Product description
This quality control product is ideally suited as reference material in clinical genomics workflows. In particular:
– Validation and development of extraction protocols
– control in sequencing protocols (e.g. Whole Genome Sequencing (WGS), Whole Exome Sequencing (WES), Amplicon Sequencing) and PCR protocols
– Determination of the detectiont limit of a method
– Calibration and development of instruments and workflows in DNA processing (e.g. DNA fragmentation via acoustic shearing, enzymatic digestion or sonication)
– Analyze the performance of your NGS pipeline by comparing to freely available datasets
– routine performance monitoring (Research Use Only)
Product Overview
Format: FFPE (Formalin Fixed Paraffin Embedded)
Unit size: 5 FFPE curls
Quantity per vial: 1 FFPE curl
Expected DNA yield: ≥ 400 ng (using Qiagen AllPrep DNA/RNA FFPE kit)
Expected RNA yield: ≥ 400 ng (using Qiagen AllPrep DNA/RNA FFPE kit)
Thickness of one curl/cut: 10 µm
Mutations:
Wild type for most tumor relevant mutations. The genome was sequenced using various methods (see below) and tested orthogeneously for specific mutations using ddPCR.
Allelic frequency: No
Storage: 2-8 °C
Expiry: stable for 24 months from date of manufacturing (as supplied)
Quality Control (DNA)
Allelic Frequency (metrologically traceable): ddPCR (Bio-Rad)
Quantification (metrologically traceable): Fluorometric dsDNA measurement (Qubit)
DNA Quality: Agarose gel electrophoresis
Quality Control (RNA)
RNA Quantification: Fluorometric RNA measurement (Qubit)
Quality Control (other)
Cell Density:
1. Visual via microscopy
2. Calibrated measurement
Technical Background
Derived from:
The Genome In A Bottle (GIAB) cell line from the Personal Genome Project (PGB): GM24385 (HG002- NA24385 – huAA53E0 – Ashkenazim son)
Bioinformatics:
– Lot specific sequencing files: LOT Search
– High-confidence variant calls: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio
– Raw datasets and bam files, currently including 10X Genomics, BioNano, Complete Genomics regular and LFR, 300x Illumina paired-end, Illumina 6kb mate-pair, 1000x Ion exome, custom moleculo libraries, ~0.05x Oxford Nanopore, and 70x/30x/30x PacBio: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/
* GRCh38 · COSMIC v90
