Sample Prep & Sequencing: Quality Control
The NWGC performs multiple QC steps on DNA samples prior to sequencing.
All samples are tested using the Quant-iT Broad Range dsDNA kit (Invitrogen) to measure DNA concentration.
Sample Sex Assay
All samples are tested using an ABI TaqMan assay specific for X/Y chromosomal regions. A definitive sex genotype is generated for each sample. These data will be compared against the reported sex from the submitted sample manifest.
The investigator will receive an email and a report detailing any QC failures. Samples that fail QC are not eligible to proceed into the sequencing pipeline. QC issues will need to be resolved by the investigator before the project can proceed to sequencing.
Resolution of QC Failures
If a sample has failed due to a sex conflict or due to insufficient concentration, the investigator may submit a replacement sample by filling out a new manifest describing the replacement sample. Submission of replacement samples will delay the release of data for the project.
If a replacement sample is not available, a single sample may be excluded from the project. In cases where the failing sample is critical to the analysis (i.e. the proband in a trio) the entire family will be excluded.
Prior to sequencing, all samples are genotyped using one of the following methods:
- 547,644 markers found on the Illumina Infinium HumanCoreExome Bead Chip.
- 64 high frequency, exome-specific SNPs using custom made OpenArray plates via QuantStudio 12K.
These genotyping data are used to assure that the sequencing data are concordant with the DNA sample fingerprint and that sample tracking integrity is maintained. The Human CoreExome data can also be used for linkage analysis. The investigator will be informed if a sample fails the genotyping assay twice and the sample will not be eligible to proceed into the sequencing pipeline.