Patrick B. O. Tan

Implementing Reproductive Carrier Screening to Include Diverse Asian Populations: Insights from Singapore

The paper describes the implementation of a reproductive carrier screening program in Singapore, focusing on diverse Asian populations and highlighting community engagement and initial outcomes.

Telomere variant sequences encode the genetic blueprint for allele-specific telomere length

The paper identifies heritable telomere variant sequences that determine allele-specific telomere length and shows their role in telomere maintenance and inheritance.

TIM3+ Tumor Associated M2 Macrophages Impair Antitumor T Cell Immunity and Promote Gastric Cancer Progression and Peritoneal Metastasis

This study shows TIM3 on M2 macrophages promotes gastric cancer progression and metastasis by suppressing T cell immunity, and TIM3 blockade combined with immunotherapy and chemotherapy improves outcomes.

High-throughput plasma proteomic platforms: Insights from a multi-ethnic Asian cohort

The paper compares three proteomic platforms in a multi-ethnic Asian cohort, finding limited overlap, platform-specific performance metrics, and ethnicity-related protein differences.

Gene-Family Encoding Boosts Domain-Adapted Single-Cell Language Models

This paper introduces gene-family encoding to improve domain-adapted single-cell language models, showing better performance in embedding-based and generative tasks on gastric-cancer data.

A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population

The paper presents a high-quality, gapless diploid reference genome for an Indian population, revealing extensive structural variation and improved performance for genomic analysis in South Asian samples.

A Computational Framework for Analysis of cfDNA Fragmentation Profiles

This study introduces NDRDiff, a computational framework for analyzing cfDNA fragmentation profiles to infer gene expression and identify differentially expressed genes in cancer.

Single-cell Pharmacogenomic Landscapes of Epigenetic Drug Resistance Revealed by Gastric Cancer Perturb-seq

This study uses Perturb-seq to analyze pharmacogenomic interactions in gastric cancer, revealing gene-drug relationships and resistance mechanisms.

Scaling Precision Medicine: Singapore's PRECISE-SG100K Genomic Engine

The paper describes the development of a national genomic infrastructure in Singapore to scale precision medicine, achieving high throughput and operational efficiency in genome sequencing.

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

Nuclear regulatory disturbances precede and predict the development of Type-2 diabetes in Asian populations

The paper identifies DNA methylation biomarkers predictive of Type-2 diabetes in Asian populations and shows their utility in risk stratification.

Spatially Resolved Tumor Ecosystems and Cell States in Gastric Adenocarcinoma Progression and Evolution

This study integrates spatial transcriptomics and single-cell data from gastric cancer samples to reveal tumor ecosystem dynamics, evolutionary trajectories, and immune microenvironment features.

Spatially resolved niche and tumor microenvironmental alterations in gastric cancer peritoneal metastases

This study identifies transcriptomic and immune features of gastric cancer peritoneal metastases, highlighting predictive markers and therapeutic targets in the tumor microenvironment.

Metabolome-wide association of carotid intima media thickness identifies FDX1 as a determinant of cholesterol metabolism and cardiovascular risk in Asian populations.

Fragle: Universal ctDNA quantification using deep learning of fragmentomic profiles

Fragle quantifies ctDNA from fragment length profiles using deep learning, showing high accuracy and improved detection limits across multiple datasets and sequencing types.

The landscape of tolerated genetic variation in humans and primates

The paper uses primate genetic data to predict human variant pathogenicity with a deep learning classifier trained on 4.3 million common missense variants.

A global catalog of whole-genome diversity from 233 primate species

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

RAPTOR: A Five-Safes approach to a secure, cloud native and serverless genomics data repository

RAPTOR provides a secure, cloud-native genomics repository with a five-safes framework to ensure compliance and data protection for genomic research.

Variation in predicted COVID-19 risk among lemurs and lorises

The paper analyzes ACE2 gene sequences in strepsirrhine primates to assess their susceptibility to SARS-CoV-2, finding high variability and potential risk in some species.

Family History Assessment Significantly Enhances Delivery of Precision Medicine in the Genomics Era

This study shows that family history collection improves the detection of pathogenic variants in genomic data, enhancing precision medicine by identifying high-risk individuals.

Whole genome and RNA sequencing of 1,220 cancers reveals hundreds of genes deregulated by rearrangement of cis-regulatory elements

The paper identifies hundreds of genes deregulated by SVs in cancer, showing increased expression linked to SV breakpoints and enhancer elements.

Large-scale whole-genome sequencing of three diverse Asian populations in Singapore

This study presents whole-genome sequencing data from 4,810 Singaporeans across three ethnic groups, revealing genetic structure, admixture, and improved imputation for Asian and Oceanian populations.

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

This study identifies alternative promoters as key regulators in the cancer transcriptome using RNA-Seq data from 1,188 cancer samples.

Recurrent PD-L1 Structural Rearrangements in Natural Killer/T Cell Lymphoma Patients with Complete Response to PD-1 Blockade Therapy

The paper identifies recurrent PD-L1 structural rearrangements and JAK3 mutations in NKTL patients achieving CR with PD-1 blockade therapy, suggesting genomic screening may improve patient selection.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

The paper analyzes RNA alterations across 27 cancer types using whole-genome sequencing data, identifying gene expression associations with DNA variants and structural fusions.

Revealing unidentified heterogeneity in different epithelial cancers using heterocellular subtype classification

The paper classifies epithelial cancers into five heterocellular subtypes, revealing previously unrecognized heterogeneity and identifying tissue-independent properties across cancer types.