RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL)
RNA-sequencing (RNA-seq) efforts in acute lymphoblastic leukaemia (ALL) have identified numerous prognostically significant genomic alterations which can guide diagnostic risk stratification and treatment choices when detected early. However, a full RNA-seq Bioinformatics workflow is time-consuming and costly in a clinical setting where rapid detection and accurate reporting of clinically relevant alterations are essential. To accelerate the identification of ALL-specific alterations (including gene fusions, single nucleotide variants and focal gene deletions), we developed the rapid screening tool RaScALL, capable of identifying more than 100 prognostically significant lesions directly from raw sequencing reads. RaScALL uses the k-mer based targeted detection tool km and known ALL variant information to achieve a high degree of accuracy for reporting subtype defining genomic alterations compared to standard alignment-based pipelines. Gene fusions, including difficult to detect fusions involving EPOR and DUX4, were accurately identified in 98% (164 samples) of reported cases in a 180-patient Australian study cohort and 95% (n=63) of samples in a North American validation cohort. Pathogenic sequence variants were correctly identified in 75% of tested samples, including all cases involving subtype defining variants PAX5 p.P80R (n=12) and IKZF1 p.N159Y (n=4). Accurate detection of intragenic IKZF1 deletions resulting in aberrant transcript isoforms was also detectable with 98% accuracy. Importantly, the median analysis time for detection of all targeted alterations averaged 22 minutes per sample, significantly shorter than standard alignment-based approaches, ensuring accelerated risk-stratification and therapeutic triage.
- 180 samples
- DAC: EGAC00001002790
- Technology: NextSeq 500
SAHMRI data transfer agreement to access exam data files
DATA TRANSFER AGREEMENT [XXX] (Recipient) South Australian Health and Medical Research Institute Limited (SAHMRI) Party and Notice details Date 2022 Parties Name ABN Short form name Recipient Notice details Name SOUTH AUSTRALIAN HEALTH AND MEDICAL RESEARCH INSTITUTE LIMITED ABN 54 141 228 346 Short form name SAHMRI Notice details SAHMRI Building, North Terrace, Adelaide SA 5000 Australia Attention : Professor Steve Wesselingh Executive Director with a copy to Ms Heather Croucher SAHMRI’s General Counsel Steve.wesselingh@sahmri.com cc: heather.croucher@sahmri.com BACKGROUND A. SAHMRI owns the Data. B. The Recipient has requested SAHMRI to provide the Recipient with the Data for the purposes of the Research Project. C. SAHMRI has agreed to provide the Data to the Recipient for the purposes of the Research Project, on the terms and conditions of this Agreement. 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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS00001006460 | Other |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.