Whole genome sequencing is carried out to produce a complete set of genetic data, including coding and non-coding regions of DNA, in order to identify genetic variants not just within the exon regions, but intron regions as well. Studies have found out that approximately 15% of disease-causing variants are found in the non-coding regions, and the whole exome sequencing (WES) method would not have been able to detect them. This is because WES only covers the protein coding sequences, which only consist about 1% of the entire genome. While WES does cover most of the protein coding regions, WGS provides a complete coverage, detecting mutations in promoter regions, enhancers, suppressors, etc.
At MyGenome, we utilise the DNBseq™ technology to perform WGS. DNA fragments are amplified via Rolling Circle Amplification (RCA) to produce DNA nanoballs. Each amplicon is produced based on the original template, hence there will be low amplification bias and no error accumulation. This allows us to produce accurate data with 99.9% SNP precision/sensitivity and 99% indel precision/sensitivity. We also utilise a patterned array, whereby each spot on the flow cell is uniformly shaped and distanced. This allows high imaging efficiency, high density, high sequencing accuracy, while low duplicate rate and no index hopping. Lastly, the cPAS chemistry is used to incorporate a fluorescent probe to a DNA anchor on the DNB, followed by high-resolution digital imaging.
When gene expression profiling was introduced, it allowed scientists to reliably detect cancer formations at their early stages, increasing the chances of survival of cancer patients. However, the conventional methods of gene expression profiling require the conversion of mRNA transcripts to cDNA, followed with PCR amplification, and as with PCR amplification, production of biased data is often the major problem, which would lead to unreproducible results.
At MyGenome, we perform gene expression profiling with a digital counting technique. Conversion step of RNA to DNA is removed, instead RNA is tagged and counted at its native level, with a patented molecular barcoding technology. Therefore, there will be no PCR bias and error, producing highly reproducible results.
Quantitative PCR, or real-time PCR, is an evolution to the conventional PCR amplification as quantification of amplicons can be monitored during the amplification process instead of after the PCR reaction. The ability to measure amplicons during the exponential phase of the PCR amplification removes the post-PCR processing step, thus data is produced at higher precision, sensitivity, and resolution. It is becoming the gold standard test for accurate, sensitive and fast diagnosis for a large range of infectious agents. It is widely used for detection and quantification of chromosomal translocations and viral load, to monitor minimal residual disease after treatment and to show graft-versus lymphoma effects.