The pitfalls of platform comparison: DNA copy number array technologies assessed
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE16400 | GEO | 2009/12/03
SECONDARY ACCESSION(S): PRJNA116291
REPOSITORIES: GEO
Similar Datasets
Project description: Not available
| S-EPMC2797821 | biostudies-literature
Project description: Not available
| S-EPMC3146450 | biostudies-literature
Project description: Not available
| S-EPMC4015297 | biostudies-literature
Project description:We sequenced two tumor/normal pairs obtained from two paediatric medulloblastoma patients (MB14 and MB24) with at least 30x coverage on all commonly used next-generation sequencing platforms for whole genome sequencing (SOLiD 4, 5500xl SOLiD, Illumina's HiSeq2000, and Complete Genomic' technology). The normal tissue samples came from venous blood. We compared their ability to call single nucleotide variations (SNVs) in whole-genome sequencing data with high confidence. As gold standard for SNV calling, we used genotypes determined by Affymetrix SNP 6.0 Array Technology (total of 907,551 SNPs after quality filtering).
2013-06-01 | E-MTAB-1159 | biostudies-arrayexpress
Project description:Two reference pools comprised of different miRNA content were hybridized to four different miRNA microarray platforms (Agilent, LC Sciences, Exiqon and a homemade chip (generated from an Inviteogen Ncode probeset)) This dataset includes the reference samples on the Agilent miRNA array. Keywords: miRNA Two reference pools were created from commercially available reference RNA (FirstChoice® mouse Total RNA including the small fraction (Catalogue # AM7800-AM7828, Ambion, Streetsville, ON)). Reference #1 contained equal parts of mouse testicle, ovary and 10-12 day embryo. Reference #2 contained liver, heart and lung. These references were hybridized to four different miRNA microarray platforms (two in two colour, two in one-colour, with 4 replicates each). Data from each platform were normalized by cyclic lowess and analysed by correlation analyses both within and between platforms.
2010-10-18 | E-GEOD-19669 | biostudies-arrayexpress
Project description: Not available
| S-EPMC4526866 | biostudies-literature
Project description:A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quality CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.
2009-02-18 | GSE14740 | GEO
Project description:: A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quali ty CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.
2009-02-18 | GSE14745 | GEO
Project description:A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quali ty CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA.
2009-02-18 | GSE14742 | GEO
Project description:A major challenge to the study of tumor DNA copy number (CN) in clinical specimens is the lack of appropriate fresh frozen samples and thus a dependence on Formalin-Fixed Paraffin Embedded (FFPE) banked samples, which typically have more extensive clinical follow up information. However, on most high density CN platforms, DNA from FFPE tissues generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking. Molecular Inversion Probe (MIP) technology has been applied successfully to obtain high quality CN and genotype data from DNA isolated from cell lines and frozen tumor samples. Since the MIP probes require only a small (~40 bp) target binding site, we reasoned they may be well suited to assess FFPE samples. In this study, we successfully applied MIP technology with a panel of 50,000 markers to CN determination in FFPE samples. Using an input of 37 ng genomic DNA, we demonstrated high quali ty CN data with MIP technology from 93 FFPE samples from seven diverse collections. We found that the performance of FFPE DNA for CN determination was comparable to that of DNA obtained from matched frozen tumor, with only a modest loss in performance of DNA. Various collections of FFPE samples have been assayed by MIP.
2010-05-06 | E-GEOD-14742 | biostudies-arrayexpress