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QIAseq RNAscan Custom Panel (Qiagen)

CH Carina Heydt
CW Christina B. Wölwer
OC Oscar Velazquez Camacho
SW Svenja Wagener-Ryczek
RP Roberto Pappesch
JS Janna Siemanowski
JR Jan Rehker
FH Florian Haller
AA Abbas Agaimy
KW Karl Worm
TH Thomas Herold
NP Nicole Pfarr
WW Wilko Weichert
TK Thomas Kirchner
AJ Andreas Jung
JK Jörg Kumbrink
WG Wolfgang Goering
IE Irene Esposito
RB Reinhard Buettner
AH Axel M. Hillmer
SM Sabine Merkelbach-Bruse
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A QIAseq RNAscan Custom Panel was designed targeting known fusion breakpoints and novel fusions in ALK, ROS1, RET, BRAF, MET, FGFR1-3, NTRK1-3 (Additional file 1: Table S1). For each sample, 200 ng of DNase digested RNA was used for cDNA synthesis by reverse transcription. For library preparation the QIAseq RNAscan Custom Panel (Qiagen) was used following manufacturer’s instructions. Purified libraries were quantified using the Qubit dsDNA Assay Kit (Thermo Fisher Scientific) and library quality was assessed using the Fragment Analyzer (Agilent). Libraries were pooled to equimolar concentration and sequenced using a NextSeq 500 (Illumina). Results were analyzed using the CLC Genomics Workbench v12.0 (Qiagen). A fusion was classified as “PASS” with a p-value below 0.005 and a minimum number of 2 fusion-supporting reads. The time for analysis heavily relied on the used hardware. On our local hardware one sample took around 15 h.

Copyright and License information: The Author(s) ©2021
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