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

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001003155	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'	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.	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.	Illumina HiSeq 2000	43

Publications	Citations
Germline SAMD9 mutation in siblings with monosomy 7 and myelodysplastic syndrome. Schwartz JR, Wang S, Ma J, Lamprecht T, Walsh M, Song G, Raimondi SC, Wu G, Walsh MF, McGee RB, Kesserwan C, Nichols KE, Cauff BE, Ribeiro RC, Wlodarski M, Klco JM. Leukemia 31: 2017 1827-1830	62
The genomic landscape of pediatric myelodysplastic syndromes. Schwartz JR, Ma J, Lamprecht T, Walsh M, Wang S, Bryant V, Song G, Wu G, Easton J, Kesserwan C, Nichols KE, Mullighan CG, Ribeiro RC, Klco JM. Nat Commun 8: 2017 1557	159
Clonal dynamics of donor-derived myelodysplastic syndrome after unrelated hematopoietic cell transplantation for high-risk pediatric B-lymphoblastic leukemia. Schwartz JR, Walsh MP, Ma J, Lamprecht T, Wang S, Wu G, Raimondi S, Triplett BM, Klco JM. Cold Spring Harb Mol Case Stud 4: 2018 a002980	5
Germline SAMD9 and SAMD9L mutations are associated with extensive genetic evolution and diverse hematologic outcomes. Wong JC, Bryant V, Lamprecht T, Ma J, Walsh M, Schwartz J, Del Pilar Alzamora M, Mullighan CG, Loh ML, Ribeiro R, Downing JR, Carroll WL, Davis J, Gold S, Rogers PC, Israels S, Yanofsky R, Shannon K, Klco JM. JCI Insight 3: 2018 121086	80
Etiology of oncogenic fusions in 5,190 childhood cancers and its clinical and therapeutic implication. Liu Y, Klein J, Bajpai R, Dong L, Tran Q, Kolekar P, Smith JL, Ries RE, Huang BJ, Wang YC, Alonzo TA, Tian L, Mulder HL, Shaw TI, Ma J, Walsh MP, Song G, Westover T, Autry RJ, Gout AM, Wheeler DA, Wan S, Wu G, Yang JJ, Evans WE, Loh M, Easton J, Zhang J, Klco JM, Meshinchi S, Brown PA, Pruett-Miller SM, Ma X. Nat Commun 14: 2023 1739	27