### General information

Author: Author: Lund university, https://www.lunduniversity.lu.se/
Contact e-mail: kajsa.paulsson@med.lu.se
DOI: 10.17044/scilifelab.21953117
License: CC BY-NC-ND 4.0
This readme file was last updated: 2023-01-31

Please cite as: Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukemia 

### Dataset description

This is a data record for a dataset used for somatic single nucleotide variants analysis of high hyperdiploid acute lymphoblastic leukemia (ALL) in the manuscript: Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukemia. The dataset is manually curated. It included 22 samples with high hyperdiploid ALL collected from the Division of Clinical Genetics, Lund University, Sweden. All samples were subjected to whole genome sequencing and somatic variants were identified by the GDC DNA-Seq analysis pipeline (Zhang et al.,2021). The data was stored in variant call format (vcf) and the interpretation of the file is available at: https://docs.gdc.cancer.gov/Data/File_Formats/VCF_Format/. The dataset is manually curated.

Please note that we cannot guarantee accuracy of any of the information provided in this dataset. We do our best at maintaining the dataset but we do not take responsibility in case any of the provided information turns out to be incorrect or incomplete. We do not recommend using this dataset for analyses/projects which require complete accuracy.

Researchers are welcome to use the data contained in the dataset for any projects. Please cite this metadata record upon use or when published. We encourage reuse using the same CC BY-NC-ND 4.0 License.


### Available variables

- 'entity': The variant call format file, somatic variants calling result. 
- 'title': Clonal origin and development of high hyperdiploidy in childhood acute lymphoblastic leukemia
- 'authors': Eleanor L Woodward, Minjun Yang, Larissa H Moura-Castro, Hilda van den Bos, Rebeqa Gunnarsson, Linda Olsson-Arvidsson, Diana CJ Spierings, Anders Castor, Nicolas Duployez, Marketa Zaliova, Jan Zuna, Bertil Johansson, Floris Foijer, Kajsa Paulsson
- 'type': journal article
- 'published': publication date assigned by the journal if available (NB: may not be accurate or up to date and may also be in a coming issue)
- 'abstract': High hyperdiploid acute lymphoblastic leukemia (HeH ALL), one of the most common childhood malignancies, is driven by nonrandom aneuploidy (abnormal chromosome numbers) mainly comprising chromosomal gains. In this study, we investigate how aneuploidy in HeH ALL arises. Single cell whole genome sequencing of 2,847 cells from nine primary cases and one normal bone marrow reveals that HeH ALL generally display low chromosomal heterogeneity, indicating that they are not characterized by chromosomal instability and showing that aneuploidy-driven malignancies are not necessarily chromosomally heterogeneous. Furthermore, most chromosomal gains are present in all leukemic cells, suggesting that they arose early during leukemogenesis. Copy number data from 577 primary cases reveals selective pressures that were used for in silico modeling of aneuploidy development. This shows that the aneuploidy in HeH ALL likely arises by an initial tripolar mitosis in a diploid cell followed by clonal evolution, in line with a punctuated evolution model.
---- 'Type': Journal article
---- 'Category': Genomics & transcriptomics
---- 'Funder': Swedish Research Council, grant numbers 2020-01164 and 2020-00997
- 'created': 2023-01-30
- 'modified': 2023-01-31