FAQs

Yes, we provide raw data for Whole Exome Sequencing (WES) and panel orders.

Raw data are typically a resource for researchers or experts that are skilled at bioinformatics. Raw data require specialized bioinformatic tools to open the files and further analyze or visualize them.

Blueprint Genetics delivers raw data in BAM and/or VCF file formats.

VCF (Variant Call Format) is a standard file format storing a list of sequence variants and their genomic positions. The VCF file does not contain detailed annotations of the variants such as the gene name or population frequency of the variant. It is ~2 MB in size.

BAM (Binary sequence Alignment Map) is a standard file format that contains sequence reads mapped to the human reference genome, including base quality and mapping quality scores.  BAM files are ~5-30 GB in size.

Please note that the file size for raw data is large and the data require further processing with bioinformatic tools to produce meaningful results. Links to commonly used and freely available tools are provided below.

• For whole exome sequencing (WES) cases, we provide unannotated VCF or BAM files.
• For panels, we provide unannotated VCF files including genetic variants detected in panel target regions, unless the full Clinical Exome raw data set is specifically requested in which case we can provide it as either VCF or BAM files.
• Note that WES raw data are not available for panel orders.
• For Single genes, raw data are only available in VCF file format.

The data can be requested by the health care provider who placed the original order or by a health care provider with whom the results have been shared in Nucleus.

Any raw data requests from an organization or institution other than the original ordering organization or institution require a PHI Release form signed by the patient / legal representative. Please contact our Support for further assistance at support.us@blueprintgenetics.com.

Download the correct form to request raw data for the order in question. Complete the Raw Data Request form and send it to us by land mail or fax.  Please do not send by e-mail. Please note there are separate Raw Data Request forms for WES raw data and panel raw data.

Alternatively, you can request raw data at the time you order a single gene, panel, or WES for your patient by sending the Raw Data Request form with the patient sample and test requisition or by attaching the form to Nucleus at the time you create your order. Please note that it is now possible to attach documents in Nucleus after placing an order.

The data can be requested up to 2 years after the initial report.

The data are delivered approximately 1 month after the results are reported, and the request and all required forms are received.

You will receive an email notification and instructions for downloading the data from our Support team. There will be a download link which will remain active for 30 days. Please download the data as soon as you receive the download link to ensure enough time for technical assistance should it be needed. If the data are not retrieved during that 30-day window, a new link can be requested by contacting Support.

Raw data for WES and panels requested within two years after the original report is provided at no cost. For Panel orders, Clinical Exome raw data are available for a fee. Contact our Client Support for more information on pricing.

The file size can be large, so we recommend that you reserve several hours for the download. It is possible to use a web browser to download the files, but we encourage you to use a command line utility to download files on a computer that is capable of storing and processing large quantities of data.

• The VCF file size (~2 MB) is not typically problematic in size for a regular computer. VCF files require bioinformatic tools for processing. However, it can be opened in any text editor or Excel after unzipping the gz-formatted VCF file.
• With BAM files (~20-30 GB), it is important to use a computer that is capable of storing and processing large quantities of data. One can use bioinformatic tools to access the BAM file and make variant calls (which generates a VCF) or visualize sequence reads and variants.

Analysis of the raw sequence data requires bioinformatics expertise and software.

For annotation and analysis of sequence variants in the VCF file there are several commercial and noncommercial tools available. Commonly used and freely available command line tools include:

• VEP (https://www.ensembl.org/info/docs/tools/vep/index.html)
• ANNOVAR (http://annovar.openbioinformatics.org/en/latest/)
• SnpEff (http://snpeff.sourceforge.net)

There are also several commercial and noncommercial web browser-based or stand-alone software for variant annotation and analysis. For sequence read analysis, GATK is one of the most commonly used toolkits https://software.broadinstitute.org/gatk/.

To visualize the content of VCF or BAM files in genomic context the Integrative Genome Browser (IGV) can be used, both as a stand-alone application and a web-browser interface.

http://software.broadinstitute.org/software/igv/.

Blueprint Genetics provides technical instructions and general assistance for receiving and downloading the data. However, we do not provide assistance with the bioinformatic analysis of the raw data. To support the work of clinicians, Blueprint Genetics has already provided a thorough clinical analysis and interpretation of the data in the Clinical Statement.