Library Construction & Sequencing: Frequently Asked Questions
Sample Submission
What types of samples are accepted?
We accept DNA and RNA samples that are plated in our designated barcoded plates.
What are the DNA requirements for submission?
Requirements for submission vary depending on the scope of a project. Please contact us for more information.
When submitting a manifests for multiple plates, can I submit one spreadsheet, but put the different plates on separate tabs?
No, please submit one manifest spreadsheet per DNA plate.
Can I use subjects first and last names as sample IDs?
No, do not use subject names. Please do not send any information that links to subject identity.
Can I alter the submission manifest?
You may add columns, but do not remove columns or change the names of any of the columns.
There are hidden rows in the manifest, may I remove them?
No, those are hidden rows that are needed for entering the manifest into our LIMS.
May I send my samples at room temperature?
Since we do not accept samples in screw-top lids, please do not send samples at room temperature. Samples that are packed frozen and that stay frozen during delivery are much less likely to contaminate each other.
I am in the Seattle area. May I pick up my plate and bring it back when I’ve aliquoted out my DNA?
Yes, please feel free to drop by the lab. We can send instructions for how to reach us.
QC
What happens to samples that fail QC?
Samples that fail QC are not eligible to proceed into the sequencing pipeline. 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.
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 describing the replacement sample. Submission of replacement samples will delay the release of data for your project.
Sequencing
What is the turnaround time for sequencing?
Turnaround time greatly depends on the size and scope of a project and what is currently in our queue. However, on average it takes approximately 8-12 weeks after all samples in the project pass QC for data to be released. Projects with a large number of samples may require extra time for sequencing before all samples are finished.
Data Delivery
How will I know when my data are available?
You will receive an email notifying you of data release.
What data do I get back from the NWGC?
You will receive the following files: bam, bam index, multi-sample vcf, sample ID lookup table, genotype data (if applicable), and SeattleSeq annotation.
Can the NWGC provide FASTQ files in addition to bam files?
You can generate FASTQ files from the BAMs received in data release. Instructions.