Ashkenazim Son FFPE Reference Standard curl

This quality control product is ideally suited for:

– 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

– Determining the limit of detection (LOD) of the analytical 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

Expiration: 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)

Bioinformatic information available from public sources:
– 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