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dbGaP phs001072 Genomic Analysis of Relapsed Pediatric Acute Lymphoblastic Leukemia - pht005356.v1.p1

- 6/23/23 - 4 forms, 1 itemgroup, 3 items, 1 language
Itemgroup: pht005356
Principal Investigator: Adolfo Ferrando, MD, PhD, Columbia University, New York, NY, USA MeSH: Leukemia, Lymphoid,Lymphoblastic Leukemia, Acute, T-Cell,Precursor B-Cell Lymphoblastic Leukemia https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001072 Although multi-agent combination chemotherapy is curative in a significant fraction of childhood acute lymphoblastic leukemia (ALL) patients, 20% of cases relapse and most die due to chemo-refractory disease. Here we used whole-exome and whole-genome sequencing to analyze the mutational landscape and pattern of clonal evolution at relapse in pediatric ALL cases. These analyses showed that ALL relapses originate from a common ancestral precursor clone of the diagnosis and relapsed populations and frequently harbor mutations implicated in chemotherapy resistance. RAS-MAPK pathway activating mutations in NRAS, KRAS and PTPN11 were present in 24/55 (44%) cases in our series. Notably, while some cases showed emergence of RAS mutant clones at relapse, in others, RAS mutant clones present at diagnosis were replaced by RAS wild type populations. Mechanistically, functional dissection of mouse and human wild type Kras and mutant Kras (Kras G12D) isogenic leukemia cells demonstrated induction of methotrexate resistance, but also improved response to vincristine, in mutant Kras- expressing lymphoblasts. These results identify chemotherapy driven selection as a central mechanism of leukemia clonal evolution and pave the road for the development of tailored personalized therapies for the treatment of relapsed ALL.

pht005357.v1.p1

1 itemgroup 8 items

pht005354.v1.p1

1 itemgroup 5 items

pht005355.v1.p1

1 itemgroup 5 items

dbGaP phs001350 Pancreatitis after Treatment for Acute Lymphoblastic Leukemia (SJIRB XPD04-123 and XPD05-078) - pht009877.v1.p1

- 2/27/23 - 5 forms, 1 itemgroup, 5 items, 1 language
Itemgroup: pht009877
Principal Investigator: Mary V. Relling, PharmD, St. Jude Children's Research Hospital MeSH: Leukemia, Lymphoid,Pancreatitis https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001350 A complication of acute lymphoblastic leukemia (ALL) treatment is acute pancreatitis, which is one of the common causes of asparaginase intolerance. To determine clinical and genetic risk factors for pancreatitis, we studied a cohort of children and young adults with ALL enrolled on COG trials (9904/9905/9906, AALL0232) and on St. Jude trial Total XV. We performed a genome-wide association study using germline DNA collected from blood in patients at remission in this cohort of 5185 patients and in an independent case-control group of 213 patients on AALL0331. The frequency of pancreatitis in the cohort was 2.3% (117 of 5185). No common variants reached genome-wide significance, but a rare nonsense variant rs199695765 in CPA2, encoding carboxypeptidase A2, was highly associated with pancreatitis (odds ratio = 587, 95% confidence interval 66.8-5166, P = 9.0 x 10-9). A gene-level analysis showed an excess of additional CPA2 variants in patients who did versus those who did not develop pancreatitis (P = 0.018). Sixteen CPA2 SNPs were associated (P 0.05) with pancreatitis, and 13 of 24 patients who carried at least one of these variants developed pancreatitis. Biological functions that were overrepresented by common variants modestly associated with pancreatitis included purine metabolism and cytoskeleton regulation.

pht009878.v1.p1

1 itemgroup 2 items

pht009879.v1.p1

1 itemgroup 5 items

pht009880.v1.p1

1 itemgroup 5 items

Eligibility

1 itemgroup 1 item

dbGaP phs001372 Integrated Single-Cell Analysis in Chronic Lymphocytic Leukemia - pht006533.v1.p1

- 2/7/23 - 4 forms, 1 itemgroup, 3 items, 1 language
Itemgroup: pht006533
Principal Investigator: Catherine Wu, Dana-Farber Cancer Institute, Boston, MA, USA MeSH: Leukemia, Lymphoid https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001372 Intratumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted mutation detection in DNA and RNA isolated from thousands of single cells from five CLL samples. By clearly resolving phylogenic relationships, we uncovered mutated LCP1 and WNK1 as novel CLL drivers, supported by functional evidence demonstrating their impact on CLL pathways. Integrative analysis of somatic mutations with transcriptional states prompts the idea that convergent evolution generates phenotypically similar cells in distinct genetic branches, thus creating a cohesive expression profile in each CLL sample despite the presence of genetic heterogeneity. Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells leading to increased understanding of driving events in malignancy. Reprinted from Genome Research, with permission from Publisher.

pht006534.v1.p1

1 itemgroup 4 items

pht006535.v1.p1

1 itemgroup 5 items

pht006532.v1.p1

1 itemgroup 3 items

dbGaP phs000621 Genome Wide Association Studies in ECOG 2997 Trial - pht003330.v1.p1

- 11/15/22 - 5 forms, 1 itemgroup, 11 items, 1 language
Itemgroup: pht003330
Principal Investigator: Richard Weinshilboum, MD, Mayo Clinic MeSH: Leukemia, Lymphoid https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000621 The ECOG 2997 trial was a randomized controlled trial for patients with previously untreated CLL comparing fludarabine monotherapy to the combination of fludarabine and cyclophosphamide. The initial clinical findings of this study were published in the Journal of Clinical Oncology in 2007 (JCO 25:793-8). Additional laboratory studies have also published (JCO 25:799-804).

pht003331.v1.p1

1 itemgroup 10 items

Eligibility

1 itemgroup 45 items

pht003328.v1.p1

1 itemgroup 5 items

pht003329.v1.p1

1 itemgroup 7 items

Eligibility NCT00560794 Acute Lymphoblastic Leukemia - Eligibility

- 9/20/21 - 1 form, 2 itemgroups, 24 items, 2 languages
Itemgroups: Inclusion Criteria, Exclusion Criteria
ODM derived from http://clinicaltrials.gov/show/NCT00560794

Eligibility Lymphocytic Leukemia NCT00935792

- 5/28/18 - 1 form, 1 itemgroup, 10 items, 1 language
Itemgroup: Criteria
Everolimus and Alemtuzumab in Treating Patients With Recurrent Chronic Lymphocytic Leukemia or Small Lymphocytic Lymphoma; ODM derived from: https://clinicaltrials.gov/show/NCT00935792

Eligibility Childhood Acute Lymphoblastic Leukemia in Remission NCT00022737

- 6/18/16 - 1 form, 1 itemgroup, 18 items, 1 language
Itemgroup: Inclusion Criteria
Combination Chemotherapy With or Without Peripheral Stem Cell Transplant in Treating Children With Acute Lymphoblastic Leukemia; ODM derived from: https://clinicaltrials.gov/show/NCT00022737

Eligibility Leukemia NCT00005596

- 1/19/16 - 1 form, 1 itemgroup, 6 items, 1 language
Itemgroup: Criteria
Combination Chemotherapy in Treating Children With Newly Diagnosed Acute Lymphoblastic Leukemia; ODM derived from: https://clinicaltrials.gov/show/NCT00005596

Eligibility Acute Lymphocytic Leukemia NCT01600781

- 1/19/16 - 1 form, 2 itemgroups, 11 items, 1 language
Itemgroups: Criteria, Exclusion Criteria
Effect of Oral Supplementation With a Fibre Enriched Paediatric Sip Feed For Children With Acute Lymphocytic Leukemia; ODM derived from: https://clinicaltrials.gov/show/NCT01600781

Eligibility Acute Lymphocytic Leukemia NCT00773149

- 1/19/16 - 1 form, 2 itemgroups, 14 items, 1 language
Itemgroups: Inclusion Criteria, Exclusion Criteria
Alemtuzumab (CAMPATH 1H) Associated to G-CSF in Adult Patients With Refractory Acute Lymphocytic Leukemia; ODM derived from: https://clinicaltrials.gov/show/NCT00773149

Eligibility Acute Lymphoid Leukemia NCT01037764

- 1/19/16 - 1 form, 2 itemgroups, 14 items, 1 language
Itemgroups: Inclusion Criteria, Exclusion Criteria
Donor-specific Allogeneic Hematopoietic Cell Transplantation for Acute Lymphoblastic Leukemia (ALL); ODM derived from: https://clinicaltrials.gov/show/NCT01037764

Eligibility Acute Lymphocytic Leukemia NCT00089596

- 1/19/16 - 1 form, 2 itemgroups, 19 items, 1 language
Itemgroups: Inclusion Criteria, Exclusion Criteria
Infusion of Specially Treated Umbilical Cord Stem Cells After Chemoradiation Treatment for Blood Cancers; ODM derived from: https://clinicaltrials.gov/show/NCT00089596

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