GEO series

An East-Asian polymorphism underlies BCR-ABL mutation-independent resistance to tyrosine kinase inhibitors in chronic myelogenous leukemia

GSE28303 Homo sapiens (human) Genome variation profiling by high throughput sequencing 6 samples Submitted 2012/02/27 Platform GPL9138Platform GPL9442

At a glance

human · 6 samples

Organism: Homo sapiens (human)
Topic: Chronic myeloid leukemiaThis series is part of our curated briefing on it.
Samples: 6 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

We used massively parallel DNA sequencing of paired-end ditags (DNA-PET) to identify structural genetic factors associated with disease progression and drug-resistance in representative samples from four CML patients and one CML cell line. The functional consequences of our genetic findings were evaluated in primary CML cells and cell lines, and validated in a larger CML cohort.

Read the full summary ↓

We discovered a novel intronic deletion that correlated with imatinib-resistance, and was subsequently confirmed to be a polymorphism in normal East-Asian, but not African or Caucasian, populations. We found that the polymorphism favored expression of transcripts lacking a pro-apoptotic domain, which is critical for imatinib-induced cell death. A CML cell line containing the polymorphism also exhibited BCR-ABL-independent imatinib-resistance.

This dataset

Open GSE28303 in finder → Find more human datasets → Chronic myeloid leukemia landscape →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE28303_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

Also filed as BioProject PRJNA139493 and SRA study SRP006673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22426421) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 6 more — browse all 6 samples with per-sample file links →

More Chronic myeloid leukemia datasets

GSE275701 Neddylation Status Determines the Therapeutic Sensitivity of BCR-ABL1-targeting Tyrosine Kinase Inhibitors in Chronic Myeloid Leukemia 12 samples same disease briefing · shares bcr-abl, inhibitors
GSE267912 CDK6 kinase inhibition opens up metabolic dependencies in BCR-ABL+ leukemia 45 samples same disease briefing · shares bcr-abl
GSE235463 Effect of knockdown PHF8 on the transcriptional regulation of BCR-ABL1 fusion gene on CML cell line K562 4 samples same disease briefing · shares bcr-abl
GSE276122 Combined targeting of GPX4 and BCR-ABL tyrosine kinase selectively compromises BCR-ABL+ leukemia stem cells 4 samples same disease briefing · shares bcr-abl
GSE281956 Oxidation Resistance 1 (Oxr1) Dysregulation Promotes TKI Resistance and Blast Crisis in Chronic Myeloid Leukemia. 59 samples same disease briefing · shares resistance
GSE292088 Martinostat as a Novel HDAC Inhibitor to Overcome Tyrosine Kinase Inhibitor Resistance in Chronic Myeloid Leukemia 15 samples same disease briefing · shares resistance
GSE198142 Selective translational control by PABPC1 phase separation regulates blast crisis and target therapy resistance of chronic myeloid leukemia 8 samples same disease briefing · shares resistance
GSE280879 Selective translational control by PABPC1 phase separation regulates blast crisis and target therapy resistance of chronic myeloid leukemia [RNA-seq] 6 samples same disease briefing · shares resistance

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.