresponding primary tumors. Furthermore, the gene expression profiles of the two new liver cancer cell lines closely resemble those of the primary tumors. Targeted therapy of PDTX from an aggressive hepatocellular malignant neoplasm with the MEK1 inhibitor trametinib and pan-class I PI3 kinase inhibitor NVP-BKM120 resulted in significant growth inhibition, thus confirming this PDTX model as a valuable tool to study tumor biology and patient-specific therapeutic responses.

CONCLUSIONS: The novel metastatic xenograft model and the isogenic xenograft-derived cell lines described in this study provide reliable tools for developing mutation- and patient-specific therapies for pediatric liver cancer.

LAY SUMMARY: Pediatric liver cancer is a rare but serious disease and no experimental animal model currently captures the complexity and metastatic capability of these tumors. We have established a novel animal model using human tumor tissue that recapitulates the genetic and biological characteristics of this cancer. We demonstrate that our patient-derived animal model, as well as two new cell lines, are useful tools for experimental therapies.

%B J Hepatol %V 65 %P 325-33 %8 2016 Aug %G eng %N 2 %1 https://www.ncbi.nlm.nih.gov/pubmed/27117591?dopt=Abstract %R 10.1016/j.jhep.2016.04.009 %0 Journal Article %J Mod Pathol %D 2015 %T BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children. %A Peters, Tricia L %A Kumar, Vijetha %A Polikepahad, Sumanth %A Lin, Frank Y %A Sarabia, Stephen F %A Liang, Yu %A Wang, Wei-Lien %A Lazar, Alexander J %A Doddapaneni, Harshavardhan %A Chao, Hsu %A Muzny, Donna M %A Wheeler, David A %A Okcu, M Fatih %A Plon, Sharon E %A Hicks, M John %A López-Terrada, Dolores %A Parsons, D Williams %A Roy, Angshumoy %K Adolescent %K Adult %K Aged %K Child %K Cyclin B %K Female %K Humans %K Male %K Middle Aged %K Oncogene Fusion %K Proto-Oncogene Proteins %K Repressor Proteins %K Sarcoma %K Soft Tissue Neoplasms %K Young Adult %X

The BCOR-CCNB3 fusion gene, resulting from a chromosome X paracentric inversion, was recently described in translocation-negative 'Ewing-like' sarcomas arising in bone and soft tissue. Genetic subclassification of undifferentiated unclassified sarcomas may potentially offer markers for reproducible diagnosis and substrates for therapy. Using whole transcriptome paired-end RNA sequencing (RNA-seq) we unexpectedly identified BCOR-CCNB3 fusion transcripts in an undifferentiated spindle-cell sarcoma. RNA-seq results were confirmed through direct RT-PCR of tumor RNA and cloning of the genomic breakpoints from tumor DNA. Five additional undifferentiated sarcomas with BCOR-CCNB3 fusions were identified in a series of 42 pediatric and adult unclassified sarcomas. Genomic breakpoint analysis demonstrated unique breakpoint locations in each case at the DNA level even though the resulting fusion mRNA was identical in all cases. All patients with BCOR-CCNB3 sarcoma were males diagnosed in mid childhood (7-13 years of age). Tumors were equally distributed between axial and extra-axial locations. Five of the six tumors were soft-tissue lesions with either predominant spindle-cell morphology or spindle-cell areas interspersed with ovoid to round cells. CCNB3 immunohistochemistry showed strong nuclear positivity in five tumors before oncologic therapy, but was patchy to negative in post-treatment tumor samples. An RT-PCR assay developed to detect the fusion transcript in archival formalin-fixed tissue was positive in all six cases, with high sensitivity and specificity in both pre- and post-treated samples. This study adds to recent reports on the clinicopathologic spectrum of BCOR-CCNB3 fusion-positive sarcomas, a newly emerging entity within the undifferentiated unclassified sarcoma category and describes a simple RT-PCR assay that in conjunction with CCNB3 immunohistochemistry can be useful in diagnosing these tumors.

%B Mod Pathol %V 28 %P 575-86 %8 2015 Apr %G eng %N 4 %1 https://www.ncbi.nlm.nih.gov/pubmed/25360585?dopt=Abstract %R 10.1038/modpathol.2014.139 %0 Journal Article %J Hematology Am Soc Hematol Educ Program %D 2015 %T Biological and clinical significance of somatic mutations in Langerhans cell histiocytosis and related histiocytic neoplastic disorders. %A Allen, Carl E %A Parsons, D Williams %K Cell Differentiation %K Clinical Trials as Topic %K Enzyme Activation %K Erdheim-Chester Disease %K Exome %K Genome, Human %K Genotype %K GTP Phosphohydrolases %K Histiocytosis, Langerhans-Cell %K Humans %K MAP Kinase Kinase 1 %K MAP Kinase Signaling System %K Membrane Proteins %K Mutation %K Phosphatidylinositol 3-Kinases %K Proto-Oncogene Proteins B-raf %K Sequence Analysis, DNA %K Xanthogranuloma, Juvenile %X

Langerhans cell histiocytosis (LCH), juvenile xanthogranuloma (JXG), and Erdheim-Chester disease (ECD) represent histiocytic disorders with a wide range of clinical manifestations. Until recently, mechanisms of pathogenesis have been speculative and debate has focused on classification of these conditions as reactive versus neoplastic. Genomic studies have been challenged by scarce tissue specimens, as well as heterogeneous nature of the lesions with variable infiltration of pathologic histiocytes. Whole-exome sequencing recently revealed a very low frequency of somatic mutations in LCH, JXG, and ECD compared to other neoplastic disorders. However, at least in the cases of LCH and ECD, there is a very high frequency of activating mutations in MAPK pathway genes, most notably BRAF-V600E, as well as MAP2K1, in LCH and NRAS in ECD. In ECD, recurrent mutations in the PI3K pathway gene PIK3CA have also been described. The heterogeneous clinical manifestations of these disorders may therefore be the cumulative result of activation of MAPK mutations (along with modifying signals from other pathways) at distinct stages of myeloid differentiation. Implications of this model include redefinition of LCH, JXG, and ECD as a group of clinically diverse myeloid neoplastic disorders with a common mechanism of pathogenesis. This model supports refocusing therapeutic strategies for these diseases on a personalized approach based on specific mutations and the cell(s) of origin.

%B Hematology Am Soc Hematol Educ Program %V 2015 %P 559-64 %8 2015 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26637772?dopt=Abstract %R 10.1182/asheducation-2015.1.559 %0 Journal Article %J J Law Med Ethics %D 2015 %T Pediatric Cancer Genetics Research and an Evolving Preventive Ethics Approach for Return of Results after Death of the Subject. %A Scollon, Sarah %A Bergstrom, Katie %A McCullough, Laurence B %A McGuire, Amy L %A Gutierrez, Stephanie %A Kerstein, Robin %A Parsons, D Williams %A Plon, Sharon E %K Adult %K Child %K Child, Preschool %K Death %K Disclosure %K Genetic Research %K Genomics %K Humans %K Neoplasms %K Research Subjects %X

The return of genetic research results after death in the pediatric setting comes with unique complexities. Researchers must determine which results and through which processes results are returned. This paper discusses the experience over 15 years in pediatric cancer genetics research of returning research results after the death of a child and proposes a preventive ethics approach to protocol development in order to improve the quality of return of results in pediatric genomic settings.

%B J Law Med Ethics %V 43 %P 529-37 %8 2015 Fall %G eng %N 3 %1 https://www.ncbi.nlm.nih.gov/pubmed/26479562?dopt=Abstract %R 10.1111/jlme.12295 %0 Journal Article %J Nat Commun %D 2015 %T Recurrent internal tandem duplications of BCOR in clear cell sarcoma of the kidney. %A Roy, Angshumoy %A Kumar, Vijetha %A Zorman, Barry %A Fang, Erica %A Haines, Katherine M %A Doddapaneni, Harshavardhan %A Hampton, Oliver A %A White, Simon %A Bavle, Abhishek A %A Patel, Nimesh R %A Eldin, Karen W %A John Hicks, M %A Rakheja, Dinesh %A Leavey, Patrick J %A Skapek, Stephen X %A Amatruda, James F %A Nuchtern, Jed G %A Chintagumpala, Murali M %A Wheeler, David A %A Plon, Sharon E %A Sumazin, Pavel %A Parsons, D Williams %K Case-Control Studies %K Child, Preschool %K Female %K Gene Duplication %K Gene Expression Profiling %K Gene Expression Regulation, Neoplastic %K Humans %K Immunoblotting %K Immunohistochemistry %K Infant %K Kidney Neoplasms %K Male %K Mutation %K Neoplasm Recurrence, Local %K Proto-Oncogene Proteins %K Repressor Proteins %K Reverse Transcriptase Polymerase Chain Reaction %K RNA, Messenger %K Sarcoma, Clear Cell %K Sequence Analysis, DNA %K Sequence Analysis, RNA %K Tandem Repeat Sequences %X

The X-linked BCL-6 co-repressor (BCOR) gene encodes a key constituent of a variant polycomb repressive complex (PRC) that is mutated or translocated in human cancers. Here we report on the identification of somatic internal tandem duplications (ITDs) clustering in the C terminus of BCOR in 23 of 27 (85%) pediatric clear cell sarcomas of the kidney (CCSK) from two independent cohorts. We profile CCSK tumours using a combination of whole-exome, transcriptome and targeted sequencing. Identical ITD mutations are found in primary and relapsed tumour pairs but not in adjacent normal kidney or blood. Mutant BCOR transcripts and proteins are markedly upregulated in ITD-positive tumours. Transcriptome analysis of ITD-positive CCSKs reveals enrichment for PRC2-regulated genes and similarity to undifferentiated sarcomas harbouring BCOR-CCNB3 fusions. The discovery of recurrent BCOR ITDs defines a major oncogenic event in this childhood sarcoma with significant implications for diagnostic and therapeutic approaches to this tumour.

%B Nat Commun %V 6 %P 8891 %8 2015 Nov 17 %G eng %1 https://www.ncbi.nlm.nih.gov/pubmed/26573325?dopt=Abstract %R 10.1038/ncomms9891 %0 Journal Article %J Blood %D 2014 %T Mutually exclusive recurrent somatic mutations in MAP2K1 and BRAF support a central role for ERK activation in LCH pathogenesis. %A Chakraborty, Rikhia %A Hampton, Oliver A %A Shen, Xiaoyun %A Simko, Stephen J %A Shih, Albert %A Abhyankar, Harshal %A Lim, Karen Phaik Har %A Covington, Kyle R %A Treviño, Lisa %A Dewal, Ninad %A Muzny, Donna M %A Doddapaneni, Harshavardhan %A Hu, Jianhong %A Wang, Linghua %A Lupo, Philip J %A Hicks, M John %A Bonilla, Diana L %A Dwyer, Karen C %A Berres, Marie-Luise %A Poulikakos, Poulikos I %A Merad, Miriam %A McClain, Kenneth L %A Wheeler, David A %A Allen, Carl E %A Parsons, D Williams %K Dendritic Cells %K Disease Progression %K Erdheim-Chester Disease %K HEK293 Cells %K Histiocytosis, Langerhans-Cell %K Histiocytosis, Sinus %K Humans %K MAP Kinase Kinase 1 %K MAP Kinase Signaling System %K Mutation, Missense %K Proto-Oncogene Proteins B-raf %K Xanthogranuloma, Juvenile %X

Langerhans cell histiocytosis (LCH) is a myeloproliferative disorder characterized by lesions composed of pathological CD207(+) dendritic cells with an inflammatory infiltrate. BRAFV600E remains the only recurrent mutation reported in LCH. In order to evaluate the spectrum of somatic mutations in LCH, whole exome sequencing was performed on matched LCH and normal tissue samples obtained from 41 patients. Lesions from other histiocytic disorders, juvenile xanthogranuloma, Erdheim-Chester disease, and Rosai-Dorfman disease were also evaluated. All of the lesions from histiocytic disorders were characterized by an extremely low overall rate of somatic mutations. Notably, 33% (7/21) of LCH cases with wild-type BRAF and none (0/20) with BRAFV600E harbored somatic mutations in MAP2K1 (6 in-frame deletions and 1 missense mutation) that induced extracellular signal-regulated kinase (ERK) phosphorylation in vitro. Single cases of somatic mutations of the mitogen-activated protein kinase (MAPK) pathway genes ARAF and ERBB3 were also detected. The ability of MAPK pathway inhibitors to suppress MAPK kinase and ERK phosphorylation in cell culture and primary tumor models was dependent on the specific LCH mutation. The findings of this study support a model in which ERK activation is a universal end point in LCH arising from pathological activation of upstream signaling proteins.

%B Blood %V 124 %P 3007-15 %8 2014 Nov 06 %G eng %N 19 %1 https://www.ncbi.nlm.nih.gov/pubmed/25202140?dopt=Abstract %R 10.1182/blood-2014-05-577825 %0 Journal Article %J Genome Med %D 2014 %T Obtaining informed consent for clinical tumor and germline exome sequencing of newly diagnosed childhood cancer patients. %A Scollon, Sarah %A Bergstrom, Katie %A Kerstein, Robin A %A Wang, Tao %A Hilsenbeck, Susan G %A Ramamurthy, Uma %A Gibbs, Richard A %A Eng, Christine M %A Chintagumpala, Murali M %A Berg, Stacey L %A McCullough, Laurence B %A McGuire, Amy L %A Plon, Sharon E %A Parsons, D Williams %X

BACKGROUND: Effectively 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.

METHODS: A 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.

RESULTS: Over 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.

CONCLUSIONS: An 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.

%B Genome Med %V 6 %P 69 %8 2014 %G eng %N 9 %1 https://www.ncbi.nlm.nih.gov/pubmed/25317207?dopt=Abstract %R 10.1186/s13073-014-0069-3