Joanna Tan
A5071096894- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Lung Cancer Treatments and Mutations
- Single-cell and spatial transcriptomics
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
- Genomics and Rare Diseases
- Genetic Associations and Epidemiology
- Chronic Myeloid Leukemia Treatments
- Research Data Management Practices
- Cancer-related gene regulation
- RNA Interference and Gene Delivery
- Ethics in Clinical Research
- Gut microbiota and health
- Extracellular vesicles in disease
- Genetic factors in colorectal cancer
- Genomic variations and chromosomal abnormalities
- Diet and metabolism studies
- Kruppel-like factors research
- Maternal and fetal healthcare
- Histone Deacetylase Inhibitors Research
- Skin and Cellular Biology Research
- Protein Degradation and Inhibitors
North West London Pathology
2025
Imperial College London
2025
Genome Institute of Singapore
2014-2024
Agency for Science, Technology and Research
2020-2024
Global Inkjet Systems (United Kingdom)
2020
National University of Singapore
2020
Australian Physiotherapy Association
2018
Genome rearrangements, a hallmark of cancer, can result in gene fusions with oncogenic properties. Using DNA paired-end-tag (DNA-PET) whole-genome sequencing, we analyzed 15 gastric cancers (GCs) from Southeast Asians. Rearrangements were enriched open chromatin and shaped by structure. We identified seven rearrangement hot spots 136 fusions. In three out 100 GC cases, found recurrent between CLDN18, tight junction gene, ARHGAP26, encoding RHOA inhibitor. Epithelial cell lines expressing...
A population of cell clusters circulating in cancer patients consist tumor-derived endothelial cells reflecting features the tumor vasculature.
Asian populations are under-represented in human genomics research. Here, we characterize clinically significant genetic variation 9051 genomes representing East Asian, South and severely Austronesian-speaking Southeast ancestries. We observe disparate risk burden attributable to ancestry-specific recurrent variants identify individuals with specific ancestries discordant their self-reported ethnicity, mostly due cryptic admixture. About 27% of severe recessive disorder genes appreciable...
Selection of the target site is an inherent question for any project aiming directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as sites in human genome Although several characterised integration literature, most these do not meet criteria set out a GSH and limited that extensively. Here, we conducted computational analysis using publicly available data to identify 25 unique putative reside active chromosomal compartments. We validated stable expression minimal...
Colorectal cancer with metastases limited to the liver (liver-limited mCRC) is a distinct clinical subset characterized by possible cure surgery. We performed high-depth sequencing of over 750 cancer-associated genes and copy number profiling in matched primary, metastasis normal tissues characterize genomic progression 18 patients liver-limited mCRC. High depth Illumina use three different variant callers enable comprehensive accurate identification somatic variants down 2.5% allele...
Asian nonsmoking populations have a higher incidence of lung cancer compared with their European counterparts. There is long-standing hypothesis that the increase in never-smokers due to environmental factors such as second-hand smoke. We analyzed whole-genome sequencing 30 cancers. Unsupervised clustering mutational signatures separated patients into two categories either all or smokers ex-smokers. In addition, nearly one third ex-smokers and classified never-smoker-like cluster. The...
Background Roux-en-Y gastric bypass is an established treatment option for type 2 diabetes and obesity. However, the optimal lengths small intestinal limbs remain controversial with variation in practice. A longer biliopancreatic limb length of 150 cm (‘Long Limb’) was hypothesised to better improve glycaemia compared standard a 50 (‘Standard Limb’). The aim trial evaluate short-term mechanistic outcomes long-term clinical safety Long Limb versus Standard bypass. Methods We undertook...
Objective To establish new trimester-specific reference ranges for thyroid function tests - stimulating hormone (TSH), free thyroxine (fT4) and triiodothyronine (fT3) in a diverse multi-ethnic population using the Abbott Alinity analyser, accordance with 2017 American Thyroid Association Guidelines Diagnosis Management of disease during Pregnancy Postpartum. Design Reference (defined as 2.5th-97.5th centile) were established TSH, fT4 fT3 from prospective samples 663 iodine-replete healthy...
Purpose We evaluated differences in a 313-variant breast cancer polygenic risk score (PRS313) across genomic platforms and their impact on stratification. Methods compared PRS313 derived from genotyping arrays (Global Screening Array [GSA], OncoArray-500K [OncoArray], Global Diversity [GDA], custom Axiom_PrecipV1 array [ThermoFisher]) low-coverage genome sequencing (lc-WGS) 2 cell lines 92 individuals. Probes were designed for all variants ThermoFisher (success rate: 259/313). Sanger was...
Abstract Background Clustering is a crucial step in the analysis of single-cell data. Clusters identified an unsupervised manner are typically annotated to cell types based on differentially expressed genes. In contrast, supervised methods use reference panel labelled transcriptomes guide both clustering and type identification. Supervised approaches have their distinct advantages limitations. Therefore, they can lead different but often complementary results. Hence, consensus approach...
Abstract The transcriptomic diversity of cell types in the human body can be analysed unprecedented detail using single (SC) technologies. Unsupervised clustering SC transcriptomes, which is default technique for defining types, prone to group cells by technical, rather than biological, variation. Compared de-novo (unsupervised) clustering, we demonstrate multiple benchmarks that supervised uses reference transcriptomes as a guide, robust batch effects and data quality artifacts. Here,...
Genomic researchers increasingly utilize commercial cloud service providers (CSPs) to manage data and analytics needs. CSPs allow grow Information Technology (IT) infrastructure on demand overcome bottlenecks when combining large datasets. However, without adequate security controls, the risk of unauthorized access may be higher for stored cloud. Additionally, regulators are mandating patterns specific protocols storage use genomic data. While CSP provides tools regulatory compliance,...
Single cell genomics offers an unprecedented resolution to interrogate genetic heterogeneity in a patient's tumour at the intercellular level. However, DNA yield per is insufficient for today's sequencing library preparation protocols. This necessitates amplification which key source of experimental noise. We provide evaluation two protocols using micro-fluidics based whole exome sequencing, scenario commonly used single genomics. The results highlight their respective biases and relative...
Clustering is a crucial step in the analysis of single-cell data. Clusters identified using unsupervised clustering are typically annotated to cell types based on differentially expressed genes. In contrast, supervised methods use reference panel labelled transcriptomes guide both and type identification. Supervised strategies have their distinct advantages limitations. Therefore, they can lead different but often complementary results. Hence, consensus approach leveraging merits paradigms...
Abstract Structural variants (SVs) are significant contributors to inter-individual genetic variation associated with traits and diseases. Current SV studies using whole-genome sequencing (WGS) have a largely Eurocentric composition, little known about diversity in other ancestries particularly from Asia. Here, we present WGS catalogue of 152,655 SVs 8,392 Singaporeans East Asian, Southeast Asian South ancestries, which ~75% (113,446 SVs) novel. We show that populations can be stratified by...
Abstract Structural variants (SVs) are significant contributors to inter-individual genetic variation associated with traits and diseases. Current SV studies using whole-genome sequencing (WGS) have a largely Eurocentric composition, little known about diversity in other ancestries, particularly from Asia. Here, we present WGS catalogue of 73,035 SVs 8392 Singaporeans East Asian, Southeast Asian South which ~65% (47,770 SVs) novel. We show that populations can be stratified by their global...
Motivation The transcriptomic diversity of the hundreds cell types in human body can be analysed unprecedented detail using single (SC) technologies. Though clustering cellular transcriptomes is default technique for defining and subtypes, strongly influenced by technical variation. In fact, prevalent unsupervised algorithms cluster cells technical, rather than biological, Results Compared to de novo (unsupervised) methods, we demonstrate multiple benchmarks that supervised clustering, which...
Summary Selection of the target site is an inherent question for any project aiming directed transgene integration. Genomic safe harbour (GSH) loci have been proposed as sites in human genome Although several characterised integration literature, most these do not meet criteria set out a GSH and limited that extensively. Here, we conducted computational analysis using publicly available data to identify 25 unique putative reside active chromosomal compartments. We validated stable expression...