Lei Sun, University of Toronto

Research

Complex Traits Confounding Data Quality Genome-Wide Association Studies Genotyping Error Heterogeneity Robust Association Methods Sex

Latest papers

Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.
PLoS genetics · 2026
Detecting latent interaction effects when analyzing binary traits.
PLoS genetics · 2025 · senior author
Winner's curse in rare variant analysis: effect size estimation bias depends on effect direction and the association method used.
Frontiers in genetics · 2025 · senior author

All 87 publications

Latest funding

Novel robust methods for complex binary traits
NSERC · 2024 · Principal investigator
$44,000
Chasing stochastics, a multidisciplinary approach to develop genetic models predicting the likelihood of stochastic events.
SSHRC · 2023 · Co-investigator
$250,000
Banff International Research Station
NSERC · 2022 · Co-investigator
$2,982,528

All 16 grants and awards

87 publications.

01

Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.

Garg E, Romain J, Sun L, Paterson AD

PLoS genetics2026

DOI: 10.1371/journal.pgen.1012280 PMID: 42743265

02

Detecting latent interaction effects when analyzing binary traits.

Zhang Z, Lawless JF, Paterson AD, Sun L

PLoS genetics2025Senior author

DOI: 10.1371/journal.pgen.1011822 PMID: 40845140

03

Winner's curse in rare variant analysis: effect size estimation bias depends on effect direction and the association method used.

Soave D, Hayalioglu M, Sun L

Frontiers in genetics2025Senior author

DOI: 10.3389/fgene.2025.1416673 PMID: 40860341

04

Integrative Proteogenomic Analyses Provide Novel Interpretations of Type 1 Diabetes Risk Loci Through Circulating Proteins.

Lu T, Manousaki D, Sun L, Paterson AD

Diabetes2025

DOI: 10.2337/db24-0380 PMID: 39761376

05

Characterization of gene-environment interactions for vitamin D through variance quantitative trait loci: a UK Biobank-based genetic epidemiology study.

Lu T, Zhang W, Robinson-Cohen C, Engelman CD, Lu Q, de Boer IH, Sun L, Paterson AD

The American journal of clinical nutrition2025

DOI: 10.1016/j.ajcnut.2025.01.021 PMID: 39855341

06

The X chromosome's influences on the human brain.

Jiang Z, Sullivan PF, Li T, Zhao B, Wang X, Luo T, Huang S, Guan PY, Chen J, Yang Y, Stein JL, Li Y, Liu D, Sun L, Zhu H

Science advances2025

DOI: 10.1126/sciadv.adq5360 PMID: 39854466

07

Chromosome X-wide common variant association study in autism spectrum disorder.

Mendes M, Chen DZ, Engchuan W, Leal TP, Thiruvahindrapuram B, Trost B, Howe JL, Pellecchia G, Nalpathamkalam T, Alexandrova R, Salazar NB, McKee EA, Rivera-Alfaro N, Lai MC, Bandres-Ciga S, Roshandel D, Bradley CA, Anagnostou E, Sun L, Scherer SW

American journal of human genetics2025

DOI: 10.1016/j.ajhg.2024.11.008 PMID: 39706197

08

Perfect collinearity not created equal: measuring and visualizing the severity of multi-collinearity of modern omics data

Deng WQ, Craiu RV, Sun L

Statistical Applications in Genetics and Molecular Biology2025Senior author

DOI: 10.1515/sagmb-2025-0043

09

Association of whole-person eigen-polygenic risk scores with Alzheimer's disease.

Kharaghani A, Tio ES, Milic M, Bennett DA, De Jager PL, Schneider JA, Sun L, Felsky D

Human molecular genetics2024

DOI: 10.1093/hmg/ddae067 PMID: 38679805

10

Genome-wide association study of susceptibility to Pseudomonas aeruginosa infection in cystic fibrosis.

Lin B, Gong J, Keenan K, Lin F, Lin YC, Mésinèle J, Calmel C, Mohand Oumoussa B, Boëlle PY, Guillot L, Corvol H, Waters V, Sun L, Strug LJ

The European respiratory journal2024

DOI: 10.1183/13993003.00062-2024 PMID: 39117430

Novel robust methods for complex binary traits

Principal investigatorNSERC2024Discovery Grants Program - Individual

Principal investigators: Sun, Lei

Keywords: statistical methodology; statistical genetics and genomics; applied statistics; robust association methods; binary outcomes; interaction; non-collapsibility; heterogeneity; meta-analysis; complex human traits

$44,000

Chasing stochastics, a multidisciplinary approach to develop genetic models predicting the likelihood of stochastic events.

Co-investigatorSSHRC2023New Frontiers in Research Fund - Exploration

Principal investigators: Breetvelt, Elemi

Keywords: regional burden; Dario Rerio; Genetic Risk Prediction; Genetic Epidemiology; Scoliosis; Schizophrenia; ASD; precision medicine; translation research

$250,000

Banff International Research Station

Co-investigatorNSERC2022Discovery Institutes Support Grants

Principal investigators: Pramanik, Malabika M

$2,982,528

Methods for including the X chromosome in genetic association studies to advance disease gene mapping

Nominated PICIHR2021Project Grant

Principal investigators: Sun, Lei; Paterson, Andrew D

Keywords: Complex Traits; Confounding; Data Quality; Genome-Wide Association Studies; Genotyping Error; Heterogeneity; Robust Association Methods; Sex; X Chromosome; Y Chromosome

$765,000

Back to the future: fast and accurate identification of shared genomic segments for disease gene mapping using population-based linkage analysis to take advantage of founder effects

Principal investigatorCIHR2019Project Grant

Principal investigators: Paterson, Andrew D; Sun, Lei

Keywords: Crpytic Relatedness; Founder Effects; Genetic; Haplotype

$680,852

Robust and set-based association analyses of complex genetic data

Principal investigatorNSERC2018Discovery Grants Program - Accelerator Supplements

Principal investigators: Sun, Lei

$120,000

Robust allele-based association analyses of complex genetic data

Principal investigatorNSERC2018Discovery Grants Program - Individual

Principal investigators: Sun, Lei

$312,000

Statistical methods and computational tools for next-generation genetic studies of complex traits

Nominated PICIHR2013Operating Grant

Principal investigators: Sun, Lei

Keywords: Complex Human Traits; Cystic Fibrosis Modifier Genes; Genetic Epidemiology; High-Throughput Genetic And Gemomic Data; Statistical Genetics; Type 1 Diabetes Complications

$667,641

Joint analyses of multiple genetic variants and multiple trait phenotypes

Principal investigatorNSERC2013Discovery Grants Program - Individual

Principal investigators: Sun, Lei

$115,000

Modification of Cystic Fibrosis Phenotypes in the Pancreas and Gut

Co-investigatorCIHR2011Operating Grant

Principal investigators: Strug, Lisa J

Keywords: Association; Cystic Fibrosis; Diabetes; Gene Modifiers; Heritability; Intestinal Obstruction; Modifiers; Pancreatic Function; Population-Based Study; Statistical Genetics

$1,070,395

From CIHR, NSERC and SSHRC funding decisions: CIHR since 2008, NSERC since 1991 and SSHRC since 1998, including their latest published competition results.

Frequent collaborators

Biostatistics Division
Medicine
Epidemiology Division
Anesthesia
Psychiatry & Behavioural Neurosciences
Mathematics and Statistics
Psychology
Other

Co-authors at University of Toronto, colored by department. Thicker lines mean more shared papers; select anyone to open their profile and their own map.

Felix Ratjen

Faculty

5 shared papers, latest 2023

Michael Parkins

Medicine

4 shared papers, latest 2023

Ruslan Dorfman

Anesthesia

4 shared papers, latest 2012

Wei Deng

Psychiatry & Behavioural Neurosciences

3 shared papers, latest 2025

Meng-Chuan Lai

Faculty

2 shared papers, latest 2025

Brett Trost

Faculty

2 shared papers, latest 2025

Tanja Gonska

Faculty

2 shared papers, latest 2022

Evdokia Anagnostou

Psychology

2 shared papers, latest 2025

Mary Jackson

Medicine

2 shared papers, latest 2021

France Gagnon

Dalla Lana School of Public Health

2 shared papers, latest 2024

Angelo Canty

Mathematics and Statistics

2 shared papers, latest 2015

Osvaldo Espin Garcia

Biostatistics Division

1 shared papers, latest 2022

Rafal Kustra

Biostatistics Division

1 shared papers, latest 2008

Rinku Sutradhar

Institute of Health Policy, Management, and Evaluation

1 shared papers, latest 2008

Wei Wang

Faculty

1 shared papers, latest 2019

Clement Zai

Epidemiology Division

1 shared papers, latest 2012

Daniel Felsky

Department of Psychiatry

1 shared papers, latest 2024

Despoina Manousaki

Pédiatrie

1 shared papers, latest 2025

Joseph Beyene

Health Research Methods, Evidence, and Impact

1 shared papers, latest 2014

Geoffrey Liu

Epidemiology Division

1 shared papers, latest 2019

Jordan Lerner-Ellis

Department of Laboratory Medicine and Pathobiology

1 shared papers, latest 2024

Guillaume Pare

Pathology & Molecular Medicine

1 shared papers, latest 2019

Write to this professor

A short, specific email works best. This draft uses one of their recent papers; replace the parts in brackets with your own details before sending.

Applying for

Paper to mentionMention their NSERC grant from 2024

Subject: Prospective PhD student: Complex Traits Dear Professor Sun, My name is [your name], and I am a [your current degree or role] at [your institution]. I am applying for a PhD position starting in [term and year]. I read your paper "Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project." (2026), and it connects closely to my own work on [your research topic]. [One or two sentences on what you did and what you learned.] I also saw your NSERC-funded project "Novel robust methods for complex binary traits" (2024), and I would be glad to contribute to work in that direction. Are you accepting new PhD students for [term and year]? I have attached my CV and transcripts, and I would be glad to talk at a time that suits you. Thank you for your time. Kind regards, [your name]