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Verifying NGS Samples – Dr. Yu Accelerates Oncology Research in Taiwan

Written by | Published: 02.13.2017

Prof. Sung-Liang Yu, National Taiwan University College of Medicine,

Prof. Sung-Liang Yu, National Taiwan University College of Medicine, recently shared some of his thoughts on omics and collaboration in oncology research. A portion of our (translated) discussion with Dr. Yu follows.

Tell us a Bit About Your Lab.

Dr. Yu: The Taiwanese government established a national program to address gaps between basic research and clinical service. This translational research program led to growth in pharmacogenomics, genetic analysis using next-generation sequencing (NGS), and biotechnology in general.

My work is in genetics, focused on clinical oncology research. Using NGS screening, we find many candidates for [bio]markers and potential drug targets. Our goal is to verify those targets using epidemiological and biological verifications. From there, we look for collaborations to turn our research findings into products.

What Tools Are You Using For NGS Screening?

Dr. Yu: For clinical research, the Oncomine™ Focus Assay is good because we don’t want to identify too many mutations for which clinical significance is unknown. On the other hand, the Oncomine™ Comprehensive Cancer Panel helps us to discover novel findings, and to better understand the underlying mechanism that may be involved in tumor progression, distal metastasis, and drug resistance.

If our sample quality is an issue, for example when we have very little or very poor quality samples, we will choose Ion Torrent™ Systems. The short turnaround time is good, as is the small input amount. While other systems struggle with [formalin-fixed] paraffin-embedded (FFPE) block samples and cfDNA samples, these perform well on Ion Torrent™ Systems. The higher error rates due to chemistry are a disadvantage, but for those poor samples, we can accept the data with a higher error rate.

If I choose other systems, I cannot get the data. We spend more time verifying [target] candidates discovered by Ion Torrent Systems, but it doesn’t matter; we have the opportunity to identify the right candidate.

What Trends do You See Emerging in Oncology Research?

Dr. Yu: Many recent achievements in cancer therapy arose from research to understand omics—genomic and proteomics. Our ongoing ability to improve the efficacy of therapies, and to reduce adverse effects, is rooted in our understanding of omics—this understanding will be a great help to advancing therapies in the future.

That said, cooperation among different experts is a major opportunity. We need physicians, basic scientists, statisticians, pharmaceutical experts, and leaders with a global view who can help us understand different and new kinds of knowledge. This isn’t a scientific bottleneck.

For Research Use Only. Not for use in diagnostic procedures.

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