ID
45096
Description
Principal Investigator: Charles Mullighan, MD, Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA MeSH: Leukemia, T-cell https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000340 *CREST* The accurate identification of structural variations using whole-genome DNA sequencing data generated by next-generation sequencing technology is extremely difficult. To address this challenge, we have developed CREST, an algorithm that uses sequencing reads with partial alignments to the reference human genome (so-called soft-clipped reads) to directly map the breakpoints of somatic structural variations. We applied CREST to paired tumor/normal whole genome sequencing data from five cases of T-lineage acute lymphoblastic leukemia (T-ALL). A total of 110 somatic structural variants were identified, 80% of which were validated by genomic PCR and Sanger sequencing. The validated structural variants included 31 inter-chromosomal translocations, 19 intra-chromosomal translocations, one inversion, 22 deletions and 16 insertions. A comparison of the results generated with CREST to those obtained using the traditional paired-end discordant mapping methods demonstrate CREST to have a much higher sensitivity and specificity. In addition, application of CREST to publicly available whole-genome sequencing data from the human melanoma cancer cell line COLO-829 demonstrated the identification of 50 novel structural variations not detected using the standard methods, 20 of which were selected for validation with a 90% success rate. These data demonstrate that direct mapping of soft-clipped reads offers an improved method for detecting structural variants at the nucleotide level of resolution. *T-ALL* Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was characterized by activating mutations in genes regulating cytokine receptor and RAS signalling (67% of cases; *NRAS*, *KRAS*, *FLT3*, *IL7R*, *JAK3*, *JAK1*, *SH2B3* and *BRAF*), inactivating lesions disrupting haematopoietic development (58%; *GATA3*, *ETV6*, *RUNX1*, *IKZF1* and *EP300*) and histone-modifying genes (48%; *EZH2*, *EED*, *SUZ12*, iSETD2/i and iEP300/i). We also identified new targets of recurrent mutation including iDNM2/i, iECT2L/i and iRELN/i. The mutational spectrum is similar to myeloid tumours, and moreover, the global transcriptional profile of ETP ALL was similar to that of normal and myeloid leukaemia haematopoietic stem cells. These findings suggest that addition of myeloid-directed therapies might improve the poor outcome of ETP ALL.
Lien
https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000340
Mots-clés
Versions (2)
- 22/08/2022 22/08/2022 - Simon Heim
- 12/10/2022 12/10/2022 - Adrian Schulz
Détendeur de droits
Charles Mullighan, MD, Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, USA
Téléchargé le
22 août 2022
DOI
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Licence
Creative Commons BY 4.0
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dbGaP phs000340 Sequencing of ETP T-ALL
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- Subject ID, consent group, subject sources, subject source ID, and affection status of patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Sample ID, Subject ID, sample sources, and sample source ID of patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Subject ID, age at diagnosis, treatment protocol, patient relapse, bone marrow transplants, genetic lesions, gender, ethnicity, and vital status of patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Sample ID, tumor status, body site where from sample was collected, analyte type, histological type of samples, and primary tumor location of samples obtained from patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Sample IDs and GEO accession IDs of samples obtained from patients diagnosed with hypodiploid acute lymphoblastic leukemia.
Similar models
Eligibility Criteria
- StudyEvent: SEV1
- Eligibility Criteria
- Subject ID, consent group, subject sources, subject source ID, and affection status of patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Sample ID, Subject ID, sample sources, and sample source ID of patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Subject ID, age at diagnosis, treatment protocol, patient relapse, bone marrow transplants, genetic lesions, gender, ethnicity, and vital status of patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Sample ID, tumor status, body site where from sample was collected, analyte type, histological type of samples, and primary tumor location of samples obtained from patients diagnosed with hypodiploid acute lymphoblastic leukemia.
- Sample IDs and GEO accession IDs of samples obtained from patients diagnosed with hypodiploid acute lymphoblastic leukemia.
C1301359 (UMLS CUI [1,2])
C3640076 (UMLS CUI [1,3])
C0027651 (UMLS CUI [1,4])
C0012854 (UMLS CUI [1,5])
C0021430 (UMLS CUI [1,6])
C0370003 (UMLS CUI [1,7])