Genotyping Only Projects: Frequently Asked Questions
How long will it take to receive my results?
Sample timeline is highly dependent on project sample size and QC resolution turnaround time. Typically this ranges from 7-28 days. If there are QC fails and replacement samples are being sent, this will delay release dates. Our project managers will do our best to communicate estimated timelines with you.
What happens to samples that fail QC?
Samples that fail QC are not eligible to proceed. A single sample may be excluded from the project or in cases where the failing sample is critical to the analysis (i.e. the proband in a trio) the entire family will be excluded.
What if I’ve received notification that one or more of my samples has failed QC?
If a clerical error on the manifest has caused the sample to fail the sex check, you may notify the NWGC of the need to correct a manifest.
If a sample has failed due to a sex conflict or due to insufficient concentration, you may submit a replacement sample by filling out a new manifest and describing the replacement sample. New barcoded plasticware will be sent to you for your resubmission. Submission of replacement samples will delay the start of your project.
Why did my sample fail on the genotyping/methylation assay?
Each Illumina Infinium Array kit has a typical call rate cutoff that varies based on the chip used. (generally ~98%). The Illumina data analysis software calculates and reports a detection p-value, which represents the confidence that a given transcript is expressed above the background defined by negative and positive control probes, providing a good overall QC indicator. An unusually low number of detected transcripts could result from a number of causes such as high background on the array, low signal, poor stringency or poor sample quality. This sample may not have had a similar number of transcripts detected compared to all other samples on the BeadChip, resulting in a call rate below the assay threshold.
In what format will I receive my results?
Our project managers will work with you to generate a custom final report for your samples. The file type for your results will depend on the type of genotyping assay technology selected. Raw data files (idat) may also be sent upon request.