Genomic Landscape of Pediatric Myelodysplastic Syndromes - EGA European Genome-Phenome Archive

Study ID	Alternative Stable ID	Type
EGAS00001002202		Other

Study ID

Alternative Stable ID

Type

EGAS00001002202

Other

Study Description

Pediatric myelodysplastic syndromes (MDS) are a rare disease and unlike their adult counterpart, very little is known about their genomic landscape. We characterized a cohort of patients from a single institution by whole exome sequencing, as well as a subset of patients by whole genome sequencing, RNA-sequencing and targeted deep sequencing. We found a spectrum of mutations, both somatic and germline, that are distinct from those observed in adult MDS. In turn, we observed mutations commonly observed in other pediatric myeloid tumors.

Dataset ID	Description	Technology	Samples
EGAD00001003155	WES files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes' WES files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'	Illumina HiSeq 2000	6
EGAD00001003156	WGS files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes' WGS files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'	Illumina HiSeq 2000	4
EGAD00001003781	Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files. Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files.	Illumina HiSeq 2000	94
EGAD00001003782	When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files. When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files.	Illumina HiSeq 2000	43

Dataset ID

Description

Technology

Samples

EGAD00001003155

WES files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

Illumina HiSeq 2000

EGAD00001003156

WGS files for SJMDS paper titled 'Genomic Landscape of Pediatric Myelodysplastic Syndromes'

Illumina HiSeq 2000

EGAD00001003781

Paired whole exome sequencing for 32 primary MDS, 14 MDS/MPN, and 8 AML-MRC cases (total = 54). Normal comparator genomic DNA was extracted from lymphocytes purified by flow cytometry. Bulk myeloid cells were used as a source of tumor gDNA. Files uploaded are mapped BAM files.

Illumina HiSeq 2000

EGAD00001003782

When available (25 primary MDS, 12 MDS/MPN, and 6 AML-MRC cases), high quality RNA (stranded-total) was submitted for RNA-seq. RNA was extracted from bulk myeloid cells which was used as the tumor population. Files uploaded are mapped BAM files.

Illumina HiSeq 2000

Study

Study Description

Study Datasets 4 datasets.

Who archives the data?

Publications

Citations

The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure.