Cancer Research Malaysia (CRMY) houses nine science units, each serving a unique purpose ranging from laboratory research to social engagement initiatives. Continuing with our Behind The Scenes series, we now engage with Dr. Pan Jia Wern, Deputy Head of Genomics and Bioinformatics (GB). He will be shedding light on the department’s projects, notable accomplishments, and the dedicated team that stands as the foundation within this unit.
1. Could you please explain the role and responsibilities of the Genomics and Bioinformatics unit within CRMY?
The Genomics and Bioinformatics department at CRMY plays a crucial role by supporting various scientific teams. Our responsibilities revolve around managing and interpreting complex data to aid in understanding and treating cancer better.
We provide essential technical support, ensuring that the tools and resources required for different research projects are available and working efficiently.
One of our main tasks is dealing with special information from tumors, which are the unhealthy cells that cause cancer. The information comes in two forms; DNA (provides the code for the cell’s activities) and RNA (converts that code into proteins to carry out cellular functions) which hold important information about what causes cancer. Additionally, we manage special pictures of tumor tissues called digital pathology data. These pictures help scientists understand what tumors look like up close. But the most exciting part is when we use computers to study all this information and look for special signs that can help predict how a cancer might behave or how it could respond to different treatments. It’s a bit like detectives looking for clues which can be used to create new cancer vaccines or to find new uses for existing drugs, all with the aim of treating cancer better.
2. What technologies or tools does the GB unit utilize to analyse and interpret genomic data effectively?
Our department uses a variety of high-tech tools and clever methods to make sense of the genetic data we are working with. One of the tools is called next-generation sequencing, that helps scientists to read and understand the genetic information in tumors. It’s like a super-powered microscope that can read the tiny details of our genes.
We also use another tool called AI and machine learning, which is like having a computer that can learn and make smart guesses. These tools help us find hidden patterns in the data that human eyes might miss. To handle all this data and processing, we rely on cloud computing, which is like a super-fast and secure storage and processing space on the internet. And in order to help others see and understand our team’s discoveries, we use data visualisation to transform dull numbers into vibrant images that narrate a tale using graphs and charts.
3. Why is the GB unit considered crucial or significant in the overall operations of CRMY?
Our Science Unit holds a key role within CRMY for some good reasons. First off, in today’s world of biology, computers are like trusty companions. We are computer experts who provide crucial help to other teams whenever they need it. Imagine how computers help you with your homework – that’s what we do for the other teams with their research.
Furthermore, we play a vital part in translating patient data into concrete targets and biomarkers. These become the building blocks for other teams to further investigate, validate, and eventually test in clinical trials. In essence, we bridge the gap between raw data and real-world applications.
4. How many individuals are currently part of the GB unit, and what are their respective roles and expertise?
There are 5 people within the GB unit (me included) and each person contributing different skills and experience. At the moment, the team comprises the following members:
- Dr Pan Jia Wern – As the Deputy Head who leads the unit, I oversee the multifaceted projects undertaken by the unit, ensuring their effective execution and alignment with the department’s goals.
- Dr Yeo Li Fang – Her specialty is studying the gut microbiome in connection with cancer. Through projects like MIBIO and MyBrCa 2.0, Li Fang investigates how these microorganisms in the gut can impact people with cancer.
- Haslina Makmur – Her focus lies in digital pathology and spatial analysis. Halina dedicates her time to analysing immune markers from breast cancer image data, paving the way for insights into the immune response.
- Tan Min Hui – Her work is to investigate fusion transcripts and neoantigens where she engages in selecting targets for other teams like CIIT (Cancer Immunology & Immunotherapy), aiming to enhance cancer treatment strategies.
- Tan Zi Ching – She is the resident AI and machine learning expert. Zi Ching assists in diverse projects that use AI and machine learning analysis, contributing valuable insights to the team’s endeavors.
5. Can you expand on the collaborative efforts between the Genomics and Bioinformatics unit and other science units within CRMY?
Collaboration is at the heart of our work and we try to join forces with every science unit within CRMY to enhance our research:
- CPPS (Cancer Prevention and Population Science) – We combine our tumor data with their clinical and genetic information to uncover new insights about cancer.
- CIIT (Cancer Immunology & Immunotherapy) – We work together to find potential targets for creating cancer vaccines. Once we suggest these targets, CIIT tests them to see if they are effective.
- TCB (Translational Cancer Biology) – We contribute by assisting in the analysis and validation of targets for repurposing drugs in head and neck cancer. This teamwork accelerates the process of finding effective treatments for this specific type of cancer.
- DH (Digital Health) – We support their computing needs for the Mobile Mouth Screening Anywhere project or more simply known as MeMoSA, by helping to set up cloud computing to gather and analyse data. This is where digital health and data science intertwine to improve healthcare outcomes.
- CT (Clinical Trial) – We offer valuable biomarkers to be used in clinical trials. These biomarkers help figure out how well treatments are working. We also provide technical support for these trials, ensuring the data is properly analysed and interpreted.
- CL (Core Lab) – They gather and prepare tissue samples, which our team will subsequently analyse by processing the data from sequencing these samples. This contributes to a comprehensive research process aimed at gaining deeper insights.
6. Could you provide examples of how the findings from genomics and bioinformatics research have directly impacted clinical practice or patient outcomes?
Our research has directly influenced patient care. For example, our findings provided biomarkers for important trials like AUROR and TENOR. These trials have given patients access to new treatments, especially in Asia. AUROR is the first trial in Asia using a genetic marker common in Asians whereas TENOR explores if a treatment helps aggressive breast cancer patients survive longer. These clinical trials are an example of how our research can lead to better treatments and outcomes.
7. What specific research projects or studies is the GB unit currently involved in, and what are their objectives?
We are engaged in a range of impactful research projects, each carrying distinct objectives. For starters, we are studying neoantigens, unique markers in cancer cells, to develop groundbreaking cancer vaccines. By analysing genetic data from cancer patients, we also work to uncover new biomarkers for better cancer treatment, especially in immunotherapy. Using artificial intelligence, the team also hopes to automate the analysis of digital pathology data to swiftly identify patients needing immediate attention.
Additionally, the department is also investigating the connection between tumors and the gut microbiome in cancer patients, aiming to better understand how microbiomes affect responses to immunotherapy. Furthermore, we are conducting detailed analyses of combined tumor and genetic data to discern how Asian patients’ needs differ from others, potentially leading to specialized treatments. These ongoing projects showcase the department’s commitment to advancing cancer care through innovative research.
8. What would you consider to be the most significant achievement of the Genomics and Bioinformatics Unit to date?
I’m proud to say that our greatest achievement to date is leading significant clinical trials like AUROR and TENOR because we provided vital data and scientific reasoning to kick-start these trials. AUROR is especially notable as the pioneering trial in Asia using a genetic marker common in Asians, a big step towards personalised cancer treatment for Asians. Meanwhile, the TENOR study explores if a PARP inhibitor can enhance survival for aggressive triple negative breast cancer patients.
9. What is the most significant challenge that the Genomics and Bioinformatics Unit has encountered and how it was addressed?
One of the biggest hurdles our team faced was handling vast amounts of data. We had to start from scratch, creating systems and pipelines to manage it effectively, essentially laying the groundwork for efficient data handling. Furthermore, the significant computing power required for data processing led us to depend on cloud computing services, though this approach comes with significant cost considerations. We managed to handle the issues by combining tailored systems and making careful use of external resources.
10. Looking ahead, where do you envision the Genomics and Bioinformatics Unit in terms of advancements and contributions to the field in the next 10 years?
Well, in the next 10 years we envision remarkable progress and contributions in the field of bioinformatics, especially with the integration of new AI tools. Our aim is to apply those tools to uncover new biomarkers and targets specific to Asian cancer patients, thereby leading to impactful clinical trials that reshape medical practices. The GB unit is also working to become the go-to team for all computational needs across CRMY, collaborating closely with other science units.
Head of the GB Unit
Dr Pan Jia Wern earned his PhD in Biology from Duke University in 2017, focusing on the neuronal development of Drosophila fruit flies. Upon completing his studies, he returned to Malaysia and became a valued member of Cancer Research Malaysia, assuming the role of a dedicated bioinformatician. Throughout his tenure at Cancer Research Malaysia, Dr Jia Wern has been instrumental in building and defining one of the most expansive genomic and transcriptomic databases of Asian breast tumors. This significant effort has resulted in numerous innovative discoveries and the initiation of two pioneering clinical trials centered around precision medicine, specifically tailored to benefit breast cancer patients in Malaysia.
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