Nasa Sinnott-Armstrong
A5002455648- Genetic Associations and Epidemiology
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Genetic and phenotypic traits in livestock
- Metabolomics and Mass Spectrometry Studies
- Epigenetics and DNA Methylation
- Genetic Mapping and Diversity in Plants and Animals
- Sleep and related disorders
- SARS-CoV-2 detection and testing
- Genetic factors in colorectal cancer
- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Cancer-related gene regulation
- Single-cell and spatial transcriptomics
- Evolution and Genetic Dynamics
- Cancer-related molecular mechanisms research
- SARS-CoV-2 and COVID-19 Research
- Nutrition, Genetics, and Disease
- Biosensors and Analytical Detection
- Genomics and Rare Diseases
- Circadian rhythm and melatonin
- Sleep and Wakefulness Research
Stanford University
2017-2024
Fred Hutch Cancer Center
2022-2024
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2022-2024
Institute for Molecular Medicine Finland
2021-2024
University of Helsinki
2021-2024
University of Washington
2024
Brotman Baty Institute
2024
Broad Institute
2018-2023
Harvard University
2021-2023
Massachusetts Institute of Technology
2021-2023
The discovery of drivers cancer has traditionally focused on protein-coding genes
Several recent papers have reported strong signals of selection on European polygenic height scores. These analyses used effect estimates from the GIANT consortium and replication studies. Here, we describe a new analysis based UK Biobank (UKB), large, independent dataset. We find that using UKB are strongly attenuated or absent. also provide evidence previous were confounded by population stratification. Therefore, conclusion adaptation now lacks support. Moreover, these discrepancies...
Wastewater-based epidemiology may be useful for informing public health response to viral diseases like COVID-19 caused by SARS-CoV-2. We quantified SARS-CoV-2 RNA in wastewater influent and primary settled solids two treatment plants inform the preanalytical analytical approaches assess whether or harbored more targets. The samples resulted higher detection frequencies than corresponding samples. Likewise, was readily detected using one-step digital droplet (dd)RT-PCR with two-step RT-QPCR...
Organoids recapitulate brain development Gene expression changes and their control by accessible chromatin in the human during is of great interest but limited accessibility. Trevino et al. avoided this problem developing three-dimensional organoid models forebrain examining accessibility gene at single-cell level. From analysis, they matched developmental profiles between fetal samples, identified transcription factor binding profiles, predicted how factors are linked to cortical...
Physical interactions between distal regulatory elements have a key role in regulating gene expression, but the extent to which these vary cell types and contribute cell-type-specific expression remains unclear. Here, address questions as part of phase III Encyclopedia DNA Elements (ENCODE), we mapped cohesin-mediated chromatin loops, using interaction analysis by paired-end tag sequencing (ChIA-PET), analysed 24 diverse human types, including core ENCODE lines. Twenty-eight per cent all...
Genome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety complex diseases and other traits. We describe UK Biobank GWAS results for three molecular traits—urate, IGF-1, testosterone—with better-understood biology than most find that many significant hits are readily interpretable. observe huge enrichment associations near genes involved in relevant biosynthesis, transport, or signaling pathways. show how data illuminate each trait, including...
Published and unpublished reports show that SARS-CoV-2 RNA in publicly owned treatment work (POTW) wastewater influent solids is associated with new COVID-19 cases or incidence sewersheds, but methods for comparing data collected from diverse POTWs to infer information about the relative of laboratory-confirmed cases, scaling allow such comparisons, have not been previously established. Here, we N1 N2 concentrations normalized by PMMoV can be used compare laboratory confirmed across POTWs....
With hundreds of copies rDNA, it is unknown whether they possess sequence variations that form different types ribosomes. Here, we developed an algorithm for long-read variant calling, termed RGA, which revealed in human rDNA loci are predominantly insertion-deletion (indel) variants. We full-length rRNA sequencing (RIBO-RT) and situ (SWITCH-seq), showed translating ribosomes variation rRNA. Over 1,000 variants lowly expressed. However, tens abundant distinct subtypes with structures near...
Genome-wide epigenomic maps have revealed millions of putative enhancers and promoters, but experimental validation their function high-resolution dissection driver nucleotides remain limited. Here, we present HiDRA (High-resolution Dissection Regulatory Activity), a combined computational method for genome-wide testing regulatory regions. We test ~7 million accessible DNA fragments in single experiment, by coupling chromatin extraction with self-transcribing episomal reporters...
Abstract Epigenetic landscapes can shape physiologic and disease phenotypes. We used integrative, high resolution multi-omics methods to delineate the methylome landscape characterize oncogenic drivers of esophageal squamous cell carcinoma (ESCC). found 98% CpGs are hypomethylated across ESCC genome. Hypo-methylated regions enriched in areas with heterochromatin binding markers (H3K9me3, H3K27me3), while hyper-methylated polycomb repressive complex (EZH2/SUZ12) recognizing regions. Altered...
Whereas coding variants often have pleiotropic effects across multiple tissues, noncoding are thought to mediate their phenotypic by specific tissue and temporal regulation of gene expression. Here, we investigated the genetic functional architecture a genomic region within FTO that is strongly associated with obesity risk. We show on common haplotype modify regulatory properties several enhancers targeting IRX3 IRX5 from megabase distances. demonstrate these affect expression in including...
In China, pottery containers first appeared about 20000 cal. BP, and became diverse in form during the Early Neolithic (9000-7000 BP), signaling emergence of functionally specialized vessels. China is also well-known for its early development alcohol production. However, few studies have focused on connections between two technologies. Based analysis residues (starch, phytolith, fungus) adhering to from sites north here we demonstrate that three material changes occurring signal innovation...
Abstract During the current COVID-19 pandemic, testing kit and RNA extraction availability has become a major limiting factor in ability to determine patient disease status accurately quantify prevalence. Current strategies rely on individual tests of cases matching restrictive diagnostic criteria detect SARS-CoV-2 RNA, asymptomatic mild cases. Testing these individuals is one effective way understand reduce spread COVID-19. Here, we develop pooled strategy identify low-risk individuals....
Abstract The Notch pathway is a conserved cell-cell communication that controls cell fate decisions. Here we sought to determine how activation inhibits the neuroendocrine in lungs, an archetypal process for decisions orchestrated by signaling has remained poorly understood at molecular level. Using intratumoral heterogeneity small-cell lung cancer as tractable model system, uncovered role transcriptional regulators REST and YAP promoters of non-neuroendocrine transition. We further...
Summary Infections can lead to persistent or long-term symptoms and diseases such as shingles after varicella zoster, cancers human papillomavirus, rheumatic fever streptococcal infections 1, 2 . Similarly, infection by SARS-CoV-2 result in Long COVID, a condition characterized of fatigue pulmonary cognitive dysfunction 3–5 The biological mechanisms that contribute the development COVID remain be clarified. We leveraged COVID-19 Host Genetics Initiative 6, 7 perform genome-wide association...
Narcolepsy type 1 (NT1) is caused by a loss of hypocretin/orexin transmission. Risk factors include pandemic 2009 H1N1 influenza A infection and immunization with Pandemrix®. Here, we dissect disease mechanisms interactions environmental triggers in multi-ethnic sample 6,073 cases 84,856 controls. We fine-mapped GWAS signals within HLA (DQ0602, DQB1*03:01 DPB1*04:02) discovered seven novel associations (CD207, NAB1, IKZF4-ERBB3, CTSC, DENND1B, SIRPG, PRF1). Significant at TRA DQB1*06:02 loci...