Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Affymetrix SNP 6.0 array data for chordoma samples

ABSTRACT: Chordomas are rare, low to intermediate grade malignant bone tumors of the axial skeleton, believed to originate from the notochord. Treatment options are limited and mainly restricted to surgical excision, as chordomas have been proven to be largely resistant to conventional ionizing radiation and chemotherapy. Therefore a new cell line was established. The cell line has been characterized by immunohistochemistry,western blot and karyotyping using cobra fish technology. Copy number variations (CNV) and loss-of heterozygosity (LOH) from fibroblasts, tumor tissue, low and high cell line passage was evaluted by using Affymetrix 6.0SNP Arrays. DNA isolated from the patients MNCs was used as control. The cell line MUG-Chor1 is highly similar to genetic profiles of chordomas and provides therefore a powerful tool for further investigations. Affymetrix SNP 6.0 arrays were performed according to the manufacturer's directions on DNA extracted from cryo material or cell lines. Copy number analysis of Affymetrix SNP 6.0 arrays was performed for 4 samples. 60 samples from HapMap database were used as references for copy number inference.

ORGANISM(S): Homo sapiens

SUBMITTER: Carina Fischer

PROVIDER: E-GEOD-25720 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Establishment and detailed functional and molecular genetic characterisation of a novel sacral chordoma cell line, MUG-Chor1.

Rinner Beate B Froehlich Elke Verena EV Buerger Karin K Knausz Heike H Lohberger Birgit B Scheipl Susanne S Fischer Carina C Leithner Andreas A Guelly Christian C Trajanoski Slave S Szuhai Karoly K Liegl Bernadette B

International journal of oncology 20111014 2

Chordomas are rare, low to intermediate grade malignant bone tumors of the axial skeleton. Current treatment options are limited to surgical procedures, as chordomas are largely resistant to conventional radiation and chemotherapy. Cell lines are valuable tools for exploring molecular mechan-isms involved in tumorigenesis and they have a fundamental impact on the development of new anticancer agents. To date, only two chordoma cell lines exist world-wide. In the present study we report a third c ...[more]

PMID: 22002331

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Project description:Generating sufficient DNA for high-throughput genetic analysis has always been a challenge for clinical settings where the amount of source DNA is limited. Multiple displacement amplification (MDA) has been proposed as a promising candidate for such situations. Previous work with lower-resolution arrays confirmed the utility of single-cell MDA products for large-size (~30 Mb) genome variation screening. We tested the performance of single-cell MDA products on the SNP 6.0 arrays to examine the performance of single-cell MDA in SNP genotyping, copy number polymorphism, de novo copy number variation (CNV) and loss of heterozygosity (LOH) analysis. Our data show that for SNP genotyping, single-cell MDA did not obtain complete genome coverage or high sequence fidelity. For CNV calling, single-cell MDA introduced stochastic amplification artifacts in log2 ratio profiles, reducing the robustness of CNV calling; however, by adjusting smooth window size, it is still possible to analyze large chromosomal aberrations, and homozygous deletions as small as 500 kb can still be identified from the noisy log2 ratio profiles. Our results also suggest that even with a modified protocol (reduction of reaction volume, addition of a molecular crowding reagent, minimization of reaction time), single-cell MDA presented little improvement over the unmodified protocol, but by increasing the number of cells as template to 5M-bM-^@M-^S10 cells, SNP 6.0 array results comparable to those of 10 ng genomic DNA MDA could be obtained. Algorithms like PICNIC improved the CNV calling, suggesting that better algorithms can better utilize single-cell MDA array results. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell line samples, and multiple displacement samples. Genotyping, Copy number and LOH analysis of Affymetrix SNP 6.0 arrays was performed for 3 samples of unamplified cell line genomic DNA, 2 samples of DNA obtained by multiple displacement amplification from 10ng genomic DNA, 3 single-cell multiple displacement amplification (MDA) products, single cell modified MDA amplification product, 5-cell modified MDA amplification product, 10-cell modified MDA amplification product.

Dataset Information

Affymetrix SNP 6.0 array data for chordoma samples

Publications

Establishment and detailed functional and molecular genetic characterisation of a novel sacral chordoma cell line, MUG-Chor1.

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