Browse
Submit Data
Databases
API
Help
Login

Dataset Information

24 Views

2 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 7

Prediction of response to anti-EGFR antibody-based therapies by multigene sequencing in colorectal cancer patients

ABSTRACT: We investigated a panel of 21 genes by parallel sequencing on the Ion Torrent Personal Genome Machine platform. We sequenced 65 CRCs that were treated with cetuximab or panitumumab ( 37 samples were responsive and 28 were resistant).

INSTRUMENT(S): Ion Torrent PGM

ORGANISM(S): Homo Sapiens

DISEASE(S): Colorectal Adenocarcinoma

SUBMITTER: Laura Lupini Cristian Bassi

PROVIDER: E-MTAB-3883 | ArrayExpress | 2015-10-22

REPOSITORIES: ArrayExpress

ACCESS DATA

Json Xml

Dataset's files

Source:

primary

			Action	DRS
	E-MTAB-3883.ID-5035.bam	Bam
	E-MTAB-3883.ID_5031.bam	Bam
	E-MTAB-3883.ID_5032.bam	Bam
	E-MTAB-3883.ID_5033.bam	Bam
	E-MTAB-3883.ID_5034.bam	Bam

Items per page:

1 - 5 of 68

Publications

Prediction of response to anti-EGFR antibody-based therapies by multigene sequencing in colorectal cancer patients.

Lupini Laura L Bassi Cristian C Mlcochova Jitka J Musa Gentian G Russo Marta M Vychytilova-Faltejskova Petra P Svoboda Marek M Sabbioni Silvia S Nemecek Radim R Slaby Ondrej O Negrini Massimo M

BMC cancer 20151027

<h4>Background</h4>The anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (moAbs) cetuximab or panitumumab are administered to colorectal cancer (CRC) patients who harbor wild-type RAS proto-oncogenes. However, a percentage of patients do not respond to this treatment. In addition to mutations in the RAS genes, mutations in other genes, such as BRAF, PI3KCA, or PTEN, could be involved in the resistance to anti-EGFR moAb therapy.<h4>Methods</h4>In order to develop a comprehensive ...[more]

PMID: 26508446

Similar Datasets

Targeted next generation sequencing of cfDNA from lung cancer patients enrolled in the GALAXY-1 trial (NCT01348126)

Project description:We evaluated whether targeted next-generation sequencing (NGS) using the Ion Torrent Personal Genome Sequencer of cfDNA could identify prognostic or predictive factors for overall survival (OS) or progression free survival (PFS) within a large cohort of patients with advanced lung adenocarcinoma enrolled in the GALAXY-1 trial.

2018-01-10 | E-MTAB-5749 | ArrayExpress

Prediction of response to anti-EGFR antibody-based therapies by multigene sequencing in colorectal cancer patients.

Project description:The anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (moAbs) cetuximab or panitumumab are administered to colorectal cancer (CRC) patients who harbor wild-type RAS proto-oncogenes. However, a percentage of patients do not respond to this treatment. In addition to mutations in the RAS genes, mutations in other genes, such as BRAF, PI3KCA, or PTEN, could be involved in the resistance to anti-EGFR moAb therapy.In order to develop a comprehensive approach for the detection of mutations and to eventually identify other genes responsible for resistance to anti-EGFR moAbs, we investigated a panel of 21 genes by parallel sequencing on the Ion Torrent Personal Genome Machine platform. We sequenced 65 CRCs that were treated with cetuximab or panitumumab. Among these, 37 samples were responsive and 28 were resistant.We confirmed that mutations in EGFR-pathway genes (KRAS, NRAS, BRAF, PI3KCA) were relevant for conferring resistance to therapy and could predict response (p = 0.001). After exclusion of KRAS, NRAS, BRAF and PI3KCA combined mutations could still significantly associate to resistant phenotype (p = 0.045, by Fisher exact test). In addition, mutations in FBXW7 and SMAD4 were prevalent in cases that were non-responsive to anti-EGFR moAb. After we combined the mutations of all genes (excluding KRAS), the ability to predict response to therapy improved significantly (p = 0.002, by Fisher exact test).The combination of mutations at KRAS and at the five gene panel demonstrates the usefulness and feasibility of multigene sequencing to assess response to anti-EGFR moAbs. The application of parallel sequencing technology in clinical practice, in addition to its innate ability to simultaneously examine the genetic status of several cancer genes, proved to be more accurate and sensitive than the presently in use traditional approaches.

2015-01-01 | S-EPMC4624582 | BioStudies

whole-exome sequencing of colorectal cancer tumour bulks from opposite side of the neoplasm (A/B) to infer tumour evolutionary dynamics and reconstruct the timeline of progression

Project description:We performed whole-exome sequencing of tumour bulks from opposite side of the neoplasm (A/B). From each we selected a panel of sub-clonal mutations and profiled multiple single tumour glands from the same neoplasm using high depth targeted re-sequencing. The aim was to infer tumour evolutionary dynamics and reconstruct the timeline of progression

2014-12-22 | E-MTAB-2247 | ArrayExpress

A comprehensive map of L1HS-Ta retrotransposons in a panel of human cells obtained by ATLAS-seq.

Project description:We used ATLAS-seq to comprehensively map the genomic location of LINE-1 elements belonging to the youngest and potentially polymorphic subfamily (L1HS-Ta). This was performed in a panel of 12 human primary or transformed cell lines (BJ, IMR90, MRC5, H1, K562, HCT116, HeLa S3, HepG2, MCF7, HEK-293, HEK-293T, 2102Ep). In brief, ATLAS-seq relies on the random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, suppression PCR-amplification of L1HS-Ta element junctions, and Ion Torrent sequencing using single-end 400 bp read chemistry. A notable aspect of ATLAS-seq is that we can obtain both L1 downstream and upstream junctions (3'- and 5'-ATLAS-seq libraries, respectively), for full-length L1 elements. Note that a 10-nt sample-specific barcode has been removed at the 5' end of the reads in the .fastq files upon demultiplexing. This was achieved using cutadapt v1.9.2.dev0 (with the following parameters: -e 0.1 -q 10 -m 25 -g <barcode_name>=^<barcode_sequence>)

2016-05-24 | E-MTAB-4676 | ArrayExpress

Targeted next generation sequencing of genomic DNA from PLC, JEG3 and JEG3R cells

Project description:A comparison between a human placental cell line (3A sub E placental, aka, PLC), human choriocarcinoma methotrexate-sensitive JEG3, and methotrexate-resistant JEG3R. This comparison focused on genomic 'hot spot' regions that are frequently mutated in human cancer genes.

2022-02-19 | E-MTAB-11432 | ArrayExpress

RNA-seq data from the pilot study of the 'Personal Genome Project UK': PGP-UK10

Project description:This study consists of 10 whole genome RNA-seq profiles which have been generated from blood samples collected from ten different volunteers in the Personal Genome Project UK

2018-03-04 | E-MTAB-6523 | ArrayExpress

Ampliseq transcriptomic array of REF seq. genes in Snai1 knock out triple negative breast cancer cells

Project description:Aim of this study is to unveil the global transcriptomic expression levels upon Knockout of Snai1 in triple negative breast cancer cells Hs578T.

2018-04-25 | E-MTAB-5244 | ArrayExpress

Identification of de novo LINE-1 (L1) retrotransposon integration sites in HeLa S3 cells by ATLAS-seq-neo (unselected insertions)

Project description:We used ATLAS-seq-neo to map the sites of integration of an engineered LINE-1 (L1) retrotransposon into the genome of HeLa S3 cells. In brief, we transfected cells with a plasmid-borne L1.3 element carrying a neomycin-resistance-based retrotransposition cassette, as well as a hygromycin-resistance cassette on the plasmid backbone. For this set of experiments, cells were only selected for transfection (hygromycin) but not for retrotransposition (neomycin). Then we prepared ATLAS-seq-neo libraries. Each sample corresponds to an independent transfection and pool of hygromycin-resistant cells. ATLAS-seq-neo relies on the random mechanical fragmentation of the genomic DNA to ensure high-coverage, ligation of adapter sequences, suppression PCR-amplification of the 3' end L1 junction with its flanking genomic sequence, and Ion Torrent sequencing using single-end 400 bp read chemistry. The primer used for suppression PCR specifically targets the engineered element and not endogenous copies as in the original ATLAS-seq protocol (Philippe et al. eLife 2016). For some libraries, the linker-ligated genomic DNA was digested with BamHI, which cuts downstream of L1 polyA site in the plasmid backbone, to limit amplification from the plasmid and enrich for retrotransposition-mediated insertion events into the genomic DNA.

2019-04-03 | E-MTAB-7644 | ArrayExpress

Identification of de novo LINE-1 (L1) retrotransposon integration sites in HeLa S3 cells by ATLAS-seq-neo

2019-04-04 | E-MTAB-6933 | ArrayExpress

Effect of a KRAS peptide nucleic acid clamp on the Ion Torrent sequencing protocol

Project description:To test whether the addition of a peptide nucleic acid (PNA) clamp, which binds WT KRAS at codon 12, can increase the efficacy of mutation detection for KRASG12D within a targeted NGS setting. We tested the effect of clamping the wild-type KRAS sequence in a reference standard (Tru-Q 7, 1.3% Tier from Horizon Diagnostics, Cambridge, UK) with a KRAS c.35G>A mutation (KRASG12D) at an allelic frequency (AF) of 1.3% assessed by digital droplet PCR (ddPCR). We then re-tested the PNA on circulating-free DNA from a patient harbouring a KRASG12D mutation (at an AF of 3.2%, determined by ddPCR). Multiple runs were conducted using 10, 5, 2.5 and 1ng of DNA input.

2017-07-29 | E-MTAB-5718 | ArrayExpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data