Ordering and sample preparation
The order process begins with you providing your patient’s medical history. This is done through Nucleus, our online portal where you can order tests, track samples, and receive your test results. The entire process is transparent, showing you at every stage what is happening with your patient’s sample.
When we receive the sample, we first check to ensure it meets the quality criteria required to produce an accurate result. If the sample is blood or saliva, it’s run through an extraction robot to acquire the DNA. We then perform a series of molecular biology techniques to prepare the sample DNA for sequencing.
First, the DNA is sheared into fragments, each comprised of about 1,000 nucleotides. Next, a synthetic DNA sequence is added to both ends of each DNA fragment during adapter ligation. These synthetic ends allow the DNA fragment to interact with the sequencing system, while also tagging the DNA to a specific patient sample. Finally, the adapted DNA fragments are copied multiple times in a process called enrichment, which produces enough of the necessary DNA for successful sequencing.
All of the methods used in this preparatory phase are tested and trusted methods of DNA sequencing preparation. A reference DNA is also prepared alongside the samples to serve as the control during sequencing. As the sequencing results for this reference DNA are known, it ensures high-quality, reliable results.
Targeted sequencing with OS-SeqTM NGS technology
When ordering targeted panels only a specific, targeted portion of the genome is sequenced using OS-Seq, making the process very fast and efficient. The prepared DNA is then loaded into the sequencing instrument. The sequencing machine uses the OS-Seq proprietary molecular biology method for selecting specific sites in the genome, while sequencing is done using standard protocol. The beauty of OS-Seq technology is that a patient’s DNA is tested using a targeted panel comprised of several disorders with similar genetic causes. As only a specific portion of the genome is sequenced, the process is very fast.
Fluids flush through the sequencing lanes in the flow cells, where the DNA fragments react with reagents and are immobilized at specific locations. When millions of DNA segments have clustered to spots on a flow cell surface, fluorescent nucleotides latch on to the exposed ligated ends of the DNA strands and images are captured. When the image capture is complete, fresh fluorescent nucleotides are added and the imaging process is repeated. The images reveal all the bases (and their order) that the sequences are comprised of. The information content on the images is then converted to raw data and extracted to text files.
Whole Exome Sequencing
Blueprint Genetics Whole Exome products target all protein-coding genes of the genome. They have been developed to maximize diagnostic yields, first of all, by generating high-quality and uniform sequencing data across the whole exome. Blueprint Genetics utilizes high-quality exome capture technology and next-generation sequencing methods to obtain deep and uniform, clinical-grade whole-exome sequencing data. When a Whole Exome product is ordered, samples are sent to Blueprint Genetics laboratory, where samples are processed as described above. DNA samples are then shipped to BGI* and after generation of exome sequencing data at BGI, data is delivered by a secure connection to Blueprint Genetics. Each exome batch is subjected to thorough quality control measures, after which raw sequence reads are transformed into variants by our proprietary bioinformatics pipeline. Finally, the variants are analyzed and interpreted in-house by our team of geneticists and clinicians.
Data analysis and interpretation
Sequencing creates a massive amount of raw data, which requires heavy processing to become clinically relevant information. The proprietary automated bioinformatics pipeline developed and used by Blueprint Genetics produces fast, reliable results. All of the software, equipment, and algorithms used are industry-standard in the field of molecular genetics, but specific parameters have been adjusted and other customizations have been made to improve data processing and analysis.
The first step in analyzing the results is quality filtering on the raw sequencing reads. This allows any uncertain nucleotides to be trimmed out of the data pool. Once the highest-quality reads have been isolated, they are aligned with the human reference genome so variant calling can begin. Variants are differences from the reference genome – hundreds may be found in any patient’s DNA, but not all the variants will be clinically relevant to the suspected disease diagnosis.
To aid in variant interpretation, Blueprint Genetics uses a comprehensive, proprietary mutation database containing only disease-related mutations. This database is comprised of information from more than 2,500 scientific publications and publicly available genetic databases. The output of the bioinformatics pipeline is a Sequence Analysis Report, which contains the detailed results of the test, related literature links, the pathogenicity evaluation, and the quality assessment.
A comprehensive clinical report
The final phase of Blueprint Genetics’ all-inclusive process is the geneticist’s statement, supported by the insight of a specialized clinician. For positive results, the report generally includes valuable insights into potential treatments while highlighting any risks the disease presents to the patient. The concluding statement is delivered to you through Nucleus, by mail, or by fax, depending on your preferences.
If the results are negative, the statement helps move toward a potential future diagnosis by ruling out one or more possibilities. The geneticist’s statement may also include recommendations for a different, more comprehensive panel when deemed beneficial. In this event, Blueprint Genetics does not generally require a new sample to run the different panel, so it’s easy for you to order a new panel if needed.
*BGI has been selected and audited as the laboratory generating whole-exome sequencing data for Blueprint Genetics Whole Exome products. BGI is one of the leading next-generation sequencing laboratories in the world, has CAP accreditation and a proven track record with providing next-generation sequencing for several international clinical collaborators. Blueprint Genetics ensures high quality and uniform sequence data for each exome by inclusion of stringent quality control steps in the analysis process.