Targeted deep sequencing on Pediatric MDS

Targeted NGS using custom panels with SAMD9, SAMD9L genes and 22 single nucleotide polymorphisms (SNP) on chromosome 7q (allele frequency >35% in all ethnic sub-populations in gnomAD) (Ampliseq #IAD10417) was performed in 667/669 cases. Additionally, 559 cases were sequenced using 28 pediatric MDS genes (GATA2, RUNX1, HOXA9, CEBPA, GATA1, KRAS, NRAS, CBL, PTPN11, ASXL1, EZH2, SETBP1, FLT3, KIT, JAK2, JAK3, CSF3R, MPL, SH2, BCOR, BCORL1; RAD21, STAG2, CTCF, TP53, PTEN, CALR, VPS45; Ampliseq #IAD51150). Libraries for targeted NGS were prepared using NEBNext Ultra II DNA library prep kit (New England BioLabs, cat#E7645S/L) per manufacturer’s instruction and samples were sequenced on an Illumina Miseq 2000 with 2 x 150 bp reads. The BAM files are uploaded here.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

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
EGAD00001007856	The dataset consists of - 126 whole exome sequencings (SAMD9/9Lmut: 64; GATA2mut 24, MDS wildtype 38/471) performed using SureSelect Human All Exon V6 enrichment (Agilent, cat# 5190-8863). The generated libraries were sequenced on the Illumina Hiseq 2500 with 150bp paired-end reads. FASTQ files were processed using SeqNext platform (JSI medical system, Germany), with gene-based alignment to a virtual panel of 300 genes (including 28 MDS-associated genes, SAMD9, and SAMD9L), consisting of genes relevant to bone marrow failure, MDS predisposition, and hematological cancers as per the Pan-Cancer studies with cohorts of >10,000 cancers. The respective BAM files are provided. - Custom panel targeting SAMD9, SAMD9L, and 22 single nucleotide polymorphisms (SNP) on chromosome 7q (allele frequency >35% in all ethnic sub-populations in gnomAD) (Ampliseq #IAD104171) were performed in 666/669 cases. And Custom panel targeting 28 MDS-associated genes (GATA2, RUNX1, HOXA9, CEBPA, GATA1, KRAS, NRAS, CBL, PTPN11, ASXL1, EZH2, SETBP1, FLT3, KIT, JAK2, JAK3, CSF3R, MPL, SH2, BCOR, BCORL1; RAD21, STAG2, CTCF, TP53, PTEN, CALR, VPS45) was performed in 544 cases (Ampliseq #IAD51150). Both custom panel libraries were prepared using NEBNext Ultra II DNA library prep kit (New England BioLabs, cat#E7645S/L) per manufacturer’s instruction and samples were sequenced on an Illumina Miseq 2000 with 2 x 150 bp reads. The respective BAM files are provided - 4 SAMD9/9L patients were subjected to MissionBio custom single-cell panel (CO-112) targeting 250 heterozygous gnomAD population polymorphisms on 7q arm and 69 amplicons in SAMD9/9L and other cancer genes. All libraries were sequenced on an Illumina NovaSeq6000 with 150 base-paired ending multiplexed runs. Fastq files were processed using the Tapestri Pipeline V2 and python-based Mosaic package (multi-omics analysis, data visualization). The derived BAM and loom files are provided.	Illumina HiSeq 2500 Illumina MiSeq Illumina NovaSeq 6000	437

Publications	Citations
Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes. Sahoo SS, Pastor VB, Goodings C, Voss RK, Kozyra EJ, Szvetnik A, Noellke P, Dworzak M, Starý J, Locatelli F, Masetti R, Schmugge M, De Moerloose B, Catala A, Kállay K, Turkiewicz D, Hasle H, Buechner J, Jahnukainen K, Ussowicz M, Polychronopoulou S, Smith OP, Fabri O, Barzilai S, de Haas V, Baumann I, Schwarz-Furlan S, European Working Group of MDS in Children (EWOG-MDS), Niewisch MR, Sauer MG, Burkhardt B, Lang P, Bader P, Beier R, Müller I, Albert MH, Meisel R, Schulz A, Cario G, Panda PK, Wehrle J, Hirabayashi S, Derecka M, Durruthy-Durruthy R, Göhring G, Yoshimi-Noellke A, Ku M, Lebrecht D, Erlacher M, Flotho C, Strahm B, Niemeyer CM, Wlodarski MW. Nat Med 27: 2021 1806-1817	60

Publications

Citations

Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes.
Sahoo SS, Pastor VB, Goodings C, Voss RK, Kozyra EJ, Szvetnik A, Noellke P, Dworzak M, Starý J, Locatelli F, Masetti R, Schmugge M, De Moerloose B, Catala A, Kállay K, Turkiewicz D, Hasle H, Buechner J, Jahnukainen K, Ussowicz M, Polychronopoulou S, Smith OP, Fabri O, Barzilai S, de Haas V, Baumann I, Schwarz-Furlan S, European Working Group of MDS in Children (EWOG-MDS), Niewisch MR, Sauer MG, Burkhardt B, Lang P, Bader P, Beier R, Müller I, Albert MH, Meisel R, Schulz A, Cario G, Panda PK, Wehrle J, Hirabayashi S, Derecka M, Durruthy-Durruthy R, Göhring G, Yoshimi-Noellke A, Ku M, Lebrecht D, Erlacher M, Flotho C, Strahm B, Niemeyer CM, Wlodarski MW. Nat Med 27: 2021 1806-1817