Mate-pair sequencing of 12q-amplified osteosarcomas

Mate-pair sequencing of 12q-amplified osteosarcomas for the detection of structural variants. This was carried out in order to study the structure of the chromosome 12q-amplicons and whether material from other chromosomes is also intertwined and amplified in a bid to further characterise these tumours beyond CDK4 and MDM2 amplification. Mate-pair data was also used to verify gene fusions detected with RNA-seq.

Type: Whole Genome Sequencing
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000000707	Further investigation and characterisation of 12q-amplified low- and high-grade osteosarcomas with MDM2 and/or CDK4 amplification focusing on SV, copy number and gene fusion analyses. In total, 25 cases (33 samples total due to multi-sampling) were included, with some form of sequencing data available for 27 samples. Mate-pair whole genome sequencing (Illumina) is available for 19 samples, longread whole genome sequencing (PacBio HiFi) on 10 samples and RNA-sequencing (Illumina Truseq) on 21 samples. Data is available as BAM files.	NextSeq 500 unspecified	25

Publications	Citations
CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma. Saba KH, Difilippo V, Styring E, Nilsson J, Magnusson L, van den Bos H, Wardenaar R, Spierings DCJ, Foijer F, Nathrath M, Haglund de Flon F, Baumhoer D, Nord KH. NPJ Genom Med 9: 2024 42	0