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| Status |
Public on Mar 20, 2020 |
| Title |
ChIP-chip by SNP array of a case of a patient with TCF3-HLF-positive BCP-ALL |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
The TCF3-HLF translocation is a very rare rearrangement in ALL that is associated with an extremely poor prognosis. The TCF3-HLF fusion gene in the described case resulted in the fusion of the homeobox-related gene of TCF3 to the leucine zipper domain of HLF. The TCF3-HLF fusion gene product acts as a transcriptional factor leading to the dedifferentiation of mature B lymphocytes into an immature state (lymphoid stem cells). This process initiates the formation of pre-leukaemic cells. Due to the rarity of this chromosomal aberration, only a few cases have been described in the literature. The advantage of this work is the presentation of an interesting case of clonal evolution of cancer cells and the cumulative implications (diagnostic and prognostic) of the patient’s genetic alterations.
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| Overall design |
The microarray analyses were performed with the use of a CytoScan HD array. All laboratory procedures were carried out according to the manufacturers' protocols. The study was based on an analysis of scanned data files that was generated with the Chromosome Analysis Suite v 3.3 (ChAS, Thermo Fisher Scientific, Waltham, MA). Furthermore, the copy numbers of altered regions (CNAs) were calculated, and the data were normalized to a reference model (Thermo Fisher Scientific) of baseline reference intensities, NA 33 (hg19/CRCh37). The copy number states (CNS) and their breakpoints were determined with the use of the hidden Markov model (HMM) software package. The threshold levels of log2 ratio ≥0.5 and ≤0.5 were used for the categorization of the altered chromosomal regions as CNV gains and losses, respectively. The obtained data were analyzed based on two different criteria: genome-wide CNVs and leukaemia-associated region/gene-specific CNAs (leukaemia genes_all_20150505; Fullerton Overlap Map_hg19).
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| Contributor(s) |
Lejman M, Włodarczyk M |
| Citation(s) |
32245383 |
| Submission date |
Mar 20, 2020 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Monika Szelest |
| E-mail(s) |
m.wlodarczyk214@gmail.com
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| Phone |
+48515509301
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| Organization name |
Medical University of Lublin
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| Department |
Laboratory of Genetic Diagnostics
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| Street address |
ul. Antoniego Gębali 6
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| City |
Lublin |
| ZIP/Postal code |
20-093 |
| Country |
Poland |
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| Platforms (1) |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA613668 |
