A5088414680- Acute Myeloid Leukemia Research
- Hemoglobinopathies and Related Disorders
- Erythrocyte Function and Pathophysiology
- Chronic Lymphocytic Leukemia Research
- Cancer Genomics and Diagnostics
- Chromosomal and Genetic Variations
- Plant-Microbe Interactions and Immunity
- Evolution and Genetic Dynamics
- Genomic variations and chromosomal abnormalities
- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- Insect-Plant Interactions and Control
- Glycosylation and Glycoproteins Research
- Plant Virus Research Studies
- Plant pathogens and resistance mechanisms
- Plant Disease Resistance and Genetics
- Genomics, phytochemicals, and oxidative stress
- NF-κB Signaling Pathways
- Molecular Biology Techniques and Applications
- Genomics and Chromatin Dynamics
- Plant Pathogenic Bacteria Studies
- Genetic factors in colorectal cancer
- Immunodeficiency and Autoimmune Disorders
- Galectins and Cancer Biology
- Plant Pathogens and Resistance
University of Utah
2015-2024
ARUP Laboratories (United States)
2023-2024
Huntsman Cancer Institute
2020-2021
University of California, Davis
2015-2019
Plant (United States)
2015
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally spatially. These shifting pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness are therefore subject to selection, we conducted multi-year trial using lines...
Germline mutation rates in humans have been estimated for a variety of types, including single-nucleotide and large structural variants. Here, we directly measure the germline retrotransposition rate three active retrotransposon elements: L1, Alu , SVA. We used tools calling mobile element insertions (MEIs) (MELT, RUFUS, TranSurVeyor) on blood-derived whole-genome sequence (WGS) data from 599 CEPH individuals, comprising 33 three-generation pedigrees. identified 26 de novo MEIs 437 births....
The most established model of the eukaryotic innate immune system is derived from examples large effect monogenic quantitative resistance to pathogens. However, many host-pathogen interactions involve genes small medium and exhibit resistance. We used Arabidopsis-Botrytis pathosystem explore genetic architecture underlying host in a population Arabidopsis thaliana. By infecting diverse panel accessions with four phenotypically genotypically distinct isolates fungal necrotroph B. cinerea, we...
Each human genome includes de novo mutations that arose during gametogenesis. While these germline represent a fundamental source of new genetic diversity, they can also create deleterious alleles impact fitness. Whereas the rate and patterns point in are now well understood, far less is known about frequency features structural variants (dnSVs). We report family-based study among 9,599 genomes from 33 multigenerational CEPH-Utah families 2,384 Simons Foundation Autism Research Initiative....
To respond to pathogen attack, selection and associated evolution has led the creation of plant immune system that are a highly effective inducible defense system. Central this hormones jasmonic acid (JA) salicylic (SA) crosstalk between two, which may play an important role in responses specific pathogens or even genotypes. Here, we used Arabidopsis thaliana-Botrytis cinerea pathosystem test how host's functions against genetic variation pathogen. We measured defense-related phenotypes...
A central goal of studying host-pathogen interaction is to understand how host and pathogen manipulate each other promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection provide systematic map the cross-kingdom communication between two species. Here we used Arabidopsis-B. cinerea pathosystem test plant fungal interact at transcriptomic level. We assessed impact genetic diversity by utilization collection 96...
To estimate the genetic risk conferred by known amyotrophic lateral sclerosis (ALS)-associated genes to pathogenesis of sporadic ALS (SALS) using variant allele frequencies combined with predicted pathogenicity.Whole exome sequencing and repeat expansion PCR C9orf72 ATXN2 were performed on 87 patients European ancestry SALS seen at University Utah. DNA variants that change protein coding sequence 31 ALS-associated annotated determine which rare deleterious as MetaSVM. The percentage a or in...
Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by detectable hematopoietic-associated gene mutations in a person without evidence hematologic malignancy. We sought to identify additional cancer-presenting useable for CHIP detection performing data mining analysis 48 somatic mutation studies reporting at diagnoses 7,430 adult and pediatric patients with malignancies. Following extraction 20,141 protein-altering mutations, we identified 434 significantly recurrent...
Plant resistance to generalist pathogens with broad host ranges, such as Botrytis cinerea (Botrytis), is typically quantitative and highly polygenic. Recent studies have begun elucidate the molecular genetic basis of plant-pathogen interactions using commonly measured traits, including lesion size and/or pathogen biomass. However, advent digital imaging high-throughput phenomics, there are a large number additional traits available study resistance. In this study, we used analysis...
Ongoing retrotransposition of Alu, LINE-1, and SINE-VNTR-Alu elements generates diversity variation among human populations. Previous analyses investigating the population genetics mobile element insertions (MEIs) have been limited by ascertainment bias or relatively small numbers populations low sequencing coverage. Here, we use 296 individuals representing 142 global from Simons Genome Diversity Project (SGDP) to discover characterize MEI deeply sequenced whole-genome data. We report 5,742...
Despite the growing number of studies showing that genotype × environment and epistatic interactions control fitness, influences epistasis on adaptive trait evolution remain largely uncharacterized. Across three field trials, we quantified aliphatic glucosinolate (GSL) defense chemistry, leaf damage, relative fitness using mutant lines Arabidopsis thaliana varying at pairs causal GSL genes to test impact variation. We found accumulation was primarily influenced by additive genetic variation,...
Abstract We performed whole genome resequencing of 84 field isolates Botrytis cinerea , largely collected from a local set plant species. Combined with 13 previously resequenced sampled diverse locations, this gave collection 97 for studies natural variation. Alignment to the reference sequence T4 and SNP detection provided further data population genetics analysis including mapping association studies. Although much genomic diversity was captured in original isolates, additional genomes...
Alu retrotransposons account for more than 10% of the human genome, and insertions these elements create structural variants segregating in populations. Such polymorphic Alus are powerful markers to understand population structure, they represent that can greatly impact genome function, including gene expression. Accurate genotyping other mobile has been challenging. Indeed, we found genotypes previously called 1000 Genomes Project sometimes erroneous, which poses significant problems...
Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential discover in populations, various bioinformatics methods have been designed tackle problem of detecting these highly repetitive elements. However, current techniques discovery may miss rare, polymorphic Combining multiple approaches provide a better profile mobilome. AluYb8/9 focus our...
The Kashmiri population is an ethno-linguistic group that resides in the Kashmir Valley northern India. A longstanding hypothesis this derives ancestry from Jewish and/or Greek sources. There historical and archaeological evidence of ancient presence India Kashmir. Further, some accounts suggest Hebrew as well. To date, it has not been determined whether signatures or admixture can be detected population. Using genome-wide genotyping detection methods, we there are no significant substantial...
While mobile elements are largely inactive in healthy somatic tissues, increased activity has been found cancer with significant variation among different types. In addition to insertion events, have also mediate many structural events the genome. Here, better understand timing and impact of element insertions associated variants cancer, we examined their longitudinal samples four metastatic breast patients. We identified 11 or that majority these occurred early tumor progression. Most...
SRSF2 mutations are known to be associated with poor outcomes in myelodysplastic neoplasm, but studies on their prognostic impact acute myeloid leukemia (AML) remain limited. In this retrospective study, we analyzed clinical and pathologic characteristics of patients AML correlated the mutations.
Abstract Each human genome includes de novo mutations that arose during gametogenesis. While these germline represent a fundamental source of new genetic diversity, they can also create deleterious alleles impact fitness. The mutation rate for single nucleotide variants and factors significantly influence this rate, such as parental age, are now well established. However, far less is known about the frequency, distribution, features structural mutations. We report large, family-based study...
Abstract Germline mutation rates in humans have been estimated for a variety of types, including single nucleotide and large structural variants. Here we directly measure the germline retrotransposition rate three active retrotransposon elements: L1, Alu, SVA. We utilized tools calling Mobile Element Insertions (MEIs) (MELT, RUFUS, TranSurVeyor) on blood-derived whole genome sequence (WGS) data from 603 CEPH individuals, comprising 33 three-generation pedigrees. identified 27 de novo MEIs...
Abstract A central goal of studying host-pathogen interaction research is to understand how the host and pathogen manipulate each other promote their own fitness in a pathosystem. Co-transcriptomic approaches can simultaneously analyze dual transcriptomes during infection provide systematic map cross-kingdom communication between two species. Here we used Arabidopsis- B. cinerea pathosystem test plant fungal at transcriptomic level infection. We assessed impact natural genetic diversity by...
Cytogenomic SNP microarray (SNP-A) is a reliable methodology for detection of acquired copy number variants (CNVs) and regions homozygosity consistent with copy-neutral loss-of-homozygosity (CN-LOH) in patients hematologic neoplasms. In recent years, utilization SNP-A both inherited forms bone marrow failure syndromes (BMFs) has increased, large part due to emerging discoveries including identification alterations that may signify disease progression or remission.
Chronic lymphocytic leukemia (CLL) has been shown to cluster in families. First-degree relatives of individuals with CLL have an ~8 fold increased risk developing the malignancy. Strong heritability suggests pedigree studies will good power localize pathogenic genes. However, is relatively rare and heterogeneous, complicating ascertainment analyses. Our goal was identify loci using unique resources available Utah methods address intra-familial heterogeneity.