Analysis methods

Technology

Blueprint Genetics is applying a powerful molecular biology approach called next-generation sequencing to analyze patients’ DNA. Changes in DNA sequence can cause errors in proteins and result in severe medical conditions. Hereditary diseases are caused by mutations originating in germ cells and presenting in all cells of an individual. Determining the underlying DNA changes creates opportunities to diagnose hereditary diseases, estimate the prognosis, and select adequate preventive treatments.

Next-generation sequencing is enabling comprehensive analysis of thousands of clinically relevant target genes in a time frame that facilitates clinical actions. DNA sequencing detects different types of mutations exchanging single nucleotides (point mutations) or adding or removing nucleotides (insertions and deletions).

With targeted sequencing, it is possible to identify all mutations that have been previously linked to specific genetic disorders as well as novel variants in the disease-associated genes.

Blueprint Genetics’ platform

High-quality exome capture is performed using an in-house designed WES platform and the Illumina NovaSeq sequencing system.

Targeted sequencing with NGS technology

In general, targeted sequencing refers to all technologies where a selected portion of the genome is sequenced bringing cost effectiveness into the process. The most common targeted sequencing approach is whole exome sequencing (WES) where specific molecular probes are used to capture DNA from coding regions of >20,000 human genes. The process leaves out non-coding regions (>98.5%) of the human genome. In context of specific phenotype driven gene panels, the target genes may be selected before or concomitantly with sequencing or sliced out from WES data. In WES, patient’s sample is prepared by adding sample specific DNA adapters to the ends of the DNA fragments, capturing specific genomic regions by hybridization and amplifying the sequencing libraries using PCR.

In the sequencing instrument, sequencing library that has been prepared from the patient’s DNA is flushed through the sequencing flow cell. Flow cell is a fluidics device where the DNA fragments in the sequencing library are sequenced. Millions of DNA fragments attached to the flow cell surface form clusters of thousands of identical molecules. Each molecule on the flow cell is sequenced using sequencing-by-synthesis approach where fluorescently labelled nucleotides latch on to the ends of the growing DNA strands and images are captured. Sequencing proceeds in cycles where old labels are cleaved off, new labelled nucleotides are added and the imaging process is repeated. The images reveal all the bases and their order in each of the immobilized DNA fragments. The information content on the images is 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. Each exome 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.

High-quality analysis

In average, 99.4% of base pairs in target region covered at least 20x depth

Highly uniform sequencing depth across all target genes

>99.7% sensitivity and 99.9% specificity for SNPs

96.9% sensitivity for 1-10 bp indels

Reportable range of insertions 1-221 bp

Reportable range of deletions 1-210 bp