Genetics and Genomics Commons^™

Gene Gangs Of The Chloroviruses: Conserved Clusters Of Collinear Monocistronic Genes, Phillip Seitzer, Adrien Jeanniard, Fangrui Ma, James L. Van Etten, Marc T. Facciotti, David D. Dunigan

Nebraska Center for Virology: Faculty Publications

Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 + 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only …

Seqothello: Querying Rna-Seq Experiments At Scale, Ye Yu, Jinpeng Liu, Xinan Liu, Yi Zhang, Eamonn Magner, Erik Lehnert, Chen Qian, Jinze Liu

Computer Science Faculty Publications

We present SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq experiments. It takes SeqOthello only 5 min and 19.1 GB memory to conduct a global survey of 11,658 fusion events against 10,113 TCGA Pan-Cancer RNA-seq datasets. The query recovers 92.7% of tier-1 fusions curated by TCGA Fusion Gene Database and reveals 270 novel occurrences, all of which are present as tumor-specific. By providing a reference-free, alignment-free, and parameter-free sequence search system, SeqOthello will enable large-scale integrative studies using sequence-level data, an undertaking not previously practicable for many individual labs.

Antibody Epitope Specificity For Dsdna Phosphate Backbone Is An Intrinsic Property Of The Heavy Chain Variable Germline Gene Segment Used, Tatjana Srdic-Rajic, Heinz Kohler, Vladimir Jurisic, Radmila Metlas

Microbiology, Immunology, and Molecular Genetics Faculty Publications

Analysis of protein sequences by the informational spectrum method (ISM) enables characterization of their specificity according to encoded information represented with defined frequency (F). Our previous data showed that F(0.367) is characteristic for variable heavy chain (VH) domains (a combination of variable (V), diversity (D) and joining (J) gene segments) of the anti-phosphocholine (PC) T15 antibodies and mostly dependent on the CDR2 region, a site for PC phosphate group binding. Because the T15 dsDNA-reactive U4 mutant also encodes F(0.367), we hypothesized that the same frequency may also be characteristic for anti-DNA antibodies. Data obtained from an analysis of 60 spontaneously …

Genome-Wide Screening Identifies Genes And Biological Processes Implicated In Chemoresistance And Oncogene-Induced Apoptosis, Tengyu Ko

LSU Doctoral Dissertations

Anti-proliferative responses such as senescence and apoptosis are often used by normal cells to combat oncogenic insults and to prevent tumorigenesis. However, oncogenic mutations are frequently found in cancers, suggesting that additional mutations may occur to facilitate the bypass of these anti-proliferative responses. It is believed that some of these additional mutations may also contribute to the chemoresistance of cancers. This dissertation focused on identifying novel genes and biological processes implicated in chemoresistance and tumorigenesis.

Cisplatin-based chemotherapeutic regimens are frequently used for treatments of solid tumors. However, tumor cells may have inherent or acquired resistance to cisplatin, and the underlying …

Myc Distant Enhancers Underlie Ovarian Cancer Susceptibility At The 8q24.21 Locus, Anxhela Gjyshi Gustafson

USF Tampa Graduate Theses and Dissertations

Ovarian cancer is a leading cause of death among women diagnosed with cancer. Mortality rate is high because an overwhelming majority of new cases are diagnosed with late-stage disease when the survival statistics are very poor with an overall 5-year survival rate of less than 40%. Despite the large burden of disease, the etiology of ovarian cancer is not well understood. In addition to linkage studies that have identified highly penetrant cancer susceptibility genes such as BRCA1 and BRCA2, the emergence of Genome Wide Association Studies (GWAS) in the last decade has facilitated the identification of common genetic variants with …

Re-Thinking Alzheimer's Disease Therapeutic Targets Using Gene-Based Tests, Man Ki Kwok, Shi Lin Lin, C Mary Schooling

Publications and Research

Background: Alzheimer's disease (AD) is a devastating condition with no known effective drug treatments. Existing drugs only alleviate symptoms. Given repeated expensive drug failures, we assessed systematically whether approved and investigational AD drugs are targeting products of genes strongly associated with AD and whether these genes are targeted by existing drugs for other indications which could be re-purposed.

Methods: We identified genes strongly associated with late-onset AD fromthe loci of genetic variants associated with AD at genome-wide-significance and from a gene-based test applied to the most extensively genotyped late-onset AD case (n=17,008)-control (n=37,154) study, the International Genomics of Alzheimer's Project. …

A Review Of Current Knowledge Concerning The Breeding And Summer Distribution Of The Cordilleran Flycatcher (Empidonax Occidentalis) In Mexico, Harold F. Greeney, Matthew J. Miller, Charles Van Riper Iii

Occasional Papers of the Museum of Natural Science, Louisiana State University

The Cordilleran Flycatcher (Empidonax occidentalis) is one of many North American birds whose distribution crosses the US–Mexican border and for which little is presently known about summer distribution and breeding biology south of this border. In addition, the Cordilleran Flycatcher presents ornithologists with a number of challenging questions surrounding its taxonomy, migration, distribution, population structure, and species limits. In particular, there remains a good deal of uncertainty concerning the species-level relationships, seasonal movements, and the wintering and breeding distributions of both recognized subspecies of Cordilleran Flycatcher in Mexico. Using field observations, a thorough review of the literature, and …

Stochastic Difference Model For Evolutional Dynamics Of Large Antigen Repertoires In African Trypanosomes, Fan Yu

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

The Future Of Biodiversity Assessment: Using Environmental Dna And Next-Generation Sequencing To Characterize Biological Communities In The Central Highlands Of Arizona, Courtney Turner-Rathbone

Undergraduate Research Symposium - Prescott

Historically ecological surveys require significant man hours in the field, utilizing methods which can stress species being observed. In using environmental DNA (eDNA) gathered from air, soil, and water, traditional methods may be supplemented or reduced in order to more efficiently utilize funding and reduce or eliminate stress on surveyed species. Water was collected in replicates using aseptic technique from two different sites, 60 miles apart, along the Verde River. Samples were vacuum filtered within 24 hours through 0.45 μm cellulose nitrate (CN) filters to collect eDNA. DNA extraction from the filters was performed. The polymerase chain reaction (PCR) was …

Genotype Fingerprints Enable Fast And Private Comparison Of Genetic Testing Results For Research And Direct-To-Consumer Applications., Max Robinson, Gustavo Glusman

Articles, Abstracts, and Reports

Genetic testing has expanded out of the research laboratory into medical practice and the direct-to-consumer market. Rapid analysis of the resulting genotype data now has a significant impact. We present a method for summarizing personal genotypes as 'genotype fingerprints' that meets these needs. Genotype fingerprints can be derived from any single nucleotide polymorphism-based assay, and remain comparable as chip designs evolve to higher marker densities. We demonstrate that these fingerprints support distinguishing types of relationships among closely related individuals and closely related individuals from individuals from the same background population, as well as high-throughput identification of identical genotypes, individuals in …

Complete Genome Sequences Of 18 Paenibacillus Larvae Phages From The Western United States, Bryan D. Merrill, Christopher P. Fajardo, Jared A. Hilton, Ashley M. Payne, Andy T. Ward, Jamison K. Walker, Aziza Dhalai, Cameron Imahara, James Mangohig, Josh Monk, Cristian Pascacio, Padmani Rai, Alicia Salisbury, Kathie Velez, Travis J. Bloomfield, Brett Buhler, Steven G. Duncan, David A. Fuhriman, Josil George, Kiel Graves, Karli Graves, Hunter L. Hill, Michelle Kim, Bradley K. Knabe, Devin B. Ririe, Spencer L. Rogers, Casey Stamereilers, Michael B. Stephenson, Brittian K. Usher, Colton S. Ward, Jacob M. Withers

Life Sciences Faculty Research

We present here the complete genomes of 18 phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. The phages were isolated between 2014 and 2016 as part of an undergraduate phage discovery course at Brigham Young University. The phages were isolated primarily from bee debris and lysogens.

8th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The mission of the Annual Postdoctoral Science Symposium (APSS) is to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience. The MD Anderson Postdoctoral Association convened its inaugural Annual Postdoctoral Science Symposium (APSS) on August 4, 2011.

The APSS provides a professional venue for postdoctoral scientists to develop, clarify, and refine their research as a result of formal reviews and critiques of faculty and other postdoctoral scientists. Additionally, attendees discuss current research on a broad range of subjects while promoting academic interactions and enrichment and developing new collaborations.

Identification Of Target Genes For Rnai-Mediated Control Of The Twospotted Spider Mite, June-Sun Yoon, Dipak K. Sahoo, Indu B. Maiti, Subba Reddy Palli

Entomology Faculty Publications

RNA interference (RNAi) is being developed for the management of pests that destroy crops. The twospotted Spider Mite (TSSM), Tetranychus urticae is a worldwide pest due to its unique physiological and behavioral characteristics including extraordinary ability to detoxify a wide range of pesticides and feed on many host plants. In this study, we conducted experiments to identify target genes that could be used for the development of RNAi-based methods to control TSSM. Leaf disc feeding assays revealed that knockdown in the expression genes coding for proteins involved in the biosynthesis and action of juvenile hormone (JH) and action of ecdysteroids …

Involvement Of Jak/Stat Signaling And A Basement Membrane-Associated Protein During Air Sac Primordium Development In Drosophila Melanogaster, Nathan Anthony Powers

Masters Theses & Specialist Projects

Tumor metastasis currently presents the greatest obstacle for effective cancer remediation. Metastatic growth necessitates both degradation of a specialized form of extracellular matrix (ECM) known as the basement membrane (BM) and the invasion of surrounding tissues thereafter. The thoracic air sacs of fruit flies (Drosophila melanogaster), which develop and operate in a fashion comparable to the human lung, provide a unique model for identifying and characterizing factors that contribute to its own development as well as tumoral invasion. We investigated the involvement of both Janus kinase (JAK)/Signal transducer and activator of transcription (STAT) signaling and a BMassociated protein during the …

Iac Gene Expression In The Indole-3-Acetic Acid-Degrading Soil Bacterium Enterobacter Soli Lf7, Isaac V. Greenhut, Beryl L. Slezak, Johan H. J. Leveau

Plant and Soil Sciences Faculty Publications

We show for soil bacterium Enterobacter soli LF7 that the possession of an indole-3-acetic acid catabolic (iac) gene cluster is causatively linked to the ability to utilize the plant hormone indole-3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes, chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (iac cluster were genes for a major facilitator superfamily protein (mfs) and enzymes of the β-ketoadipate pathway (pcaIJD-catBCA), which channels …

Developmental Variation In Fruit Polyphenol Content And Related Gene Expression Of A Red-Fruited Versus A White-Fruited Fragraria Vesca Genotype, Sutapa Roy, Sanjay Singh, Douglas D. Archbold

Horticulture Faculty Publications

Two cultivars of F. vesca, red-fruited Baron Solemacher (BS) and white-fruited Pineapple Crush (PC), were studied to compare and contrast the quantitative accumulation of major polyphenols and related biosynthetic pathway gene expression patterns during fruit development and ripening. Developing PC fruit showed higher levels of hydroxycinnamic acids in green stages and a greater accumulation of ellagitannins in ripe fruit in comparison to BS. In addition to anthocyanin, red BS fruit had greater levels of flavan-3-ols when ripe than PC. Expression patterns of key structural genes and transcription factors of the phenylpropanoid/flavonoid biosynthetic pathway, an abscisic acid (ABA) biosynthetic gene, …

Glucose Signaling Is Important For Nutrient Adaptation During Differentiation Of Pleomorphic African Trypanosomes, Yijian Qiu, Jillian E. Milanes, Jessica A. Jones, Rooksana E. Noorai, Vijay Shankar, James C. Morris

Publications

The African trypanosome has evolved mechanisms to adapt to changes in nutrient availability that occur during its life cycle. During transition from mammalian blood to insect vector gut, parasites experience a rapid reduction in environmental glucose. Here we describe how pleomorphic parasites respond to glucose depletion with a focus on parasite changes in energy metabolism and growth. Long slender bloodstream form parasites were rapidly killed as glucose concentrations fell, while short stumpy bloodstream form parasites persisted to differentiate into the insect-stage procyclic form parasite. The rate of differentiation was lower than that triggered by other cues but reached physiological rates …

Identification Of Chst9 As A Candidate Gene For Schizophrenia From Whole Genome Sequencing, Christopher Sharp, Jingchun Chen, Marvi Moreno, Mahtab Hamid, Francisco Servin, Bita Bashy, Travis Mize

LSAMP Poster Presentations

Recent results imply that rare variants contribute to the risk of schizophrenia. We conducted whole genome sequencing for 99 subjects from 20 Chinese families (parents and at least two siblings with a schizophrenia diagnosis and one unaffected sibling). Of the 9 frameshift mutations identified in more than 2 families, one was at chromosome 10:125780762 on the Carbohydrate Sulfotransferase 15 (CHST15) gene and another at chromosome 18:24722723 on the Carbohydrate Sulfotransferase 9 (CHST9) gene. We observed these deletions in 4 affected persons of two families from whole. At least two types of mutations (one or three bases insertion) have been identified …

Set It And Forget It! A Self-Sustaining Semester-Long Literature Assignment For An Undergraduate Genetics Class. Now With A Bonus Reference Game To Emphasize Boolean Operators!, Brian Odom

Georgia International Conference on Information Literacy

Biology is the largest undergraduate major at Wingate University and Molecular Genetics is a required course for all biology majors. Some of the goals of this course are to provide technical training in skills required to function in the modern workforce. In addition to the gaining of molecular laboratory techniques, training in the use of library resources is also included in the laboratory curriculum. This training, taught by the course instructor, is a follow-up to an intensive library introduction provided by reference and instruction Librarians as part of the foundational molecular biology course taken during the freshman year.

This additional …

Complete Genome Sequences Of Paenibacillus Larvae Phages Halcyone, Heath, Scottie, And Unity From Las Vegas, Nevada, Diane G. Yost, Carolyn Chang, Lucy Leblanc, Erin Cassin, Ceara Peterman, Padmani Rai, Alicia Salisbury, Nicolas Barroga, Ramiro Cisneros, Joseph Fersini, Jonathan Juste, Juvie Ines, Gabriel Leyva, Dyanne Macalinao, Spencer Muscelli, Gustavo S. Reyes, Heather Rhoden, Rodney Tan, Erika Torres, Krystal Tran, Georgette Uriarte-Valle, Christopher Wallace, Simon Wong, Kevin Ayala-Pineda, Vanessa Cadiz, Tiffany Jeanite, Sophia Nhan, Julianne H. Grose, Christy Strong, Penny S. Amy, Philippos K. Tsourkas

Life Sciences Faculty Research

We present the complete genome sequences of four phages that infect Paenibacillus larvae, the causative agent of American foulbrood disease in honeybees. The phages were isolated from beehives and beeswax products from Las Vegas, Nevada. The genomes are 50 to 55 kbp long and use the “direct terminal repeats” DNA-packaging strategy.

Able: Blockwise Site Frequency Spectrafor Inferring Complex Population Histories And Recombination, Champak R. Beeravolu, Michael J. Hickerson, Laurent A. F. Frantz, Konrad Lohse

Publications and Research

We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE.

Using Transcriptomics To Enable A Plethodontid Salamander (Bolitoglossa Ramosi) For Limb Regeneration Research, Claudia M. Arenas Gómez, Ryan M. Woodcock, Jeramiah J. Smith, Randal S. Voss, Jean Paul Delgado

Biology Faculty Publications

Background: Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain a broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-Seq to generate a de novo reference transcriptome and identify differentially expressed genes during limb regeneration.

Results: Using paired-end Illumina sequencing technology and Trinity …

Fine Mapping Of Mhc Region In Lung Cancer Highlights Independent Susceptibility Loci By Ethnicity, Aida Ferreiro-Iglesias, Corina Lesseur, James Mckay, Rayjean J. Hung, Younghun Han, Xuchen Zong, David Christiani, Mattias Johansson, Xiangjun Xiao, Yafang Li, David C. Qian, Xuemei Ji, Geoffrey Liu, Neil Caporaso, Ghislaine Scelo, David Zaridze, Anush Mukeriya, Milica Kontic, Simona Ognjanovic, Jolanta Lissowska, Małgorzata Szołkowska, Beata Swiatkowska, Vladimir Janout, Ivana Holcatova, Ciprian Bolca, Milan Savic, Miodrag Ognjanovic, Stig Egil Bojesen, Xifeng Wu, Demetrios Albanes, Susanne M. Arnold

Markey Cancer Center Faculty Publications

Lung cancer has several genetic associations identified within the major histocompatibility complex (MHC); although the basis for these associations remains elusive. Here, we analyze MHC genetic variation among 26,044 lung cancer patients and 20,836 controls densely genotyped across the MHC, using the Illumina Illumina OncoArray or Illumina 660W SNP microarray. We impute sequence variation in classical HLA genes, fine-map MHC associations for lung cancer risk with major histologies and compare results between ethnicities. Independent and novel associations within HLA genes are identified in Europeans including amino acids in the HLA-B*0801 peptide binding groove and an independent HLA-DQB1*06 loci group. In …

Transcriptional Profiling Of Liver During The Critical Embryo-To-Hatchling Transition Period In The Chicken (Gallus Gallus), Larry A. Cogburn, Nares Trakooljul, Chuming Chen, Hongzhan Huang, Cathy H. Wu, Wilfrid Carré, Xiaofei Wang, Harold B. White Iii

Biology Faculty Research

Background

Although hatching is perhaps the most abrupt and profound metabolic challenge that a chicken must undergo; there have been no attempts to functionally map the metabolic pathways induced in liver during the embryo-to-hatchling transition. Furthermore, we know very little about the metabolic and regulatory factors that regulate lipid metabolism in late embryos or newly-hatched chicks. In the present study, we examined hepatic transcriptomes of 12 embryos and 12 hatchling chicks during the peri-hatch period—or the metabolic switch from chorioallantoic to pulmonary respiration.

Results

Initial hierarchical clustering revealed two distinct, albeit opposing, patterns of hepatic gene expression. Cluster A genes …

Effect Of Larval Starvation On Lipid Content Of Drosophila Melanogaster Over 15 Days, Fabian Leija, Allen Gibbs

LSAMP Poster Presentations

Starvation-resistant Drosophila melanogaster, common fruit flies, deriving from 121 generations of starvation selection, have resulted in genetically, behaviorally, and physiologically different individuals compared to non-resistant counterparts. Starvation-resistant Drosophila are more obese, containing twice as much lipids as control flies.This is a result of starvation-resistant fly larva feeding for 5 days and then entering the pupa stage while non-resistant flies only feed for 4 days.

In this experiment, we hope to answer the question of whether the starvation-resistant flies are genetically predisposed to be substantially more obese than wild populations or if it is a result of this alternate behavior …

Evaluating The Performance Of Gene-Based Tests Of Genetic Association When Testing For Association Between Methylation And Change In Triglyceride Levels At Gaw20, Jason Vander Woude, Jordan Huisman, Lucas Vander Berg, Jenna Veenstra, Abbey Bos, Anya Kalsbeek, Karissa Koster, Nathan Ryder, Nathan L. Tintle

Faculty Work Comprehensive List

Although methylation data continues to rise in popularity, much is still unknown about how to best analyze methylation data in genome-wide analysis contexts. Given continuing interest in gene-based tests for next-generation sequencing data, we evaluated the performance of novel gene-based test statistics on simulated data from GAW20. Our analysis suggests that most of the gene-based tests are detecting real signals and maintaining the Type I error rate. The minimum pvalue and threshold-based tests performed well compared to single-marker tests in many cases, especially when the number of variants was relatively large with few true causal variants in the set.

Data For Gaw20: Genome-Wide Dna Sequence Variation And Epigenome-Wide Dna Methylation Before And After Fenofibrate Treatment In A Family Study Of Metabolic Phenotypes, Stella Aslibekyan, Laura Almasy, Michael A. Province, Devin M. Absher, Donna K. Arnett

Epidemiology and Environmental Health Faculty Publications

GAW20 provided participants with an opportunity to comprehensively examine genetic and epigenetic variation among related individuals in the context of drug treatment response. GAW20 used data from 188 families (N = 1105) participating in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study (clinicaltrials.gov identifier NCT00083369), which included CD4+ T-cell DNA methylation at 463,995 cytosine-phosphate-guanine (CpG) sites measured before and after a 3-week treatment with fenofibrate, single-nucleotide variation at 906,600 loci, metabolic syndrome components ascertained before and after the drug intervention, and relevant covariates. All GOLDN participants were of European descent, with an average age of …

Longitudinal Data Methods For Evaluating Genome-By-Epigenome Interactions In Families, Justin C. Strickland, I-Chen Chen, Chanung Wang, David W. Fardo

Psychology Faculty Publications

Background: Longitudinal measurement is commonly employed in health research and provides numerous benefits for understanding disease and trait progression over time. More broadly, it allows for proper treatment of correlated responses within clusters. We evaluated 3 methods for analyzing genome-by-epigenome interactions with longitudinal outcomes from family data.

Results: Linear mixed-effect models, generalized estimating equations, and quadratic inference functions were used to test a pharmacoepigenetic effect in 200 simulated posttreatment replicates. Adjustment for baseline outcome provided greater power and more accurate control of Type I error rates than computation of a pre-to-post change score.

Conclusions: Comparison of all modeling approaches indicated …

Application Of Novel And Existing Methods To Identify Genes With Evidence Of Epigenetic Association: Results From Gaw20, Angga M. Fuady, Samantha Lent, Chloé Sarnowski, Nathan L. Tintle

Faculty Work Comprehensive List

Background: The rise in popularity and accessibility of DNA methylation data to evaluate epigenetic associations with disease has led to numerous methodological questions. As part of GAW20, our working group of 8 research groups focused on gene searching methods.

Results: Although the methods were varied, we identified 3 main themes within our group. First, many groups tackled the question of how best to use pedigree information in downstream analyses, finding that (a) the use of kinship matrices is common practice, (b) ascertainment corrections may be necessary, and (c) pedigree information may be useful for identifying parent-of-origin effects. Second, many groups …

Epigenome Wide Association Study Of Snp–Cpg Interactions On Changes In Triglyceride Levels After Pharmaceutical Intervention: A Gaw20 Analysis, Jenna Veenstra, Anya Kalsbeek, Karissa Koster, Nathan Ryder, Abbey Bos, Jordan Huisman, Lucas Vander Berg, Jason Vander Woude, Nathan L. Tintle

Faculty Work Comprehensive List

In the search for an understanding of how genetic variation contributes to the heritability of common human disease, the potential role of epigenetic factors, such as methylation, is being explored with increasing frequency. Although standard analyses test for associations between methylation levels at individual cytosine-phosphateguanine (CpG) sites and phenotypes of interest, some investigators have begun testing for methylation and how methylation may modulate the effects of genetic polymorphisms on phenotypes. In our analysis, we used both a genome-wide and candidate gene approach to investigate potential single-nucleotide polymorphism (SNP)–CpG interactions on changes in triglyceride levels. Although we were able to identify …