RNA-seq identified 141 nonsynonymous mutations in 93 patients (54%) the most frequent were RAS-MAPK pathway mutations. Gene expression profiling enabled further molecular classification into the following B-cell ALL (B-ALL) subgroups: high hyperdiploid (n 5 36), ETV6-RUNX1/-like (n 5 31), TCF3-PBX1 (n 5 7), KMT2A-rearranged (KMT2A-R n 5 5), intrachromosomal amplification of chromosome 21 (iAMP21) (n 5 1), hypodiploid (n 5 1), Philadelphia chromosome (Ph)-positive/Ph-like (n 5 16), DUX4-R (n 5 11), PAX5 alterations (PAX5 alt n 5 11), PAX5 P80R (n 5 1), ZNF384-R (n 5 4), NUTM1-R (n 5 1), MEF2D-R (n 5 1), and others (n 5 10). An additional 56 gene fusions were identified by RNA-seq, many of which confer prognostic or therapeutic significance. Fusion detection was 100% concordant with results obtained from conventional cytogenetic analyses. RNA-seq identified at least 1 alteration in 157 patients (91%). The Dana-Farber Cancer Institute ALL Consortium Protocol 16-001 enrolled 173 patients with ALL who consented to optional studies and had samples available for RNA-seq.
#Thai kahn san fusion trial
We examined the feasibility and utility of incorporating RNA-seq into a prospective multicenter phase 3 clinical trial for children with newly diagnosed ALL.
RNA sequencing (RNA-seq) is a powerful next-generation sequencing technology that can simultaneously identify cryptic gene rearrangements, sequence mutations and gene expression profiles in a single assay. The molecular hallmark of childhood acute lymphoblastic leukemia (ALL) is characterized by recurrent, prognostic genetic alterations, many of which are cryptic by conventional cytogenetics.
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