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Genomics & Metabolomics

Background

Genomics and metabolomics are crosscutting technologies that enables molecular dissection of disease subtypes and mechanisms. Our core is equipped with 3 next-generation sequencers (NGS) as well as supported by multiple targeted gas and liquid chromatography mass spectrometers from the Duke-NUS metabolomics core facility (led by Asst Prof Jean Paul Kovalik, www.duke-nus.edu.sg/research/research-facilities/metabolomics-facility) that was relocated to NHCS in Year 2018 to expand research capability for metabolomics analyses. These state-of-the-art equipment and skillsets enable basic science and translational research into the genome, transcriptome, proteome and metabolome of cardiometabolic diseases. This ‘one-stop’ resource allows scientists to incorporate new genomics and metabolomics data into their studies. Together with NHCS Biobank and other NHRIS core facilities, the core is aimed to build phenotype-genotype-metabolomics profiles in the Asian context, bridging the gaps in national (SG100k) and global precision medicine initiatives.

We support multiple NGS analyses based on Illumina platform such as gene panel design, targeted DNA-seq, bulk RNA-seq, miRNA-seq and single cell RNA-seq. This knowledge enable scientists to translate basic research into meaningful insight concerning challenges by many diseases.

Prof Stuart Alexander Cook.png           Pua Chee Jian Edmund.png

                                                Prof Stuart Alexander Cook            Mr Pua Chee Jian Edmund


Contacts:

For further information please contact our Genomics & Metabolomics core facility from Monday to Fridays (except public holidays), 8.30am to 5pm, at:

Email: genomics@nhcs.com.sg

Tel: (65) 6704 2199
Prof Stuart Cook | Distinguished Clinician Scientist, NHCS; Core Lead, NHRIS
Dr Edmund Pua Chee Jian | Senior Research Associate, NHRIS
Ms Lim Shiqi | Research Associate, NHRIS


Expertise

Genomics Metabolomics.png


Genomics:

(1) Clinical grade (ISO15189:2012) NGS genetic tests for inherited cardiac conditions; (2) Targeted re-sequencing of panels; (3) Whole Exome Sequencing (WES); (4) Sanger sequencing (5) mRNASeq and ChiPSeq; (6) Single-cell RNA-seq (7) Sanger sequencing; (8) Bioinformatics analyses and data storage; (9) Gene differential expression analysis (bulk/single-cell); (10) Custom gene panel design


Metabolomics analyses:

(1) Amino Acids; (2) Acyl Carnitines; (3) Free/Total Carnitines; (4) Organic Acids (TCA cycle intermediates); (5) Sphingolipids & phosphatidylcholines; (6) 1-Methylhistidine; (7) Tryptophan metabolism pathway.


Methodology

Equipment:

Illumina MiniSeq

  • Medium throughput next generation sequencer
  • Read types: paired-end; single-end
  • Read cycles: 50, 150, 300

Illumina MiSeq

  • Medium throughput next generation sequencer with longer read cycles
  • Read types: paired-end; single-end
  • Read cycles: 50, 150, 300, 600

Illumina NextSeq 500

  • High throughput next generation sequencer
  • Read types: paired-end; single-end
  • Read cycles: 75, 150, 300

Applied Biosystems 3500 Series Genetic Analyzer

  • Sanger sequencer

Perkin Elmer Caliper Sciclone G3 and LabChip GXii Touch System

    • Automated NGS library preparation and quality check
    • Up to 96 samples


      Services:

      Custom gene panel design and bioinformatics support

      • Common and rare diseases

      Targeted re-sequencing

      • Illumina TruSight panels

      Whole Exome Sequencing

      • Illumina Nextera Rapid Capture exome kit
      • Illumina Nextera Rapid Capture expanded exome kit

      Bulk RNA sequencing

      • TruSeq stranded mRNA kit
      • TruSeq total RNA kit
      • TruSeq small RNA kit

      Single cell RNA sequencing

      • Single cell gene expression kit

      Sanger sequencing

      • 8 capillaries


      Research Area

      Inherited Cardiac Conditions (ICC) are a diverse group of heart conditions including cardiomyopathy, arrhythmic disorders, aortopahties and lipid disorders such as falimial hypercholesterolemia. They can affect people of any age, and can be life-threatening so improving diagnosis is important for effective treatment. We use the commercialized TruSight Cardio panel and in-house bioinformatics pipeline to study Inherited Cardiac Condition (ICC) genes among patient/research samples to define novel pathological mutations that are unique to Asian including Singaporean. These mutations will be used to stratify sub-disease and we hope to use this information to pin down the underlying cause.

      We are also interested to investigate the fundamental cause and therapeutic targets of cardiometabolic diseases using genomics and metabolomics technologies. We provide genotyping, DNA sequencing, bulk and single cell RNA sequencing services for research projects involving heart, kidney, lung and liver in cardiometabolic diseases.

      Achievements

      We have developed jointly with Royal Brompton Hospital, a genetic test kit that uses high-throughput DNA sequencing technology to look for variation in 174 genes that can cause inherited cardiac conditions (ICC). The test panel was commercialized by Illumina as the TruSight Cardio Sequencing Kit and available globally for clinical diagnostics of inherited cardiac conditions and case-control research study. Using local case-control cohort that we have recruited over the past 8 years, we identified two common variants in TNNI3 and TNNT2 in the Chinese hypertrophic cardiomyopathy (HCM) patients. The re-classification of both troponin variants is expected to affect nearly 200,000 HCM cases worldwide in the clinical care settings. At NHCS, we also use NGS technology to sequence cases of sudden unexplained death for the Health Services Authority (HSA) and up to 30% cases have likely pathogenic variants to explain the cause of death.


      Awards

      • The President’s Technology Award 2018 was awarded to Prof Cook for his research in human genetics.
      • The lab is accredited by the Singapore Accreditation Council to ISO 15189:2012 (Medical laboratories) for clinical grade ICC genetic test


      Publications

      1. Pua, C. J., Tham, N., Chin, C. W. L., Walsh, R., Khor, C. C., Toepfer, C. N., . . . Cook, S. A. (2020). Genetic Studies of Hypertrophic Cardiomyopathy in Singaporeans Identify Variants in TNNI3 and TNNT2 That Are Common in Chinese Patients. Circ Genom Precis Med, 13(5), 424-434. doi:10.1161/circgen.119.002823 
      2. Mazzarotto, F., Tayal, U., Buchan, R. J., Midwinter, W., Wilk, A., Whiffin, N., . . . Walsh, R. (2020). Reevaluating the Genetic Contribution of Monogenic Dilated Cardiomyopathy. Circulation, 141(5), 387-398. doi:10.1161/circulationaha.119.037661 

      3. Schafer, S., de Marvao, A., Adami, E., Fiedler, L. R., Ng, B., Khin, E., . . . Cook, S. A. (2017). Titin-truncating variants affect heart function in disease cohorts and the general population. Nat Genet, 49(1), 46-53. doi:10.1038/ng.3719 

      4. Walsh, R., Buchan, R., Wilk, A., John, S., Felkin, L. E., Thomson, K. L., . . . Cook, S. A. (2017). Defining the genetic architecture of hypertrophic cardiomyopathy: re-evaluating the role of non-sarcomeric genes. Eur Heart J, 38(46), 3461-3468. doi:10.1093/eurheartj/ehw603 

      5. Pua, C. J., Bhalshankar, J., Miao, K., Walsh, R., John, S., Lim, S. Q., . . . Cook, S. A. (2016). Development of a Comprehensive Sequencing Assay for Inherited Cardiac Condition Genes. J Cardiovasc Transl Res, 9(1), 3-11. doi:10.1007/s12265-016-9673-5