Skip to main content
Researchdata.se

Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts

https://doi.org/10.48723/zt59-8x04
Full transcriptome (RNA-sequencing) from bulk CD34+ bone marrow mononuclear cells from MDS patients with ring sideroblasts. CD34+ cells were isolated from the MNC using AUTO-MACS with double-separation option (Miltenyi Biotec, Germany) and submitted for RNA extraction. RNA was extracted with RNeasy Microkit (Qiagen, Hilden, Germany) and treated with DNase, according to manufacturer instruction. RNA integrity number was estimated using Agilent RNA 6000 Pico (Agilent Technologies, Palo Alto, CA) and was greater than 6.5 for all the samples (median 8.2). The RNA-sequencing (RNA-seq) libraries were prepared from total RNA using SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian with enzymatic ribosomal depletion (Takara Bio, Japan). Libraries were sequenced using the Novaseq 6000 with paired-end 150bp configuration. The molecular data were integrated with clinical information aiming to improve prognosis prediction in this hematologic malignancy. The dataset consists of 2 files: - FASTQ_RS.tar.gz: compressed folder that includes 258 fastq files - metadata_RS.xlsx The total size of the dataset is approximately 1 TB.
Download documentation (2 files / 7.09 KiB)

Documentation files

  • readme.txt
    1.58 KiB
  • Variable_list_metadata_RS.csv
    5.51 KiB

Citation and access

Data access level:

Creator/​Principal investigator(s):

Research principal:

Data contains personal data:

Yes

Type of personal data:

Genetic and health information

Code key exists:

Yes

Sensitive personal data:

Yes

Citation:

License:

Language:

Method and outcome

Population:

Patients with Myelodysplastic neoplasms with ring sideroblasts (MDS-RS)

Study design:

  • Observational study

Description of sampling:

We studied 129 MDS patients with ring sideroblasts within a population of 834 myeloid neoplasms evaluated at Karolinska University Hospital in Stockholm between February 2004 and August 2020. CD34+ cells were isolated from the MNC using AUTO-MACS with double-separation option (Miltenyi Biotec, Germany) and submitted for RNA extraction for all cases and controls. The RNA-sequencing (RNA-seq) libraries were prepared from total RNA using SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian with enzymatic ribosomal depletion (Takara Bio, Japan). Libraries were sequenced using the Novaseq 6000 with paired-end 150bp configuration.

Time period(s) investigated:

Number of individuals/​objects:

129

Data format/​data structure:

Samples/material Existing from scientific collection/biobank

Name:

Karolinska MDS Biobank

Type(s) of sample:

Bone marrow cells; Human sample; RNA

Geographic coverage

Geographic location:

Administrative information

Responsible department/​unit:

Department of Medicine, Huddinge [H7]

Ethics Review:

Stockholm - 2017/1090-31/4

Funding

Funding agency:

Award number:

2021-01404_VR

Award title:

Disease mechanisms and targeted treatment in myelodysplastic syndromes

Funding information:

This translational research program aims at improving outcome for patients with myelodysplastic syndromes (MDS) by unravelling cellular and molecular mechanisms underlying disease features and response to treatment. Using a world-unique database of clinically annotated MDS patients who have undergone targeted DNA sequencing and RNA sequencing of CD34+ BM cells and has been complemented with comprehensive information regarding transfusion patterns and response to treatment we aim to develop novel predictive models for estimation of age-related survival loss, risk for progression, and optimal management and treatment. By using advanced culture models for human hemopoietic stem cell (HSC) biology and erythroid maturation in combination with single cell sequencing we will explore SF3B1 mutated MDS with ring sideroblasts with the aim to understand the clonal advantage of mutated over normal HSC and explore new molecular routes to prevent ineffective erythropoiesis and chronic transfusion dependency. Finally, we aim to implement and further improve recently developed methods for personalized minimal residual disease monitoring in a prospective clinical trial and thereby improve the cure rate after allogeneic stem cell transplantation in high-risk MDS. The long-term goal is to implement precision medicine in MDS in order to be able to predict and implement optimal management for each patient.

Topic and keywords

Standard för svensk indelning av forskningsämnen 2025:

Keywords:

Publications

Citation:

Todisco G, Creignou M, Bernard E, Björklund AC, Moura PL, Tesi B, Mortera Blanco T, Sander B, Jansson M, Walldin G, Barbosa I, Reinsbach SE, Hofman IJ, Nilsson C, Yoshizato T, Dimitriou M, Chang D, Olafsdottir S, Venckute Larsson S, Tobiasson M, Malcovati L, Woll P, Jacobsen SW, Papaemmanuil E, Hellström-Lindberg E. Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts. Clin Cancer Res. 2023 Jul 27:CCR-23-0538. doi: 10.1158/1078-0432.CCR-23-0538.

Contact

Metadata

Version 1
doris
ki
Published:|Updated: