Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Agilent_HGG_custom_CGH

ABSTRACT: Custom oligonucleotide array CGH. We designed two fine-tiling oligonucleotide microarrays to cover the specific amplicons observed at chromosome 2p22.1 and 10q11.21 This was undertaken using the Agilent custom array design tool e-Array (Agilent, Santa Clara, CA, USA; https://earray.chem.agilent.com/), and comprised 700 probes covering 43.56Ð43.70 Mb on chromosome 10 and 5000 probes covering 39Ð40 Mb on chromosome 10 with a median probe interval of 200 bp on 2x105K microarray. Due to limited amount of material, DNA was whole genome amplified (WGA) using the GenomePlex Complete Whole Genome Amplification Kit (Sigma, Gillingham, UK) starting with 10 ng of sample and control DNA, and following the manufacturers protocol. WGA DNA was labelled using the Agilent Genomic DNA ULS labelling kit, hybridised as per manufacturers instructions, and scanned on the Agilent 2505B Microarray Scanner System.

ORGANISM(S): Homo sapiens

SUBMITTER: Alan Mackay

PROVIDER: E-MTAB-2340 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In the study of tumor genetics, formalin-fixed paraffin-embedded (FFPE) tumors are the most readily available tissue samples. While DNA derived from FFPE tissue has been validated for array comparative genomic hybridization (aCGH) application, the suitability of such fragmented DNA for single-nucleotide polymorphism (SNP) array analysis has not been well examined. Furthermore, whole-genome amplification (WGA) has been used in the study of small precursor lesions to produce sufficient amount of DNA for aCGH analysis. It is unclear whether the same approach can be extended to SNP analysis. In this study, we examined the utility and limitations of genotyping platform performed on whole-genome amplified DNA from FFPE tumor samples for both copy number and SNP analyses. We analyzed the results obtained using DNA derived from matched FFPE and frozen tissue samples on Affymetrix 250K Nsp SNP array. Two widely used WGA methods, Qiagen (isothermal protocol) and Sigma (thermocycling protocol), were used to determine how WGA methods affect the results. We found that the use of DNA derived from FFPE tumors (without or with WGA) for high-resolution SNP array application can produce a significant amount of false positive and false negative findings. While some of these misinterpretations appear to cluster in genomic regions with high or low GC contents, the majority appears to occur randomly. Only large-scale chromosome LOH (>10Mb) can be reliably detected from FFPE tumor DNA samples (without or with WGA) but not smaller LOH or copy number alterations. Our findings here indicate a need for caution in SNP array data interpretation when using FFPE tumor-derived DNA, particularly with WGA. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved and FFPE mesenchymal tumor samples without or with WGA, as well as genomic snap-frozen non-neoplastic tissue DNA from 5 adult individuals to serve as reference DNA. WGA was performed using the REPLI-g® FFPE kit (Qiagen, Valencia, CA, USA) and GenomePlex® Tissue Whole Genome Amplification WGA5 kit (Sigma, Saint Louis, MO, USA) in parallel in accordance with the manufacturers’ protocols. A two- to eight-hour individualized reaction time was used in the Qiagen platform for each sample. A gradient amount of initial DNA (10ng, 30ng, 60ng, 100ng and 150ng) was tested followed by gel electrophoresis and qualitative multiplex PCR assay to determine the quality of post-WGA products. At least four independent experiments were concurrently performed per template amplification. Four separateWGA reaction products were pooled for each sample for subsequent microarray analysis to minimize the amplification bias and allele dropout. One of the Affymetrix GeneChip® Human Mapping 500K Array Set (Nsp 250K SNP array) was used for genotyping analysis. Four gastrointestinal stromal tumors with known cytogenetic aberrations were included. Two cases were sucessfullly amplified and passed the quality tests. A total of 12 samples were compared between each other, including frozen tissue DNA (as reference), frozen tissue DNA with WGA (two platforms), FFPE tissue DNA, and FFPE tissue DNA with WGA (two platforms) from each case.

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Agilent_HGG_custom_CGH

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