The 8‐μm thick sections were mounted on regular glass slides. After deparaffinization, the target tumor cells were macro‐dissected and collected in a 1.5‐mL tube. The target tumor cells were identified using hematoxylin–eosin (HE) staining. Genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's instructions. The concentration and quality of the extracted DNA were measured using the GeneRead DNA QuantiMIZE Kit (Qiagen) before the targeted enrichment. The coding regions and exon/intron junctions of 72 oncogenes were enriched by multiplex PCR using the QIAseq Targeted DNA Human Lung Cancer Panel (DHS‐005Z; Qiagen) according to the manufacturer's instructions and sequenced using NextSeq 500 (Illumina) in 151‐base pair (bp) paired‐end reads. The average read depth of coverage was set at 3400× to allow the detection of rare mutations and to accurately estimate variant allele frequencies.
Generead dna quantimize kit
Manufactured by Qiagen
Sourced in Germany
The GeneRead DNA QuantiMIZE Kit is a laboratory equipment product designed for the quantification of DNA samples. It provides a reliable and accurate method to determine the concentration of DNA in a given sample.
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Lab products found in correlation
5 protocols using generead dna quantimize kit
1
Targeted sequencing of lung cancer
2
FFPE DNA Extraction Optimization
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DNA was isolated from LCM caps using GeneRead DNA FFPE Tissue Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol. However, the deparaffinization step was omitted starting with the proteinase K digestion step followed by incubation at 56°C for 16 hr. Quality and amplifiable DNA material was assessed with the GeneRead DNA QuantiMIZE Kit (Qiagen, Valencia, CA).
3
Targeted NGS Gastric Cancer Panel
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The DNA extracted from captured cells was quantified and assessed on quantitative PCR (qPCR) using a GeneRead DNA QuantiMIZE kit (Qiagen), and input DNA volume for subsequent NGS adjusted according to the manufacturer's recommendations. Target exon enrichment was performed with the GeneRead DNAseq Targeted Panel V2 for gastric cancer designed to analyze 29 human gastric cancer‐relevant genes (Qiagen). Following the qPCR‐based quantification of NGS libraries using a GeneRead DNAseq Library Quant Array (Qiagen), deep sequencing was performed on the MiSeq platform according to the manufacturer's instructions (Illumina, San Diego, CA, USA) at Okayama University Hospital Biobank.
4
FFPE DNA Extraction and Assessment
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FFPE tissue sections were purchased from BioChain Institute Inc. Samples collected by BioChain were ethically approved by an Institutional Review Board established at BioChain (registered with the Office for Human Research Protections with the registration number of IRB00008283). So samples may be purchased for this study without the requirement for project-specific ethical approval. Each 10um section was used to extract genomic DNA using GeneRead DNA FFPE Kit (QIAGEN, Germany), which contains an enzymatic step to remove cytosine deamination artifacts generated during the formalin fixation process. The quality and amplifiable portion of the extracted DNA were assessed by the GeneRead DNA QuantiMIZE Kit (QIAGEN, Germany). The detailed sample information is provided in Additional file 1 : Table S1.
5
Tumor DNA Isolation and Quantification
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The tissue section used for isolation was a 1 mm core that was removed using a TMArrayer (Pathology Devices, Winchester, MD) from the previously marked tumor area. DNA was isolated using QIAmp DNA Micro Kit (Qiagen, Valencia, CA). Manufacturer's protocol was followed with a modified condition that included an RNase A treatment immediately following overnight incubation. Quality and amplifiable DNA material was assessed with the GeneRead DNA QuantiMIZE Kit (Qiagen, Valencia, CA).
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