Additional file 2: Table S2. of Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

The sequences of designed primers for amplification of selected promoters of SLC and ABC genes including annotations of transporters. (XLSX 11 kb

Additional file 5: Figure S1. of Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

A colormap of genotypes distribution among optimally and non-optimally responding patients to first-line imatinib treatment at 12 months. Each square illustrates each genotyped SNP for each patient. Red squares = minor allele homozygotes; pink squares = heterozygotes; white squares = major allele homozygotes; gray square = not analyzed. Figure S2. Genotype frequencies of the rs460089 and rs460271 in patients with optimal and non-optimal response to imatinib at 12 months. 1 – Initial cohort of 83 patients; 2 – An independent group of added patients. Note – the graphs illustrate frequencies of genotypes of rs460089, which exactly reflect genotypes frequencies of rs460271. Figure S3. Genotype frequencies of a. rs13180043 (SLC22A5) and b. rs1050152 (SLC22A4, exon 9) in patients with optimal and non-optimal response to imatinib at 12 months. Note – the graph a. illustrates frequencies of genotypes of rs13180043, which exactly reflect genotypes frequencies of rs4646298, rs13180169, rs1310186, and rs13180295. Figure S4. Relative mRNA levels of SLC22A4 and SLC22A5 in tested cell lines. a. Graph shows expression in all eight cell lines. b. Graph shows expression of cell lines carrying rs460089-GG_rs2631365-TC or rs460089-GC_rs2631365-TC genotypes. (DOCX 687 kb

Additional file 4: Table S4. of Genotypes of SLC22A4 and SLC22A5 regulatory loci are predictive of the response of chronic myeloid leukemia patients to imatinib treatment

Identified SNPs in amplified region including whole promoters of 19 selected genes in the cohort of 83 CML patients. (XLSX 20 kb

Analysis of chronic myeloid leukemia during deep molecular response by genomic PCR: a traffic light stratification model with impact on treatment-free remission

This work investigated patient-specific genomic BCR-ABL1 fusions as markers of measurable residual disease (MRD) in chronic myeloid leukaemia, with a focus on relevance to treatment-free remission (TFR) after achievement of deep molecular response (DMR) on tyrosine kinase inhibitor (TKI) therapy. DNA and mRNA BCR-ABL1 measurements by qPCR were compared in 2189 samples (129 patients) and by digital PCR in 1279 sample (62 patients). A high correlation was found at levels of disease above MR4, but there was a poor correlation for samples during DMR. A combination of DNA and RNA MRD measurements resulted in a better prediction of molecular relapse-free survival (MRFS) after TKI stop (n = 17) or scheduled interruption (n = 25). At 18 months after treatment cessation, patients with stopped or interrupted TKI therapy who were DNA negative/RNA negative during DMR maintenance (green group) had an MRFS of 80% and 100%, respectively, compared with those who were DNA positive/RNA negative (MRFS = 57% and 67%, respectively; yellow group) or DNA positive/RNA positive (MRFS = 20% for both cohorts; red group). Thus, we propose a “traffic light” stratification as a TFR predictor based on DNA and mRNA BCR-ABL1 measurements during DMR maintenance before TKI cessation