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 Mr Pua Chee Jian Edmund
For further information please contact our Genomics & Metabolomics core facility from Monday to Fridays (except public holidays), 8.30am to 5pm, at:
Tel: (65) 6704 2199
Prof Stuart Cook | Distinguished Clinician Scientist, NHCS; Core Lead, NHRISDr Edmund Pua Chee Jian | Senior Research Associate, NHRISMs Lim Shiqi | Research Associate, NHRIS
(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
(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.
Illumina NextSeq 500
Applied Biosystems 3500 Series Genetic Analyzer
Perkin Elmer Caliper Sciclone G3 and LabChip GXii Touch System
Custom gene panel design and bioinformatics support
Whole Exome Sequencing
Bulk RNA sequencing
Single cell RNA sequencing
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.
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.
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