Computational protocol: Frequent variations in cancer-related genes may play prognostic role in treatment of patients with chronic myeloid leukemia

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Protocol publication

[…] Newly diagnosed patients with Ph+ CML in chronic phase at diagnosis have been included in this study at Federal State-Funded Institution National Research Center for Hematology of the Ministry of Healthcare of the Russian Federation (Moscow, Russia) starting from June, 2012. Peripheral blood samples were collected at diagnosis after signing informed consent “Exome and transcriptome analysis of leukemic cells in chronic myeloid leukemia”. The study was conducted according to the provisions of the Declaration of Helsinki. All patients received standard treatment with TKIs and were examined at regular time periods – 3, 6, 9 and 12 months during the 1-st year of observation. The examination included clinical evaluation, complete blood count, cytogenetic and molecular tests which measured BCR-ABL expression by quantitative PCR. Patients were assigned to the groups of either optimal responders or failures according to ELN recommendations 2013 []. For the purpose of our study we evaluated response at 6 months. All failures were checked for the absence of mutations in the ABL-kinase domain of the BCR-ABL by sequencing. DNA extracted from blood samples was used for WES. WES was performed using Ion Torrent Personal Genome Machine (Thermo Fisher Scientific, Waltham, MA, USA) with 200 bp reads. Exome enrichment was performed using Ion TargetSeq™ Exome Kit which captures about 30,000 protein-coding and RNA genes and predicted microRNA-binding sites. Sequencing analysis was done in Torrent Suite software v.3.6.2. Single nucleotide variants (SNVs) were annotated with ANNOVAR [], Partek Genomics Suite (Partek, St. Louis, Missouri, USA) and Variant Effect Predictor tool []. Variants identified by whole exome sequencing, were validated by Sanger sequencing. Methods in more details are described in Additional file . […]

Pipeline specifications

Software tools ANNOVAR, Partek Genomics Suite, VEP
Application WES analysis
Organisms Homo sapiens
Diseases Neoplasms, Leukemia, Myelogenous, Chronic, BCR-ABL Positive
Chemicals Tyrosine