Stephen B. Montgomery
A5025409424- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- RNA modifications and cancer
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Genomics and Chromatin Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Phylogenetic Studies
- Genomic variations and chromosomal abnormalities
- Adipose Tissue and Metabolism
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Nutrition, Genetics, and Disease
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Genetic Syndromes and Imprinting
- Computational and Text Analysis Methods
- Genetics and Neurodevelopmental Disorders
- Genetics, Bioinformatics, and Biomedical Research
- Treatment of Major Depression
- CRISPR and Genetic Engineering
- Cardiovascular Function and Risk Factors
Stanford University
2016-2025
Stanford Medicine
2013-2024
Stanford Maternal and Child Health Research Institute
2024
California Institute of Technology
2023
Ontario Genomics
2023
Digital Research Alliance of Canada
2023
University of Geneva
2009-2022
Thermo Fisher Scientific (Sweden)
2020
University of Pennsylvania
2018-2019
Palo Alto University
2019
Characterization of the molecular function human genome and its variation across individuals is essential for identifying cellular mechanisms that underlie genetic traits diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize in gene expression levels diverse tissues body, many which are not easily accessible. Here we describe effects on 44 tissues. We find local affects majority genes, further identify inter-chromosomal 93 genes 112 loci. On basis identified effects,...
The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.
We sequenced the 29,751-base genome of severe acute respiratory syndrome (SARS)âassociated coronavirus known as Tor2 isolate. The sequence reveals that this is only moderately related to other coronaviruses, including two human HCoV-OC43 and HCoV-229E. Phylogenetic analysis predicted viral proteins indicates virus does not closely resemble any three previously groups coronaviruses. will aid in diagnosis SARS infection humans potential animal hosts (using polymerase chain reaction...
Defective Gene Detective Identifying genes that give rise to diseases is one of the major goals sequencing human genomes. However, putative loss-of-function genes, which are often some first identified targets genome and exome sequencing, have turned out be errors rather than true genetic variants. In order identify scope within genome, MacArthur et al. (p. 823 ; see Perspective by Quintana-Murci ) extensively validated genomes from 1000 Genomes Project, as well an additional European...
Abstract Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy general robustness misspecified reference sets. We apply this framework 44 GTEx tissues 100+ from GWAS meta-analysis studies, creating growing public catalog of associations seeks capture the effects variation on human...
RNA sequencing (RNA-Seq) uses the capabilities of high-throughput methods to provide insight into transcriptome a cell. Compared previous Sanger sequencing- and microarray-based methods, RNA-Seq provides far higher coverage greater resolution dynamic nature transcriptome. Beyond quantifying gene expression, data generated by facilitate discovery novel transcripts, identification alternatively spliced genes, detection allele-specific expression. Recent advances in workflow, from sample...
Studies correlating genetic variation to gene expression facilitate the interpretation of common human phenotypes and disease. As functional variants may be operating in a tissue-dependent manner, we performed profiling association with (single-nucleotide polymorphisms) on three cell types 75 individuals. We detected type-specific effects, 69 80% regulatory identified multiple expressive quantitative trait loci (eQTLs) per gene, unique or shared among positively correlated number transcripts...
Understanding the consequences of regulatory variation in human genome remains a major challenge, with important implications for understanding gene regulation and interpreting many disease-risk variants that fall outside protein-coding regions. Here, we provide direct window into genetic by sequencing RNA from 922 genotyped individuals. We present comprehensive description distribution variation--by specific expression phenotypes altered, properties affected genes, genomic characteristics...
Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex in gene expression and genetic regulation across 44 tissue sources surveyed by Genotype-Tissue Expression project (GTEx, v8 release). demonstrate that influences levels cellular composition samples body. A total 37% all genes sex-biased at least one tissue. identify cis quantitative trait loci (eQTLs)...
The genetic basis of gene expression variation has long been studied with the aim to understand landscape regulatory variants, but also more recently assist in interpretation and elucidation disease signals. To date, many studies have looked specific tissues population-based samples, there limited assessment degree inter-population variability variation. We analyzed genome-wide lymphoblastoid cell lines from a total 726 individuals 8 global populations HapMap3 project correlated levels SNPs...
The recent success of genome-wide association studies (GWAS) is now followed by the challenge to determine how reported susceptibility variants mediate complex traits and diseases. Expression quantitative trait loci (eQTLs) have been implicated in disease associations through overlaps between eQTLs GWAS signals. However, abundance strong correlation structure (LD) genome make it likely that some these are coincidental not driven same functional variants. In present study, we propose an...
Cell type composition, estimated from bulk tissue, maps the cellular specificity of genetic variants.
DNA methylation is an essential epigenetic mark whose role in gene regulation and its dependency on genomic sequence environment are not fully understood. In this study we provide novel insights into the mechanistic relationships between genetic variation, transcriptome sequencing data three different cell-types of GenCord human population cohort. We find that association expression variation among individuals likely due to mechanisms from those establishing methylation-expression patterns...
While there have been studies exploring regulatory variation in one or more tissues, the complexity of tissue-specificity multiple primary tissues is not yet well understood. We explore depth role cis-regulatory three human tissues: lymphoblastoid cell lines (LCL), skin, and fat. The samples (156 LCL, 160 166 fat) were derived simultaneously from a subset well-phenotyped healthy female twins MuTHER resource. discover an abundance cis-eQTLs each tissue similar to previous estimates (858 4.7%...
Telomere length within an individual varies in a correlated manner across most tissues.
Genomewide association studies of autoimmune diseases have mapped hundreds susceptibility regions in the genome. However, only for a few signals has causal gene been identified, and even fewer variant underlying mechanism defined. Coincident associations DNA variants affecting both risk disease quantitative immune variables provide an informative route to explore mechanisms drug-targetable pathways.Using case-control samples from Sardinia, Italy, we performed genomewide study multiple...