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Genomics",{"type":429,"tag":525,"props":2298,"children":2299},{},[2300,2302,2309],{"type":435,"value":2301},"The Clinical Pilot project was a retrospective study that evaluated the accuracy and demonstrated the feasibility of three-platform sequencing in a CAP/CLIA setting.\nThe findings of this project were published in ",{"type":429,"tag":446,"props":2303,"children":2306},{"href":2304,"rel":2305},"https://pubmed.ncbi.nlm.nih.gov/30262806/",[676],[2307],{"type":435,"value":2308},"Nature Communications",{"type":435,"value":559},{"type":429,"tag":519,"props":2311,"children":2313},{"id":2312},"clinical-research-in-als-and-related-disorders-for-therapeutic-development-consortium",[2314],{"type":435,"value":2315},"Clinical Research in ALS and Related Disorders for Therapeutic Development Consortium",{"type":429,"tag":525,"props":2317,"children":2318},{},[2319,2323,2325,2329,2331,2335,2336,2340],{"type":429,"tag":531,"props":2320,"children":2321},{},[2322],{"type":435,"value":736},{"type":435,"value":2324},": CReATe | ",{"type":429,"tag":531,"props":2326,"children":2327},{},[2328],{"type":435,"value":1332},{"type":435,"value":2330},": PBMC Germline DNA | ",{"type":429,"tag":531,"props":2332,"children":2333},{},[2334],{"type":435,"value":1991},{"type":435,"value":2039},{"type":429,"tag":531,"props":2337,"children":2338},{},[2339],{"type":435,"value":1343},{"type":435,"value":2341},": 705",{"type":429,"tag":525,"props":2343,"children":2344},{},[2345,2347,2354],{"type":435,"value":2346},"The Phenotype-Genotype-Biomarker (PGB, or PGB1) study (NCT02327845) of the Clinical Research in ALS and Related Disorders for Therapeutic Development (CReATe) Consortium was a natural history and biomarker study of patients with amyotrophic lateral sclerosis (ALS) or a related disorder, including but not limited to ALS-frontotemporal dementia (ALS-FTD), progressive muscular atrophy (PMA), primary lateral sclerosis (PLS), hereditary spastic paraplegia (HSP), and multisystem proteinopathy (MSP).\nIn addition to patients enrolled in the PGB1 Cohort (primary participants), the study also enrolled family members for limited data collection (secondary participants).\nThis dataset includes WGS data from N=705 in PGB1, including N=472 ALS/ALS-FTD, N=20 PMA, N=47 PLS, N=162 HSP, and N=4 with other related disorders.\nThe findings of the project were published in ",{"type":429,"tag":446,"props":2348,"children":2351},{"href":2349,"rel":2350},"https://translationalneurodegeneration.biomedcentral.com/articles/10.1186/s40035-025-00516-2",[676],[2352],{"type":435,"value":2353},"Translational Neurodegeneration",{"type":435,"value":559},{"type":429,"tag":519,"props":2356,"children":2358},{"id":2357},"dmg-h3k27a-clonal-evolution",[2359],{"type":435,"value":2360},"DMG-H3K27a Clonal Evolution",{"type":429,"tag":525,"props":2362,"children":2363},{},[2364,2368,2369,2373,2374,2378,2380,2384],{"type":429,"tag":531,"props":2365,"children":2366},{},[2367],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2370,"children":2371},{},[2372],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2375,"children":2376},{},[2377],{"type":435,"value":1991},{"type":435,"value":2379},": WGS, WES | ",{"type":429,"tag":531,"props":2381,"children":2382},{},[2383],{"type":435,"value":1343},{"type":435,"value":2385},": 70",{"type":429,"tag":525,"props":2387,"children":2388},{},[2389,2391],{"type":435,"value":2390},"The primary purpose of the DMG-H3K27a Clonal Evolution (H3K27A_EVOLUTION) project is to understand how clonal evolution contributes to tumor invasive spread.\nThe study performed exome sequencing and SNP array profiling on 49 multi-region autopsy samples from 11 patients with pontine DMG-H3 K27-a enrolled in a phase I clinical trial of PDGFR inhibitor crenolanib.\nAdditional objectives include deconvoluting subclonal composition and prevalence at each tumor region to study convergent evolution and invasion patterns.\nFor more information see: ",{"type":429,"tag":446,"props":2392,"children":2395},{"href":2393,"rel":2394},"http://permalinks.stjude.cloud/permalinks/h3k27a_evolution",[676],[2396],{"type":435,"value":2393},{"type":429,"tag":519,"props":2398,"children":2400},{"id":2399},"genome-4-kids",[2401],{"type":435,"value":2402},"Genome 4 Kids",{"type":429,"tag":525,"props":2404,"children":2405},{},[2406,2410,2412,2416,2417,2421,2422,2426,2428],{"type":429,"tag":531,"props":2407,"children":2408},{},[2409],{"type":435,"value":736},{"type":435,"value":2411},": Clinical Genomics, PCGP | ",{"type":429,"tag":531,"props":2413,"children":2414},{},[2415],{"type":435,"value":1332},{"type":435,"value":2187},{"type":429,"tag":531,"props":2418,"children":2419},{},[2420],{"type":435,"value":1991},{"type":435,"value":2193},{"type":429,"tag":531,"props":2423,"children":2424},{},[2425],{"type":435,"value":1343},{"type":435,"value":2427},": 571 | ",{"type":429,"tag":531,"props":2429,"children":2430},{},[2431],{"type":429,"tag":446,"props":2432,"children":2434},{"href":2292,"rel":2433},[676],[2435],{"type":435,"value":2296},{"type":429,"tag":525,"props":2437,"children":2438},{},[2439],{"type":435,"value":2440},"The goal of the Genomes 4 Kids (G4K) prospective study was to determine whether the three-platform sequencing protocol laid out in the Clinical Pilot project could generate results on a clinical timeline in practice and to evaluate the prevalence of actionable findings.\nThe study concluded with just over 300 patients, and the publication is currently in review.",{"type":429,"tag":519,"props":2442,"children":2444},{"id":2443},"g4kffpe",[2445],{"type":435,"value":2446},"G4KFFPE",{"type":429,"tag":525,"props":2448,"children":2449},{},[2450,2454,2455,2459,2460,2464,2466,2470],{"type":429,"tag":531,"props":2451,"children":2452},{},[2453],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2456,"children":2457},{},[2458],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2461,"children":2462},{},[2463],{"type":435,"value":1991},{"type":435,"value":2465},": WES | ",{"type":429,"tag":531,"props":2467,"children":2468},{},[2469],{"type":435,"value":1343},{"type":435,"value":2471},": 33",{"type":429,"tag":519,"props":2473,"children":2475},{"id":2474},"genomics-and-transcriptomics-of-relapsed-pediatric-aml-rpaml",[2476],{"type":435,"value":994},{"type":429,"tag":525,"props":2478,"children":2479},{},[2480,2484,2485,2489,2490,2494,2496,2500],{"type":429,"tag":531,"props":2481,"children":2482},{},[2483],{"type":435,"value":736},{"type":435,"value":2411},{"type":429,"tag":531,"props":2486,"children":2487},{},[2488],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2491,"children":2492},{},[2493],{"type":435,"value":1991},{"type":435,"value":2495},": RNA-seq, WGS | ",{"type":429,"tag":531,"props":2497,"children":2498},{},[2499],{"type":435,"value":1343},{"type":435,"value":2501},": 265",{"type":429,"tag":525,"props":2503,"children":2504},{},[2505,2507,2514],{"type":435,"value":2506},"The primary purpose of the Relapsed Pediatric AML Dataset (RPAML) is to identify the tumor-acquired (somatic) genome sequence and structural variants in pediatric AML at the time of disease relapse.\nAdditional objectives include the acquisition and analysis of additional genomic data, including gene expression data, mutational signatures, and germline variants that may predispose to AML or other bone marrow disorders.\nThe findings of the project were published in ",{"type":429,"tag":446,"props":2508,"children":2511},{"href":2509,"rel":2510},"https://doi.org/10.1158/2643-3230.BCD-21-0160",[676],[2512],{"type":435,"value":2513},"Blood Cancer Discovery",{"type":435,"value":559},{"type":429,"tag":519,"props":2516,"children":2518},{"id":2517},"landscape-of-pediatric-acute-myeloid-leukemia-panpaml",[2519],{"type":435,"value":1147},{"type":429,"tag":525,"props":2521,"children":2522},{},[2523,2527,2528,2532,2533,2537,2539,2543],{"type":429,"tag":531,"props":2524,"children":2525},{},[2526],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2529,"children":2530},{},[2531],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2534,"children":2535},{},[2536],{"type":435,"value":1991},{"type":435,"value":2538},": RNA-seq, WGS, WES | ",{"type":429,"tag":531,"props":2540,"children":2541},{},[2542],{"type":435,"value":1343},{"type":435,"value":2544},": 272",{"type":429,"tag":525,"props":2546,"children":2547},{},[2548,2550,2557],{"type":435,"value":2549},"Recent studies on pediatric acute myeloid leukemia (pAML) have revealed pediatric-specific driver alterations, many of which are underrepresented in the current classification schemas.\nThe PanpAML study systematically categorized 887 pAML cases into 23 mutually distinct molecular categories, including new major entities such as UBTF or BCL11B, covering 91.4% of the cohort.\nThese molecular categories were associated with unique expression profiles and mutational patterns, and were strongly associated with clinical outcomes, leading to the establishment of a new prognostic framework for pAML based on updated molecular categories and minimal residual disease.\nThe findings of the project were published in ",{"type":429,"tag":446,"props":2551,"children":2554},{"href":2552,"rel":2553},"https://doi.org/10.1038/s41588-023-01640-3",[676],[2555],{"type":435,"value":2556},"Nature Genetics",{"type":435,"value":559},{"type":429,"tag":519,"props":2559,"children":2561},{"id":2560},"medulloblastoma-preclinical-ribociclib-and-gemcitabine-mbprg",[2562],{"type":435,"value":1156},{"type":429,"tag":525,"props":2564,"children":2565},{},[2566,2570,2571,2575,2576,2580,2581,2585],{"type":429,"tag":531,"props":2567,"children":2568},{},[2569],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2572,"children":2573},{},[2574],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2577,"children":2578},{},[2579],{"type":435,"value":1991},{"type":435,"value":2238},{"type":429,"tag":531,"props":2582,"children":2583},{},[2584],{"type":435,"value":1343},{"type":435,"value":2385},{"type":429,"tag":525,"props":2587,"children":2588},{},[2589],{"type":435,"value":2590},"The MBPRG dataset comprises medulloblastoma group 3 (G3 MB) patient-derived orthotopic xenografts (PDOX) and mouse G3 MB tumor models.\nBoth human (PDOX) and mouse tumor models were treated with either ribociclib (CDK4/6 inhibitor), gemcitabine (metabolic inhibitor of DNA synthesis), or the combination of these two drugs in comparison to control (vehicle).\nThe key objective of this dataset is to evaluate the impact of this treatment and identify perturbation of gene expression/pathways at the transcriptional level in G3 MB.",{"type":429,"tag":519,"props":2592,"children":2594},{"id":2593},"medulloblastoma-preclinical-ribociclib-and-paxalisib-mbprp",[2595],{"type":435,"value":1165},{"type":429,"tag":525,"props":2597,"children":2598},{},[2599,2603,2604,2608,2609,2613,2614,2618],{"type":429,"tag":531,"props":2600,"children":2601},{},[2602],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2605,"children":2606},{},[2607],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2610,"children":2611},{},[2612],{"type":435,"value":1991},{"type":435,"value":2238},{"type":429,"tag":531,"props":2615,"children":2616},{},[2617],{"type":435,"value":1343},{"type":435,"value":2619},": 39",{"type":429,"tag":525,"props":2621,"children":2622},{},[2623],{"type":435,"value":2624},"The MBPRP dataset comprises medulloblastoma group 3 (G3 MB) and medulloblastoma Sonic hedgehog (SHH MB) patient-derived orthotopic xenografts (PDOX).\nThese human tumor models were treated with either ribociclib (CDK4/6 inhibitor), paxalisib (PI3K/mTOR inhibitor), or the combination of these two drugs in comparison to control (vehicle).\nThe key objective of this dataset is to validate the synergistic effect of the combination treatment observed in-vitro, and evaluate the impact of these treatments on gene expression/pathways at the transcriptional level in MB.",{"type":429,"tag":519,"props":2626,"children":2628},{"id":2627},"pan-acute-lymphoblastic-leukemia",[2629],{"type":435,"value":2630},"Pan-Acute Lymphoblastic Leukemia",{"type":429,"tag":525,"props":2632,"children":2633},{},[2634,2638,2640,2644,2645,2649,2650,2654],{"type":429,"tag":531,"props":2635,"children":2636},{},[2637],{"type":435,"value":736},{"type":435,"value":2639},": PanALL | ",{"type":429,"tag":531,"props":2641,"children":2642},{},[2643],{"type":435,"value":1332},{"type":435,"value":2187},{"type":429,"tag":531,"props":2646,"children":2647},{},[2648],{"type":435,"value":1991},{"type":435,"value":2238},{"type":429,"tag":531,"props":2651,"children":2652},{},[2653],{"type":435,"value":1343},{"type":435,"value":2655},": 735",{"type":429,"tag":525,"props":2657,"children":2658},{},[2659],{"type":435,"value":2660},"Pan-Acute Lymphoblastic Leukemia (PanALL) comprises cases of B-progenitor and T-lineage ALL encompassing the spectrum of ALL subtypes across the age continuum.\nSamples sequenced were obtained from multiple sites, centers and cooperative groups including St. Jude Children's Research Hospital, The Children's Oncology Group, The Alliance – Cancer and Leukemia Group B, the Eastern Cooperative Oncology Group, The Southwestern Oncology group, MD Anderson Cancer Center, City of Hope National Medical Center, Princess Margaret Cancer Center, Northern Italy Leukemia Group, and UKALL.",{"type":429,"tag":519,"props":2662,"children":2664},{"id":2663},"pediatric-acute-myeloid-leukemia-pedaml",[2665],{"type":435,"value":1181},{"type":429,"tag":525,"props":2667,"children":2668},{},[2669,2673,2674,2678,2679,2683,2684,2688],{"type":429,"tag":531,"props":2670,"children":2671},{},[2672],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2675,"children":2676},{},[2677],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2680,"children":2681},{},[2682],{"type":435,"value":1991},{"type":435,"value":1993},{"type":429,"tag":531,"props":2685,"children":2686},{},[2687],{"type":435,"value":1343},{"type":435,"value":2689},": 275",{"type":429,"tag":525,"props":2691,"children":2692},{},[2693],{"type":435,"value":2694},"The primary purpose of the Pediatric AML (PedAML) Data Set is to identify the genome sequence and structural variants that define the different molecular subtypes of pediatric AML (pAML).\nAdditional objectives include, but are not limited to, the acquisition and analysis of additional genomic data, including gene expression data and patterns of mutational cooperativity.",{"type":429,"tag":519,"props":2696,"children":2698},{"id":2697},"pediatric-brain-tumor-program",[2699],{"type":435,"value":2700},"Pediatric Brain Tumor Program",{"type":429,"tag":525,"props":2702,"children":2703},{},[2704,2708,2709,2713,2714,2718,2719,2723],{"type":429,"tag":531,"props":2705,"children":2706},{},[2707],{"type":435,"value":736},{"type":435,"value":2411},{"type":429,"tag":531,"props":2710,"children":2711},{},[2712],{"type":435,"value":1332},{"type":435,"value":1986},{"type":429,"tag":531,"props":2715,"children":2716},{},[2717],{"type":435,"value":1991},{"type":435,"value":1993},{"type":429,"tag":531,"props":2720,"children":2721},{},[2722],{"type":435,"value":1343},{"type":435,"value":2724},": 97",{"type":429,"tag":525,"props":2726,"children":2727},{},[2728,2730,2737],{"type":435,"value":2729},"The Pediatric Brain Tumor Portal (PBTP) is organized by the St. Jude Children's Research Hospital Neurobiology and Brain Tumor Program.\nInvestigators have access to specialized resources, such as an integrated support structure for preclinical modeling, including patient-derived xenograft samples.\nThe program consists of clinicians, radiation oncologists, neurobiologists, medicinal chemists, and other research faculty and staff.\nPBTP features molecular characterization for patient-derived orthotopic xenograft (PDOX) models of pediatric CNS tumors and reflects close to 10 years of effort to generate and extensively characterize in-vivo models that faithfully recapitulate pediatric brain cancer diseases.\nThe portal offers visualization tools that allow users to interrogate curated datasets and access models from our library of PDOX for functional studies of tumorigenesis or preclinical testing.\nThe findings of the project were published in ",{"type":429,"tag":446,"props":2731,"children":2734},{"href":2732,"rel":2733},"https://doi.org/10.1007/s00401-020-02171-5",[676],[2735],{"type":435,"value":2736},"Acta Neuropathol",{"type":435,"value":559},{"type":429,"tag":519,"props":2739,"children":2741},{"id":2740},"pediatric-cancer-genome-project",[2742],{"type":435,"value":2743},"Pediatric Cancer Genome Project",{"type":429,"tag":525,"props":2745,"children":2746},{},[2747,2751,2752,2756,2757,2761,2762,2766,2768],{"type":429,"tag":531,"props":2748,"children":2749},{},[2750],{"type":435,"value":736},{"type":435,"value":1980},{"type":429,"tag":531,"props":2753,"children":2754},{},[2755],{"type":435,"value":1332},{"type":435,"value":2187},{"type":429,"tag":531,"props":2758,"children":2759},{},[2760],{"type":435,"value":1991},{"type":435,"value":2193},{"type":429,"tag":531,"props":2763,"children":2764},{},[2765],{"type":435,"value":1343},{"type":435,"value":2767},": 3,031 | ",{"type":429,"tag":531,"props":2769,"children":2770},{},[2771],{"type":429,"tag":446,"props":2772,"children":2774},{"href":1077,"rel":2773},[676],[2775],{"type":435,"value":2776},"Additional Information About PCGP",{"type":429,"tag":525,"props":2778,"children":2779},{},[2780],{"type":435,"value":2781},"The Pediatric Cancer Genome Project (PCGP) is a collaboration between St. Jude Children's Research Hospital and the McDonnell Genome Institute at Washington University School of Medicine that sequenced the genomes of over 600 pediatric cancer patients.",{"type":429,"tag":519,"props":2783,"children":2785},{"id":2784},"pediatric-therapy-related-myeloid-neoplasms-tmn",[2786],{"type":435,"value":1012},{"type":429,"tag":525,"props":2788,"children":2789},{},[2790,2794,2795,2799,2800,2804,2805,2809,2811],{"type":429,"tag":531,"props":2791,"children":2792},{},[2793],{"type":435,"value":736},{"type":435,"value":2411},{"type":429,"tag":531,"props":2796,"children":2797},{},[2798],{"type":435,"value":1332},{"type":435,"value":2187},{"type":429,"tag":531,"props":2801,"children":2802},{},[2803],{"type":435,"value":1991},{"type":435,"value":2193},{"type":429,"tag":531,"props":2806,"children":2807},{},[2808],{"type":435,"value":1343},{"type":435,"value":2810},": 206 | 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