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PCGP HYPO - samples

ABSTRACT: Hypodiploid acute lymphoblastic leukemia whole genome sequencing

PROVIDER: EGAD00001000260 | EGA |

REPOSITORIES: EGA

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Germline ETV6 Mutations Confer Susceptibility to Acute Lymphoblastic Leukemia and Thrombocytopenia.

Topka Sabine S Vijai Joseph J Walsh Michael F MF Jacobs Lauren L Maria Ann A Villano Danylo D Gaddam Pragna P Wu Gang G McGee Rose B RB Quinn Emily E Inaba Hiroto H Hartford Christine C Pui Ching-Hon CH Pappo Alberto A Edmonson Michael M Zhang Michael Y MY Stepensky Polina P Steinherz Peter P Schrader Kasmintan K Lincoln Anne A Bussel James J Lipkin Steve M SM Goldgur Yehuda Y Harit Mira M Stadler Zsofia K ZK Mullighan Charles C Weintraub Michael M Shimamura Akiko A Zhang Jinghui J Downing James R JR Nichols Kim E KE Offit Kenneth K

PLoS genetics 20150623 6

Somatic mutations affecting ETV6 often occur in acute lymphoblastic leukemia (ALL), the most common childhood malignancy. The genetic factors that predispose to ALL remain poorly understood. Here we identify a novel germline ETV6 p. L349P mutation in a kindred affected by thrombocytopenia and ALL. A second ETV6 p. N385fs mutation was identified in an unrelated kindred characterized by thrombocytopenia, ALL and secondary myelodysplasia/acute myeloid leukemia. Leukemic cells from the proband in th ...[more]

PMID: 26102509

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Project description:The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), characterized by aneuploidy and poor outcome, is unknown. Here, using complementary genome-wide profiling approaches, we show that hypodiploid ALL comprises two major subtypes that differ in the severity of aneuploidy, transcriptional profile and submicroscopic genetic alterations. Near haploid cases with 24-31 chromosomes frequently harbor alterations targeting receptor tyrosine kinase- and Ras signaling (71%) and IKZF3 (AIOLOS; 13%). In contrast, low hypodiploid ALL cases with 32-39 chromosomes are characterized by TP53 alterations (88%), almost half of which are present in non-tumor cells, and have alterations of IKZF2 (HELIOS; 53%) and RB1 (41%). Both near haploid and low hypodiploid tumors exhibit activation of Ras and PI3K signaling pathways, and are sensitive to PI3K inhibition, indicating that these drugs should be explored as a new therapeutic strategy for this frequently lethal form of leukemia. Gene expression profiling was performed on 117 single diagnosis tumor samples and one relapse sample [SJHYPO117]. No control or reference samples were included.

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Project description:<p>The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.</p>

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Development of gene expression signatures with lncRNAs for 64 T-ALL patient samples

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Project description:St. Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project: Whole Genome Sequencing of Childhood Hypodiploid Acute Lymphoblastic Leukemia

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Project description:St. Jude Children's Research Hospital - Washington University Pediatric Cancer Genome Project: Whole Genome Sequencing of Childhood Hypodiploid Acute Lymphoblastic Leukemia

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