Bioinformatics
Frequently Asked Questions
Where is your lab located and where will sequencing and spatial work be performed?
Our labs are located in Singapore – both in Biopolis. Our labs are fully equipped for processing of samples to be performed in Singapore. The NLG long-read sequencing NGS lab is in the Synapse building and the spatial genomics lab is a joint lab via a research collaboration with GIS and Nanostring. All sample processing, sequencing and spatial work is done in Singapore.
What types of samples do you accept and how much is required?
For all of our work, we can accept primary samples – such as blood, tissues, microbiome samples and FFPE blocks. We can extract DNA and RNA and also slice FFPE blocks into slides in our labs. We also accept extracted DNA or RNA or histopathology slides. The amount needed is dependent on the project – for whole genome sequencing, micrograms of DNA is best. For single-cell RNA analysis, nanograms of cDNA. Reach out to our specialists to discuss your projects to learn how to best proceed with samples.
Which NGS system is the best to use? Why is long-read better than short read?
No single NGS platform is perfect. Each has their own strengths and weaknesses. Long-read sequencing is superior to short-read in many aspects. With long-read data, more complex variants are easily found – things like larger deletions, insertions, rearrangements and copy number variants – which are often missed with short read data. In addition, long read allows for phasing – or determining which variants are on the same copy in the genome – maternal or paternal – and therefore inheritance or transmission of these variants can be studied. When using long-read for RNA, complete isoforms of mRNA are often sequenced completely, meaning novel splicing events are discovered that might be missed with short-read sequencing.
Is data quality and integrity an issue with long-read sequencing?
No system has 100% perfect quality scores. The latest advances in long-read sequencing, such as PacBio’s Hifi circular consensus sequencing system and Oxford Nanopore’s latest software and chemistry have improved quality to match or beat that of short-read sequencing. Quality is a measure of the probability that a base called is not the correct base found in the source DNA. One way to improve of the quality and accuracy of base calling is to perform “deeper” sequencing – or sequence each strand multiple times – sometimes 20, 30 or 60 times for each base. Random errors are then removed. In the case of long-read sequencing, since many protocols utilize direct, native DNA in the sequencing – without any amplification – errors are minimal since the DNA polymerase in the amplification can introduce errors in short-read protocols and lead to false variants.
