Project description:Internal tandem duplications (ITD) of FLT3 predict poor prognosis in acute myeloid leukemia (AML) and often co-exist with inactivating DNMT3A mutations. In a genetically modified mouse model harboring these genetic aberrations, we analyzed the role of the adaptor protein Gab2 in this disease. We observed Gab2 to be essential for the development of Flt3-ITD driven AML in vivo, which was corroborated by RNA sequencing data of whole murine bone marrow with different Gab2 genotypes
Project description:Interpreting the genomic and phenotypic consequences of copy number variation (CNV) is essential to understand the etiology of genetic disorders. Whereas deletion CNVs obviously lead to haploinsufficiency, duplications may cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci and in some cases these copy number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has not been investigated on a large scale. Here, we fine mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). In addition, we predicted six in-frame fusion genes at sequenced duplication breakpoints. Four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These novel fusion genes could be related to clinical phenotypes and warrant further study. Though most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that may not be predicted by conventional copy number analysis. Thus, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.
Project description:Whole-genome tiling arrays were used to validate deletions and tandem duplications that were inferred based on next-generation sequencing data. The arrays were generated for six samples of the Drosophila melanogaster Genetic Reference Panel (DGRP) as well as the Berkeley reference strain. Structural variations (SVs) were assessed by comparing probe intensities within the region of interest between the sample for which the SV was predicted and the reference strain.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:Oligonucleotide expression microarray data used for expression signature associated with FLT3 internal tandem duplications(FLT3-ITD) in samples from older patients with cytogenetically normal AML
Project description:Colorectal cancer panel sequencing of 100 adenoma and carcinoma samples . Cancer Hot Spot panel sequencing of 7 samples from one poly.
Project description:The Xuanwei area is a hot spot of lung adenocarcinoma in females in China, which is strongly associated with the consumption of local smoky coal. Comprehensive characterization of its genomic and immunological landscapes is crucial for cancer prevention and the development of precision therapy. Here, we report extensive genomic, transcriptomic, and immunological profiles of 117 Xuanwei female lung adenocarcinoma (XWFA), comprising 112 pairs of tumour-normal whole-exon sequencing (WES) profiles and 33 normal and 115 tumour mRNA-seq profiles.
Project description:Chromosomal structural mutations play an important role in determining the transcriptional landscape of human breast cancers. We determined that pro-oncogenic and anti-oncogenic genes are clustered throughout the genome and that these clusters coincide with regions of segmental amplification and deletion. We constructed detailed structural mutation maps of representative breast cancers and found that tandem duplications appear to nucleate regions for amplification. Subsequent rearrangements link distant pro-oncogenic elements for co-amplification, and are associated with loss of tumor suppressors. We show that genes engaged in co-amplifications or conjoint deletions on 17q and 8q have pro-growth effects that are additive in nature. Our results suggest structural mutations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously.
Project description:Our study represents the first analysis of thymocyte transcriptomes of mice expressing the equivalent of the human p53-Y220C hot-spot oncogenic mutant