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Mark Daly

Ph.D.

Director of the Finnish Institute for Molecular Medicine (FIMM)

Founding Chief of the Analytic and Translational Genetic Unit (ATGU)

Massachusetts General Hospital

Associate Professor of Medicine at Harvard Medical School

Institute member, Broad Institute of MIT and Harvard

Dr. Mark Daly is Director of the Finnish Institute for Molecular Medicine (FIMM) at the University of Helsinki, Founding Chief of the Analytic and Translational Genetic Unit (ATGU) at Massachusetts General Hospital, Associate Professor of Medicine at Harvard Medical School, and Institute member of the Broad Institute of MIT and Harvard.

His research has historically focused on the development and application of statistical methods for the discovery and interpretation of genetic variation responsible for complex human disease and with the creation of the ATGU, he and other core faculty are focused on the interpretation of genome sequence and the use of genome information in clinical settings.  At the Broad, he is an Institute Member and Co-Director of the Program in Medical and Population Genetics, where he leads many large scale genome sequencing studies in autism and inflammatory bowel disease.

In February of 2018, he was appointed Director of the Institute of Molecular Medicine Finland (FIMM), and now divides his time between Helsinki and Boston, although he maintains his primary lab and affiliations in Boston. FIMM is a translational research institute with a focus on cancer, digital diagnostics, genetics and epidemiology and is the home of landmark efforts such as the FinnGen Project.

While developing computational and statistical methods that can be broadly applied, his group has several primary medical genetics research foci.  He has extensive research program in neuropsychiatric genetics - particularly in autism, schizophrenia and ADHD – and has led large-scale GWAS and exome sequencing efforts in this area.  His lab serves as an analytic hub for the Psychiatric GWAS Consortium, an international consortium leading the largest collaborative GWAS studies in 5 major psychiatric disorders.  He also has a longstanding effort in the mapping of genes for Crohn’s disease and ulcerative colitis where he helped found and lead an international effort that has identified more than 150 genetic risk factors and pursues the functional interpretation and clinical ramifications of these continued gene discovery efforts.  He is also co-PI of the gnomAD project and committed to ensuring the output of all ATGU genomic research is maximally accessible and useful to the clinical and research communities.

Dr. Daly has received many awards and was elected to the National Academy of Medicine in 2017. 

He studied physics at MIT, and although he initially wanted to become a lawyer or poker player, he joined Eric Lander’s lab at the Whitehead Institute as a freshman to do genetics research. He received his PhD in Human Genetics from Leiden University in 2004.

Mark Daly

Ph.D.

Director of the Finnish Institute for Molecular Medicine (FIMM)

Founding Chief of the Analytic and Translational Genetic Unit (ATGU)

Massachusetts General Hospital

Associate Professor of Medicine at Harvard Medical School

Institute member, Broad Institute of MIT and Harvard

Dr. Mark Daly is Director of the Finnish Institute for Molecular Medicine (FIMM) at the University of Helsinki, Founding Chief of the Analytic and Translational Genetic Unit (ATGU) at Massachusetts General Hospital, Associate Professor of Medicine at Harvard Medical School, and Institute member of the Broad Institute of MIT and Harvard.

His research has historically focused on the development and application of statistical methods for the discovery and interpretation of genetic variation responsible for complex human disease and with the creation of the ATGU, he and other core faculty are focused on the interpretation of genome sequence and the use of genome information in clinical settings.  At the Broad, he is an Institute Member and Co-Director of the Program in Medical and Population Genetics, where he leads many large scale genome sequencing studies in autism and inflammatory bowel disease.

In February of 2018, he was appointed Director of the Institute of Molecular Medicine Finland (FIMM), and now divides his time between Helsinki and Boston, although he maintains his primary lab and affiliations in Boston. FIMM is a translational research institute with a focus on cancer, digital diagnostics, genetics and epidemiology and is the home of landmark efforts such as the FinnGen Project.

While developing computational and statistical methods that can be broadly applied, his group has several primary medical genetics research foci.  He has extensive research program in neuropsychiatric genetics - particularly in autism, schizophrenia and ADHD – and has led large-scale GWAS and exome sequencing efforts in this area.  His lab serves as an analytic hub for the Psychiatric GWAS Consortium, an international consortium leading the largest collaborative GWAS studies in 5 major psychiatric disorders.  He also has a longstanding effort in the mapping of genes for Crohn’s disease and ulcerative colitis where he helped found and lead an international effort that has identified more than 150 genetic risk factors and pursues the functional interpretation and clinical ramifications of these continued gene discovery efforts.  He is also co-PI of the gnomAD project and committed to ensuring the output of all ATGU genomic research is maximally accessible and useful to the clinical and research communities.

Dr. Daly has received many awards and was elected to the National Academy of Medicine in 2017. 

He studied physics at MIT, and although he initially wanted to become a lawyer or poker player, he joined Eric Lander’s lab at the Whitehead Institute as a freshman to do genetics research. He received his PhD in Human Genetics from Leiden University in 2004.

Recent Publications

Gene Portals: A Framework for Integrating Clinical, Functional, and Structural Evidence into Rare Disease Variant Classification

Published On 2026 Mar 13

Journal article

Rare Mendelian disorders affect 300-400 million people globally. Although genetic testing has become widely adopted, gene-specific evidence for tailored variant interpretation remains scattered across resources. We present Gene Portals, a framework for gene-centered multimodal knowledge bases that co-localize expert-harmonized clinical data, functional assays, population variation, structural annotations and gene-specific ACMG/AMP specifications within a single resource. A modular interface...


Genome-wide association analyses of autoimmune hypothyroidism reveal autoimmune and thyroid-specific contributions and an inverse relationship with cancer risk

Published On 2026 Feb 26

Journal article

The high prevalence (>5%) of autoimmune hypothyroidism (AIHT) provides a unique opportunity to dissect genetic contributions to systemic and organ-specific autoimmunity. Here we performed a genome-wide association meta-analysis of 81,718 AIHT cases in FinnGen and the UK Biobank, identifying 418 independent signals (P < 5 × 10^(-8)). At 48 of these loci, a protein-coding variant is, or is highly correlated (r² > 0.95) with, the lead variant, including Finnish-enriched coding variants in LAG3,...