Project description:In this study we will sequence the transcriptome of Verified Matched Pair Cancer Cell line tumour samples. This will be married up to whole exome and whole genome sequencing data to establish a full catalog of the variations and mutations found.

2013-07-11 | E-ERAD-157 | biostudies-arrayexpress

EGAS00001000434-sc-20130710 - samples

| EGAD00001000630 | EGA

Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions

2014-03-07 | GSE43168 | GEO

Application of SNP microarrays to the genome-wide analysis of chromosomal instability in premalignant airway lesions

Project description:Chromosomal instability is central to the process of carcinogenesis. The detection of somatic chromosomal alterations in small premalignant lesions genome-wide remains challenging since sample heterogeneity dilutes the aberrant cell information. We introduced an analytic metric termed "delta-θ", and applied this metric to a titrated cancer cell model using a pair of cancer cell line and matched lymphoblastoid cell line. We examined heterogeneous clinical specimens including bronchial biopsies and brushings with this metric. Distinctive genomic variation were successfully detected across the whole genome in invasive cancer cases (6/6), carcinoma in situ (3/3), and high grade dysplasia (severe or moderate) (3/11). We modeled titration series (100%, 25%, 12.5%, 6.3%, 3.1%, 1.6% and 0% tumor content) mixing the genomic DNA of the cell line pair. We also investigated 30 malignant/premalignant samples from 18 patients with heavy smoking histories (6 invasive lung cancer, 3 carcinoma in situ,15 dysplasia, 3 hyperplasia and 3 normal histology) using Illumina HumanOmni2.5 and Human 660w SNP microarrays. All of them were paired with matched reference blood DNA and analyzed.

2014-03-07 | E-GEOD-43168 | biostudies-arrayexpress

Project description:LOW-LEVEL HETEROPLASMY IN HUMAN MITOCHONDRIAL GENOMES OF A CANCER-DERIVED CELL LINE PAIR

| PRJEB19247 | ENA

Whole Genome Sequencing of Tongue cancer samples and cell line

Project description:Whole Genome Sequencing of Tongue cancer samples and cell line

| PRJEB62494 | ENA