RNA-Seq Identifies Gene Expression Changes Associated with Relapse in Acute Lymphoblastic Leukemia (ALL)

In this study a team of researchers from Life Technologies and St. Jude Children’s Research Hospital have performed RNA-Seq using the SOLiD™3 system on samples from five children with acute lymphoblastic leukemia (ALL) with paired samples taken at the time of initial presentation with cancer (“initial” or “I”) and at the time of relapse (“relapse” or “R”).Raw data was processed using the analysis pipelines in Bioscope and tertiary analysis was performed using several published statistical methods. These methods identified gene sets that can select cancer relapse samples with almost 98% accuracy, and have further identified genes that were found to be correlated with tumor relapse and poor prognosis in other studies. The analysis have also identified nucleotide variants unique to the samples at the time of relapse. The researchers further note that processing of the data using a Bayesian method such as Bayseq appears to alleviate sample and run specific variation in the data. RNA-Seq is a powerful tool for exploring the biology of cancer, and these results point the way to important follow up studies that may further elucidate the causes of cancer relapse