Mutational profiling in acute lymphoblastic leukemia by RNA sequencing and chromosomal genomic array testing

Cancer Medicine

Jerry Radich¹  Olga Sala‐Torra¹  Min Fang¹  Cecilia Yeung¹  David Woolston¹  Xiaoyu Qu² 

[1] Fred Hutchinson Cancer Research Center Clinical Research Division Seattle WA USA;Seattle Cancer Care Alliance Seattle WA USA;

关键词: leukemia;    molecular pathology;    next‐generation sequencing;    RT‐qPCR;   

DOI  :  10.1002/cam4.4101

来源: DOAJ

【 摘 要 】

Abstract Background Comprehensive molecular and cytogenetic profiling of acute lymphoblastic leukemia (ALL) is important and critical to the current standard of care for patients with B‐acute lymphoblastic leukemia (B‐ALL). Here we propose a rapid process for detecting gene fusions whereby FusionPlex RNA next‐generation sequencing (NGS) and DNA chromosome genomic array testing (CGAT) are combined for a more efficient approach in the management of patients with B‐ALL. Methods We performed RNA NGS and CGAT on 28 B‐ALL samples and, in four patients, compared fixed cell pellets to paired cryo‐preserved samples as a starting material to further assess the utility of cytogenetic fixed pellets for gene expression analysis. Results Among the fixed specimens, when using alternative techniques as references, including karyotype, fluorescence in situ hybridization, CGAT, and RT‐qPCR, fusions were detected by RNA NGS with 100% sensitivity and specificity. In the four paired fixed versus fresh cryopreserved samples, fusions were also 100% concordant. Four of the 28 patients showed mutations that were detected by RNA sequencing and three of four of these mutations had well‐known drug resistance implications. Conclusions We conclude that FusionPlex is a robust and reliable anchored multiplex RNA sequencing platform for use in the detection of fusions in both fresh cryopreserved and cytogenetic fixed pellets. Gene expression data could only be obtained from fresh samples and although limited variant data are available, critical hotspot variants can be determined in conjunction with the fusions.

【 授权许可】

Unknown