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Lund University

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Sample Requirement

OncoScan for FFPE samples 

 The OncoScanassay utilizes the Molecular Inversion Probe (MIP) technology, a proven technology for identifying copy number alterations, loss of heterozygosity (LOH), and detecting somatic mutations. It offers enhanced resolution in ~900 cancer genes, and the status of frequently tested somatic mutations, all from a single assay. Data can be generated from only 80 ng of FFPE-derived DNA. This assay has been shown to perform well with highly degraded DNA, such as that derived from FFPE-preserved tumour samples of various ages and with low inputs of DNA starting material, making the assay a natural choice in cancer clinical research.

The OncoScan Assay is set-up for 23 samples and a positive control.

FFPE DNA must be extracted and handled according to recommendations in the OncoScan Assay Manual, pp 28 – 29 and Appendix E, pp 120 – 124. Samples should be delivered in a PCR-plate; at least 15 µl in a concentration of 12 ng/µl. A gel-image should also be submitted. Plate orientation A1-12, C1-12, etc.

It is mandatory to determine the sample concentration using a dsDNA specific quantification method. We strongly recommend using the PicoGreen Assay or Qubit dsDNA Quantification, both by Life Technologies. UV absorbance or NanoDrop must NOT be used at all in this assay, as it will heavily over estimate the DNA concentration. Samples must be eluted and diluted in Low EDTA 1xTE buffer. Do NOT use water.

For important and detailed information about sample handling, see the OncoScan Manual.

The SCIBLU lab will not make any further quality tests.

CytoScan

 The CytoScan HD Array is based on the proven Genome-Wide Human SNP Array 6.0 and contains more than 2.6 million markers for copy number analysis and approximately 750,000 SNPs that fully genotype with greater than 99 percent accuracy.

The CytoScan HD Array provides the power to detect known and novel chromosome aberrations across the entire human genome. This array features unbiased whole-genome coverage, excellent performance across the entire genome (>99% sensitivity and specificity for CN changes >400 kb), and the highest probe density (>2.6 million markers including 750,000 unique SNPs) to detect gene-level, copy-neutral LOH, uniparental isodisomy (UPD), and regions identical-by-descent, in addition to low-level mosaicism and sample heterogeneity 

The CytoScan Assay is presently only available for 100 samples. Please check with us.

DNA must be extracted and handled according to recommendations in the CytoScan Assay Manual, pp 21 – 22. Samples should be delivered in a PCR-plate; 5 µl, 50 ng/µl. A gel-image should also be submitted.

This protocol has been optimized using UV absorbance to determine genomic DNA concentrations. Other quantitation methods such as PicoGreen may give different readings.

The SCIBLU lab will not make any further quality tests.

DMET, Drug Metabolism

 Many of the known genetic markers that influence the metabolism of commonly prescribed drugs are not assayed by conventional microarray SNP methods due to the presence of pseudogenes or other closely related genomic sequences. DMET Plus is capable of processing these complex markers by making use of a pre-amplification step in the processing of genomic DNA. Some markers are first pre-amplified using multiplex polymerase chain reaction (mPCR) prior to joining the other markers in the DMET Plus assay flow. Genomic sequences that contain the polymorphic markers of interest are preferentially amplified through the use of highly selective Molecular Inversion Probe (MIP) [25, 26] amplification. The resulting target DNA is then labelled and hybridized to the DMET Plus Array.

The DMET Assay is set-up for 45 samples. Please contact us early.

Samples should be delivered in a PCR-plate; 17 µl, 60 ng/µl. A gel-image should also be submitted.

It is mandatory to determine the sample concentration using a dsDNA specific quantification method. We strongly recommend using the PicoGreen Assay or Qubit dsDNA Quantification, both by Life Technologies. UV absorbance or NanoDrop must NOT be used at all in this assay, as it will heavily over estimate the DNA concentration. Samples should be diluted in 1xTE buffer. Do NOT use water.

For more information about sample handling, see the DMET Manual, chapter 3.

The SCIBLU lab will not make any further quality tests.

 

Transport to SCIBLU Genomics

 Samples should be transported on dry ice. Please contact us before sending your samples to make sure that someone will receive the package. You will be placed in queue upon sample arrival.

Delivery address:              
Lunds Universitet, SCIBLU Genomics, Microarray unit
Inst. för Immunteknologi
Medicon Village, byggnad 402A, Scheelevägen 8
SE 223 63 Lund