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Systematic identification of genomic markers of drug sensitivity in cancer cells
It was found that mutated cancer genes were associated with cellular response to most currently available cancer drugs, and systematic pharmacogenomic profiling in cancer cell lines provides a powerful biomarker discovery platform to guide rational cancer therapeutic strategies. Expand
Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours
Phylogenetically conserved restriction fragments in the vicinity of EWSR1 and EWSR2, the genomic regions where the breakpoints of chromosome 22 and chromosome 11 are, respectively, have allowed identification of transcribed sequences from these regions and has indicated that a hybrid transcript might be generated by the translocation. Expand
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data
The tool Control-FREEC is presented, that enables automatic calculation of copy number and allelic content profiles from NGS data, and consequently predicts regions of genomic alteration such as gains, losses and LOH. Expand
Molecular subgroups of medulloblastoma: an international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas
A meta-analysis of all molecular and clinical data of 550 medulloblastomas brought together from seven independent studies shows how distinct the molecular subtypes are with respect to their transcriptome, DNA copy-number aberrations, demographics, and survival. Expand
Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer
The observation of bi-allelic alterations of hSNF5/INI1 in MRTs suggests that loss-of-function mutations of h snf5/inI1 contribute to oncogenesis, and the most frequently deleted part of chromosome 22q11.2 is mapped. Expand
Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition.
Functional assays in different SHH-MB xenograft models demonstrated that SHh-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant. Expand
Mesenchymal stem cell features of Ewing tumors.
Gen expression analysis comparing ETs with a variety of normal tissues shows that the profiles of different EWS-FLI1-silenced Ewing cell lines converge toward that of mesenchymal stem cells (MSC). Expand
Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma
Neuroblastoma, a tumour derived from the peripheral sympathetic nervous system, is one of the most frequent solid tumours in childhood. It usually occurs sporadically but familial cases are observed,Expand
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization
It is demonstrated that for Illumina single-end, mate-pair or paired-end sequencing, GC-contentr normalization provides smooth profiles that can be further segmented and analyzed in order to predict CNAs and FREEC (control-FREE Copy number caller) automatically normalizes and segments copy number profiles (CNPs) and calls CNAs. Expand
Integrative genomic analysis of medulloblastoma identifies a molecular subgroup that drives poor clinical outcome.
It is shown that a previously unidentified molecular subgroup, characterized genetically by c-MYC copy number gains and transcriptionally by enrichment of photoreceptor pathways and increased miR-183∼96∼182 expression, is associated with significantly lower rates of event-free and overall survivals. Expand