The benefits of bioinformatics in genomics sequencing

Dr Bongcho Kim is the new CEO of Macrogen Europe, a Netherlands-based provider of genomic sequencing services. Dr Kim’s appointment comes at a time of sustained growth for the company, which is benefitting from the rapidly expanding sequencing market. He talks to Lu Rahman and explains the important role of bioinformatics in genomics.

LR: Could you tell us about your background and career?

BK: I received a PhD in pathology from Seoul National University, studying gene expression mechanisms related to fibrosis. As a postdoc, I studied stem cell differentiation and the cellular senescence induction mechanism of cancer cells. While I was still working in research, I first came into contact with Macrogen and I used their genome analysis service.

In 2013, I joined Macrogen’s clinical service development team. I was the Head of the NGS overseas sales department and the planning and coordination department – and subsequently the managing director of the technology innovation division, responsible for the technical implementation of all of Macrogen’s services. On 1 March 2021, I was appointed CEO of Macrogen Europe BV and began my career in the Netherlands.

LR: What are the key developments and opportunities in the genomics market?

BK: The genomics market has made great strides in the last ten years due to the fast-paced development in both analytical technology and equipment. In particular, the growing capacity of sequencing equipment has led the genomics analysis market. However, in recent years, not only the research-oriented genomics market, but also the direct-to-consumer (DTC) genetic test market is expanding along with the clinical genomics market for diagnosis. Therefore, in addition to sequencing capacity, the analytic bioinformatic pipelines and the power of its content determine its competitiveness.

The future of medicine is often described as one of precision medicine or personalised medicine, and obviously genomic analysis plays a key role in this development. In the field of clinical genetic research we see this trend very clearly with a rapid increase in ways of effectively identifying genetic variations with high-depth data by targeting a customisable gene set desired by the researcher.

There are also enormous opportunities in the field of single cell RNA sequencing. With improvements in pre-sequencing steps such as library preparation it has become possible to analyse genetic variation and gene expression in unprecedented detail at the single cell level. And the possibility to combine this level of genomic detail with information on the location of a cell within a histological section – through spatial transcriptomics – opens up even more opportunities for studying individual cells.

In the field of epigenomics the increasing capabilities of ATAC-seq are very interesting. This stands for “assay for transposase-accessible chromatin using sequencing” and can be used to study chromatin accessibility, for example in cancer and other diseases. These technological improvement are likely to lead to a significant increase in their application areas.

LR: Could you give us a brief overview of Macrogen Europe?

BK: Macrogen Europe provides genomic sequencing services for clients across Europe and Africa. We work with universities and research institutes – as well as scientists working in industry and clinical research. We support our clients on projects of all sizes, ranging from just a handful of samples to large multicentre genomic studies.

Macrogen Europe came into existence in 2008 as a branch office of South Korea-based Macrogen Inc, which has been active in the genomics market since its foundation in 1997. We are based on the grounds of the Amsterdam Medical Centre (AMC) in the Netherlands (pictured) where we recently moved to a new facility with increased lab space to help us meet the increasing demand for sequencing services. In 2017, we became a subsidiary, Macrogen Europe BV, but we maintain a close collaboration with the teams in South Korea and across the globe – and benefit enormously from their genomics expertise.

We provide Sanger sequencing (also known as capillary electrophoresis sequencing, CES) and a number of next generation sequencing (NGS) workflows using platforms such as Illumina and Pacific Biosciences.

These NGS services include whole genome and whole exome sequencing, but also deep sequencing of targeted gene panels commonly used, for example, in oncology. We also offer RNA sequencing services such as whole transcriptome, mRNA and single cell RNA sequencing, which, among other applications, can help researchers in drug discovery determine changes in gene expression in response to a novel compound. A final area that has seen increased interest in recent years is metagenome sequencing used for example to analyse the interactions between a drug and the human microbiome.

LR: Why is bioinformatics an important area for drug discovery and how can it help improve efficiencies and workflows for the research market?

BK: In the era of a global Covid-19 pandemic, it is clear that there is a growing interest in producing effective vaccines and developing new drugs more precisely and rapidly. In particular, the rapid development of the Covid-19 vaccine was possible because researchers rapidly analysed the Sars-CoV-2 genome. Bioinformatics has played an essential role in the scientific understanding of biological phenomena and a vast amount of high-throughput genomic data was produced within a short period of time due to the advancement of sequencing equipment and computing sources. These recent successes have made it possible to apply similar approaches in other fields as well.

In the development of new drugs, bioinformatics makes it possible to create animal models for specific diseases more effectively. By selecting drug candidates that can directly target the cause of a disease and verify the effect of a treatment, it is possible to develop treatments more efficiently and economically than with traditional research methods. In addition, it can be used through companion diagnostics (CDx) that pre-emptively select subjects and patients based on the genomic analysis information to ensure safe and effective drug responses in clinical trials and treatments for new drugs.

By reducing the costs and time required for drug development, bioinformatics plays an important role in helping to realise personalised medicine. It does this, for example, by using available genomic information for understanding disease mechanisms, preferentially selecting molecular targets and accurately picking compounds that can control the expression pattern and function of the target.

LR: What is Macrogen Europe currently offering in bioinformatics that would be useful for drug development and discovery?

BK: We are offering a range of different bioinformatics analyses for all of our sequencing services. This includes standard as well as advanced analyses. Standard analysis can include variant calling for single nucleotide polymorphisms (SNPs) and indels, but also mapping and expression profiling in the case of RNA sequencing. Examples of advanced analyses include gene prediction, gene annotation and population analysis.

Macrogen Europe is evolving with a focus on customised precision genomics. In the past, we have mainly focused on services such as whole genome, whole exome and transcriptome sequencing, but we are now broadening our offering in various ways to meet the needs of our clients. For example, we are expanding our targeted sequencing service with bioinformatic analysis of genes desired by clients, so that they receive comprehensive reports with the analyses they need to move their projects forward. We are currently investing in additional facilities to construct an even broader range of bioinformatic pipelines.

As the first step, Macrogen Europe has recently acquired an additional NovaSeq 6000: a high-throughput sequencer that is recognised worldwide for the enormous amount of data it generates with every run. In the second step, we want to create a systematic bioinformatics analysis infrastructure and a quality control process that is unique to Macrogen Europe. To achieve this we will strengthen our computing power and secure additional data storage servers to provide fast and high-quality mass data to research institutes, hospitals and institutions across Europe. As a third step, we plan to build our own database so that we can discover and utilise new biomarkers for various diseases through excellent DNA sequencing facilities and analytic infrastructure and provide them to our clients.

LR: Where do you see this market heading – its potential and opportunities that researchers will be able to use to improve efficiency?

BK: The Covid-19 pandemic has clearly demonstrated – not just to the life science industry, but also to the wider public – the critical importance of speed in drug and vaccine development. However, the same crisis has also shown how much the industry and regulatory bodies can achieve when the stakes are higher than ever. Going forward, these achievements will be extremely valuable in determining future strategies for speeding up drug development without compromising on safety.

For us as a genomics service provider it is essential that we support scientists in this process by offering fast results, but also by offering a broad and flexible portfolio of services that makes it as easy as possible for researchers to work with us and take away bottlenecks in their workflow. We do this by offering a comprehensive end-to-end solution to those that need to minimise time investment – and a highly customisable service to organisations where seamless integration into their existing workflow is critical. This combination provides our clients with the confidence that outsourcing helps them speed up their research with reliable data and insightful analyses.

Volume 22, Issue 3 – Summer 2021

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