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A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor.

Nat Genet. Volume 49, Issue 10 p.1487-1494, 21 August 2017 10.1038/ng.3940

We performed genome-wide sequencing and analyzed mRNA and miRNA expression, DNA copy number, and DNA methylation in 117 Wilms tumors, followed by targeted sequencing of 651 Wilms tumors. In addition to genes previously implicated in Wilms tumors (WT1, CTNNB1, AMER1, DROSHA, DGCR8, XPO5, DICER1, SIX1, SIX2, MLLT1, MYCN, and TP53), we identified mutations in genes not previously recognized as recurrently involved in Wilms tumors, the most frequent being BCOR, BCORL1, NONO, MAX, COL6A3, ASXL1, MAP3K4, and ARID1A. DNA copy number changes resulted in recurrent 1q gain, MYCN amplification, LIN28B gain, and MIRLET7A loss. Unexpected germline variants involved PALB2 and CHEK2. Integrated analyses support two major classes of genetic changes that preserve the progenitor state and/or interrupt normal development.

This study characterized TARGET cases as described below:

117 Discovery Cases   651 Validation Cases
113 cases had chip-based GE   -
112 cases had mRNA-seq   -
114 had miRNA-seq   -
115 cases had CN array   -
115 cases had methylation array   -
80 cases had WGS   -
37 cases had WXS   -
-   651 cases had TCS

GE=gene expression; CN=copy number, TCS=targeted capture sequencing

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