Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts 2023-148-1 https://doi.org/10.48723/zt59-8x04 Swedish National Data Service Svensk nationell datatjänst Landing page Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts Integrated genomic and transcriptomic analysis improves disease classification and risk stratification of MDS with ring sideroblasts 2023-148-1 https://doi.org/10.48723/zt59-8x04 10.1158/1078-0432.CCR-23-0538 Todisco, Gabriele Todisco, Gabriele Hellström-Lindberg, Eva Hellström-Lindberg, Eva 2021-01404_VR 2021-01404_VR Swedish National Data Service Svensk nationell datatjänst Landing page Hematologic Diseases Blodsjukdomar Myelodysplastic Syndromes Myelodysplastiskt syndrom Myelodysplastic-Myeloproliferative Diseases Myelodysplastiska-myeloproliferativa syndrom Human health and safety Människors hälsa och säkerhet 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. Heltranskriptom-sekvensering (RNA-seq) från CD34-uttryckande mononukleära benmärgsceller från patienter med myelodysplastisk syndrom med ringsideroblaster (MDS-RS). CD34-uttryckande celler isolerades från mononukleära benmärgsceller via instrumentet AUTO-MACS med dubbelseparation (Miltenyi Biotec, Germany). RNA extraherades från CD34-uttryckande celler via RNeasy Microkit (Qiagen, Hilden, Germany) och behandlades därefter med DNase i enlighet med tillverkarens instruktion. RNA integritetsnumret uppskattades sedan via Agilent RNA 6000 Pico (Agilent Technologies, Palo Alto, CA) och var högre än 6.5 i alla prover (median 8.2). RNA sekvenseringsbiblioteken sattes upp från allt RNA via SMARTer Stranded Total RNA-Seq Kit v2 Pico Input Mammalian med enzymatisk degradering av ribosomalt RNA (Takara Bio, Japan). RNA-biblioteken sekvenserades sedan på Novaseq 6000 med ”paired-end 150bp” inställning. Slutligen kombinerade vi molekylära och kliniska data i syfte att hitta nya prognostiska markörer och förbättra karaktärisering av sjukdomen hos patienter med MDS. Datasetet består av två filer: - FASTQ_RS.tar.gz: komprimerad mapp innehållande 258 fastq-filer - metadata_RS.xlsx Datasetets totala storlek är ca 1 TB. Sweden Sverige Patients with Myelodysplastic neoplasms with ring sideroblasts (MDS-RS) Patienter med myelodysplastisk syndrom med ringsideroblaster (MDS-RS) Text Other 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.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. Access to data through SND. Access to data is restricted. Åtkomst till data via SND. Tillgång till data är begränsad. restrictedAccess 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. 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. 10.1158/1078-0432.CCR-23-0538 2023