Isolation and Whole Genome Sequencing of Tumor gDNA

Tumor gDNA samples were available from The Swedish Childhood Tumor Biobank^{20 (link)} for all Karolinska University Hospital patients. Isolation of gDNA from tumors was performed using the AllPrep DNA/RNA/Protein Mini kit (Qiagen, Hilden, Germany) and from blood (minimum 1 ml) using the QIAamp® DNA Blood Midi/Maxi kit, vacuum protocol (Qiagen), according to the manufacturer’s instructions. WGS analysis was performed on paired tumor-normal data by The Swedish Childhood Tumor Biobank as previously described and used to detect driver genetic aberrations.^{18 (link)}

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Krynina O., de Ståhl T.D., Jylhä C., Arthur C., Giraud G., Nyman P., Fritzberg A., Sandgren J., Tham E, & Sandvik U. (2024). The potential of liquid biopsy for detection of the KIAA1549-BRAF fusion in circulating tumor DNA from children with pilocytic astrocytoma. Neuro-Oncology Advances, 6(1), vdae008.

Publication 2024

AllPrep DNA/RNA/Protein Mini kit QIAamp® DNA Blood Midi/Maxi kit

Corresponding Organization : Karolinska University Hospital

Other organizations : Uppsala University Hospital, Linköping University, Linköping University Hospital, Falun Hospital

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Variable analysis

independent variables

Tumor gDNA samples from The Swedish Childhood Tumor Biobank

dependent variables

Driver genetic aberrations detected by whole-genome sequencing (WGS) analysis on paired tumor-normal data

control variables

Isolation of gDNA from tumors using the AllPrep DNA/RNA/Protein Mini kit (Qiagen)
Isolation of gDNA from blood (minimum 1 ml) using the QIAamp® DNA Blood Midi/Maxi kit, vacuum protocol (Qiagen)
WGS analysis performed on paired tumor-normal data by The Swedish Childhood Tumor Biobank as previously described

controls

No positive or negative controls were explicitly mentioned in the provided information.

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