Publications by authors named "Amrita Chattopadhyay"
Background: Sepsis is characterized by organ dysfunction as a response to infection and is one of the leading causes of mortality and loss of health. The heterogeneous nature of sepsis, along with ethnic differences in susceptibility, challenges a thorough understanding of its etiology. This study aimed to propose prediction models by leveraging genetic-risk scores and clinical variables that can assist in risk stratification of patients.
View Article and Find Full Text PDFPredicting Survival Outcomes for Patients with Ovarian Cancer Using National Cancer Registry Data from Taiwan: A Retrospective Cohort Study.
Womens Health Rep (New Rochelle)
January 2025
Background: Ovarian cancer is one of the top seven causes of cancer deaths. Incidence of ovarian cancer varies by ethnicity, where Asian women demonstrate lower incidence rates than non-Hispanic Blacks and Whites. Survival prediction models for ovarian cancer have been developed for Caucasians and Black populations using national databases; however, whether these models work for Asians is unclear.
View Article and Find Full Text PDFCurrent genome-wide association studies (GWAS) for kidney function lack ancestral diversity, limiting the applicability to broader populations. The East-Asian population is especially under-represented, despite having the highest global burden of end-stage kidney disease. We conducted a meta-analysis of multiple GWASs (n = 244,952) on estimated glomerular filtration rate and a replication dataset (n = 27,058) from Taiwan and Japan.
View Article and Find Full Text PDFCross-population enhancement of PrediXcan predictions with a gnomAD-based east Asian reference framework.
Brief Bioinform
September 2024
Article Synopsis
- Genome-wide association studies have identified thousands of genetic variants linked to complex traits, but understanding their biological functions requires precise gene expression levels.
- The PrediXcan algorithm helps predict these expression levels using single nucleotide polymorphisms, but its effectiveness for East Asian populations is uncertain due to a lack of diverse reference data.
- To address this, researchers developed Predict Asian-Population (PredictAP) as a supplementary tool for PrediXcan, using allele frequency information to improve gene expression predictions for individuals of East Asian ancestry.
Article Synopsis
- The study focuses on improving outcomes for sepsis patients by using the National Early Warning Score 2 (NEWS2) to measure treatment effectiveness in the emergency department (ED).
- It evaluated how changes in NEWS2 scores during ED stay relate to overall hospital mortality rates among sepsis patients admitted between 1997 and 2020.
- The findings suggest that a decrease in NEWS2 scores correlates with lower mortality risk, highlighting the importance of prompt and effective treatment in reducing sepsis-related deaths.
Population-Based Prognostic Models for Head and Neck Cancers Using National Cancer Registry Data from Taiwan.
J Epidemiol Glob Health
June 2024
Purpose: This study aims to raise awareness of the disparities in survival predictions among races in head and neck cancer (HNC) patients by developing and validating population-based prognostic models specifically tailored for Taiwanese and Asian populations.
Methods: A total of 49,137 patients diagnosed with HNCs were included from the Taiwan Cancer Registry (TCR). Six prognostic models, divided into three categories based on surgical status, were developed to predict both overall survival (OS) and cancer-specific survival using the registered demographic and clinicopathological characteristics in the Cox proportional hazards model.
Twnbiome: a public database of the healthy Taiwanese gut microbiome.
BMC Bioinformatics
December 2023
Article Synopsis
- Recent advancements in next generation sequencing (NGS) technology have made studying bacterial genomes in the environment more affordable and effective, allowing for the identification of previously unknown microbiome species.
- An efficient NGS data analysis pipeline needs to combine various bioinformatics tools, which can be complex and resource-intensive, presenting challenges for biologists and clinicians.
- Twnbiome, a public gut microbiome database developed from healthy Taiwanese subjects, provides an interactive and user-friendly platform for microbiota research, enabling easy data analysis and customizable results for users without a bioinformatics background.
The largest genome-wide association study for breast cancer in Taiwanese Han population.
Breast Cancer Res Treat
January 2024
Article Synopsis
- Breast cancer shows significant genetic variation, with existing research primarily focused on Caucasian populations, prompting a study in a Taiwanese cohort to broaden understanding.
- A study analyzing 152,534 participants narrowed down to 2,496 cases and 9,984 controls conducted genome-wide association studies and polygenic risk score analyses encompassing four breast cancer subtypes.
- The findings revealed 113 SNPs linked to breast cancer risk, including 50 novel variants, with strong correlations found between polygenic risk scores and the likelihood of developing breast cancer, especially for the luminal A subtype.
Article Synopsis
- Frailty is a common syndrome in older adults, linked to poor health outcomes and assessed using the Frailty Phenotype (FP) and Frailty Index (FI), but its biological mechanisms are still not well understood.
- Researchers analyzed genetic and health data from UK Biobank participants (aged 60-73), identifying significant genetic links to frailty, including notable associations with known genes related to aging and metabolism.
- The study utilized machine learning to create models that effectively distinguish between frail and non-frail individuals, achieving a high accuracy of 85%, highlighting the polygenic nature of frailty and its connections to cognitive function and cholesterol metabolism.
Article Synopsis
- Genotype imputation is important for understanding disease variants in Asian populations, which have been underrepresented in genetic studies compared to Caucasian populations.
- A new web platform called Multi-ethnic Imputation System (MI-System) has been developed to facilitate easy genotype imputation for East-Asians, providing multiple established pipelines and a unique reference panel for Taiwanese-Chinese ancestry.
- MI-System allows researchers to upload their data for imputation with minimal effort, contributing to faster research in Asian population genetics without needing extensive computational resources or bioinformatics expertise.
Article Synopsis
- The study investigates the outcomes of out-of-hospital cardiac arrest (OHCA) patients with end-stage kidney disease (ESKD) compared to those without ESKD, focusing on rates of return of spontaneous circulation (ROSC) during CPR.* -
- Results showed that ESKD patients had significantly higher rates of "any" and "sustained" ROSC and exhibited lower potassium levels and milder acidosis than non-ESKD patients during resuscitation.* -
- Findings suggest ESKD patients can achieve comparable hospital survival rates to non-ESKD patients, challenging existing beliefs that these patients are always at high risk for complications like hyperkalemia and acidosis.*
Exploring the genetic correlation of cardiovascular diseases and mood disorders in the UK Biobank.
Epidemiol Psychiatr Sci
May 2023
Article Synopsis
- Cardiovascular diseases (CVDs) are the top global cause of death, and individuals with mood disorders, especially major depressive disorder (MDD), face higher mortality and incidence rates, highlighting a significant comorbidity.
- This research utilized the UK Biobank's extensive genetic and health data to analyze genetic links between CVDs, mood disorders, and cardiometabolic traits among nearly 118,000 participants.
- Findings revealed a strong genetic correlation between CVDs and mood disorders, particularly MDD, suggesting a shared genetic background, while no significant link was found between CVDs and bipolar disorder.
Article Synopsis
- Patients with end-stage renal disease (ESRD) on long-term hemodialysis (HD) face a higher risk of out-of-hospital cardiac arrest (OHCA) but may have better chances of recovering spontaneous circulation (ROSC) compared to non-ESRD patients.
- A study using data from Taiwan analyzed over 100,000 ESRD and matched non-ESRD patients, revealing that ESRD patients had a 2.11 times higher risk of OHCA but were 2.47 times more likely to achieve ROSC.
- Additionally, survival rates after ROSC were found to be better for ESRD patients, suggesting that their prolonged exposure to toxins and regular HD may improve their vascular response and outcomes post-arrest
CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants.
BMC Bioinformatics
October 2022
Article Synopsis
- Next generation sequencing data allows for the analysis of low-frequency and rare genetic variants, which are crucial for understanding complex diseases that can't be fully explained by common variants. CLIN_SKAT is an R package developed to address the challenges of analyzing this data efficiently.
- The package provides four user-friendly functions for obtaining clinically relevant variants, conducting gene-based association analyses, and visualizing results, making it easier to interpret findings.
- CLIN_SKAT includes pre-analysis steps and customizable features to enhance the clinical relevance of its results, and it's available for free on multiple operating systems for users to download and use in R.
Article Synopsis
- Researchers successfully created the first high-entropy nanoparticles using a mix of lanthanide oxysulfides (Pr, Nd, Gd, Dy, Er) through a thermolysis process.
- Analysis via powder X-ray diffraction and electron microscopy confirmed the uniformity and distribution of lanthanides within the particles.
- The nanoparticles exhibited a noticeable blue shift in absorption and photoluminescence spectra compared to bulk samples, which indicates quantum confinement effects, supported by both experimental and theoretical insights into their electronic properties.
Article Synopsis
- The study investigates the gut microbiota of healthy Taiwanese individuals and compares it to that of chronic kidney disease (CKD) patients on different dialysis treatments to understand how kidney disease affects gut health.
- Researchers analyzed fecal samples using advanced sequencing methods to identify bacterial species and their relationships with certain demographic factors like age and gender.
- Results showed significant differences in gut microbiome composition between healthy individuals and dialysis patients, with specific bacteria linked to CKD complications, highlighting the potential of gut microbiota as a therapeutic target in managing non-communicable diseases.
Article Synopsis
- * The research involved a bi-directional Mendelian randomization analysis of 15,996 healthy Taiwanese individuals, examining the causal relationship between platelet count and hypertension.
- * The study concluded that higher platelet counts significantly increase the risk of hypertension, while the reverse effect of hypertension on platelet count was found to be insignificant.
Article Synopsis
- This study aims to improve prognosis prediction and treatment plans for stage-III pancreatic cancer patients by creating a more precise classification system based on clinical variables.
- It analyzes data from the Taiwan Cancer Registry and identifies that factors like lymph node involvement and tumor grade significantly affect patient survival rates.
- The study concludes that this new classification can help in guiding treatment decisions for patients with advanced-stage pancreatic cancer, with a noticeable difference in median survival among newly defined subgroups.
Article Synopsis
- - The study focuses on assessing cardiovascular mortality risk in an aging population through a combined score based on electrocardiographic (ECG) parameters, aiming for primary prevention strategies.
- - Conducted on over 5,300 elderly subjects in Taiwan, results showed that specific ECG abnormalities like left ventricular hypertrophy (LVH) and prolonged QTc and PR intervals were significantly linked to all-cause and cardiovascular death.
- - The research developed predictive models using an ECG abnormality score, which effectively identified high-risk groups, demonstrating robust statistical improvements in predicting outcomes related to mortality.
Article Synopsis
- Whole-genome doubling (WGD) is an important event in cancer development, particularly in breast cancer, but its effects on different breast cancer subtypes are still not fully understood.
- The study found that triple-negative breast cancer shows a higher occurrence of WGD and increased chromosomal instability (CIN), while HER2-positive tumors experienced early WGD with varying CIN levels compared to luminal types.
- The research also identified a link between WGD, homologous recombination deficiency (HRD), and a specific genetic signature in Taiwanese breast cancer patients, which could inform more personalized treatment options.
Article Synopsis
- Colon cancer is a major health issue in Taiwan, and this study aimed to create a reliable survival prediction model using data from the Taiwan Cancer Registry.
- The researchers analyzed data from over 20,000 patients diagnosed between 2007 and 2015 and developed two models, one using traditional clinical features and another including site-specific factors.
- Both models showed strong predictive performance, and the first model proved effective regardless of patients' ethnic backgrounds, potentially aiding doctors in improving treatment strategies.
High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data.
Brief Bioinform
November 2021
Article Synopsis
- A deep learning model was developed to classify individuals from mixed DNA samples using 27 short tandem repeats and 94 single nucleotide polymorphisms from massively parallel sequencing.
- The model achieved 100% accuracy in identifying major and minor contributors in 90 manually prepared DNA mixtures and effectively identified contributors in external mixed samples as well.
- The researchers also tested the model on whole exome sequencing data for breast cancer classification, showing versatility with an area under the curve of 0.85, and introduced a sliding window approach to enhance model performance.