Life Sciences Commons^™

Impact Of Fads Genotype On Polyunsaturated Fatty Acid Content In Human Milk Extracellular Vesicles: A Genetic Association Study, John J. Miklavcic, Natalie Paterson, Jennifer Hahn-Holbrook, Laura M. Glynn

Food Science Faculty Articles and Research

Background

Extracellular vesicles in human milk are critical in supporting newborn growth and development. Bioavailability of dietary extracellular vesicles may depend on the composition of membrane lipids. Single-nucleotide polymorphisms (SNPs) in the fatty acid desaturase gene cluster impact the content of long-chain polyunsaturated fatty acids in human milk phospholipids. This study investigated the relation between variation in FADS1 and FADS2 with the content of polyunsaturated fatty acids in extracellular vesicles from human milk.

Methods

Milk was obtained from a cohort of mothers (N = 70) at 2–4 weeks of lactation. SNPs in the FADS gene locus were determined using …

Taxonomic Advances Driven By The Genomic Analysis Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

This study presents new findings based on a large-scale analysis of butterfly genomic sequences. Focusing on species identification through comparative genomics, we define subspecies as populations differentiated to a lesser extent than distinct species ("species in the making"). Additionally, we propose further adjustments to the current butterfly classification. As a result, 3 subgenera, 12 species, and 4 subspecies are described as new. New subgenera are (type species in parenthesis): Hyalaus Grishin, subgen. n. (Papilio epidaus E. Doubleday, 1846) of Eurytides Hübner, [1821] (Papilionidae Latreille, [1802]) and Astria Grishin, subgen. n. (Lycaena astraea Freyer, 1851) of Glaucopsyche Scudder, 1872 …

Multi-Cancer Early Detection Testing (Mced), Ora K Gordon, Brad Bott, Nanor Parseghian, Paul Psychogios, Kimberly K Childers, Sandra Brown

Articles, Abstracts, and Reports

No abstract provided.

Population Screening For High-Risk Patient Identification Partnership With Care-Comprehensive Assessment, Risk, And Education., Ora K Gordon, Brad Bott, Nanor Parseghian, Kimberly K Childers, Sandra Brown

Articles, Abstracts, and Reports

No abstract provided.

Genomic Analysis Reveals New Species And Subspecies Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Large-scale genomic sequencing of butterfly taxa reveals new findings that are presented here. While we focus on detecting species by comparative genomics and define subspecies as groups of populations genetically differentiated from each other but not as strongly as species (that is, subspecies as species in the making), we report other adjustments to butterfly classification. As a result, 4 subgenera, 11 species, and 6 subspecies are proposed as new. New subgenera are: Rapis Grishin, subgen. n. (type species Papilio rapae Linnaeus, 1758, genus Pieris Schrank, 1801) in Pieridae Swainson, 1820 and Callitera Grishin, subgen. n. (type species Eurygona? pulcherrima …

Demographic History Shapes North American Gray Wolf Genomic Diversity And Informs Species' Conservation, Bridgett M. Vonholdt, Daniel R. Stahler, Kristin Brzeski, Marco Musiani, Rolf O. Peterson, Michael Phillips, John Stephenson, Kent Laudon, Erin Meredith, John Vucetich, Jennifer A. Leonard, Robert K. Wayne

Michigan Tech Publications, Part 2

Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, …

Type 2 Diabetes Modifies The Association Of Cad Genomic Risk Variants With Subclinical Atherosclerosis, Natalie R Hasbani, Kenneth E Westerman, Soo Heon Kwak, Han Chen, Xihao Li, Daniel Di Corpo, Jennifer Wessel, Joshua C Bis, Chloè Sarnowski, Peitao Wu, Lawrence F Bielak, Xiuqing Guo, Nancy Heard-Costa, Gregory L Kinney, Michael C Mahaney, May E Montasser, Nicholette D Palmer, Laura M Raffield, James G Terry, Lisa R Yanek, Jessica Bon, Donald W Bowden, Jennifer A Brody, Ravindranath Duggirala, David R Jacobs, Rita R Kalyani, Leslie A Lange, Braxton D Mitchell, Jennifer A Smith, Kent D Taylor, April P Carson, Joanne E Curran, Myriam Fornage, Barry I Freedman, Stacey Gabriel, Richard A Gibbs, Namrata Gupta, Sharon L R Kardia, Brian G Kral, Zeineen Momin, Anne B Newman, Wendy S Post, Karine A Viaud-Martinez, Kendra A Young, Lewis C Becker, Alain G Bertoni, John Blangero, John J Carr, Katherine Pratte, Bruce M Psaty, Stephen S Rich, Joseph C Wu, Rajeev Malhotra, Patricia A Peyser, Alanna C Morrison, Ramachandran S Vasan, Xihong Lin, Jerome I Rotter, James B Meigs, Alisa K Manning, Paul S De Vries

Journal Articles

BACKGROUND: Individuals with type 2 diabetes (T2D) have an increased risk of coronary artery disease (CAD), but questions remain about the underlying pathology. Identifying which CAD loci are modified by T2D in the development of subclinical atherosclerosis (coronary artery calcification [CAC], carotid intima-media thickness, or carotid plaque) may improve our understanding of the mechanisms leading to the increased CAD in T2D.

METHODS: We compared the common and rare variant associations of known CAD loci from the literature on CAC, carotid intima-media thickness, and carotid plaque in up to 29 670 participants, including up to 24 157 normoglycemic controls and 5513 …

Descriptions Of One Hundred New Species Of Hesperiidae, Jing Zhang, Qian Cong, Nick V. Grishin

Insecta Mundi

A century and a half since the time of Hewitson, we are experiencing a renaissance in species discovery fueled by whole genome sequencing. A large-scale genomic analysis of Hesperiidae Latreille, 1809 (Lepidoptera), including primary type specimens, reveals a deluge of species new to science. One hundred of them (one in a new genus) are described here from the New World (type localities are given in parenthesis): Drephalys (Drephalys) diovalis Grishin, new species (Ecuador: Napo), Euriphellus panador Grishin, new species (Ecuador: Esmeraldas), Euriphellus panamicus Grishin, new species (Panama: Panama), Cecropterus (Thorybes) viridissimus Grishin, new species (Ecuador: Zamora-Chinchipe), …

Genomics-Based Taxonomic Rearrangement Of Achlyodini And Carcharodini (Lepidoptera: Hesperiidae: Pyrginae), Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

Insecta Mundi

Genomic analysis of Pyrginae Burmeister, 1878 (Lepidoptera: Hesperiidae Latreille, 1809) with an emphasis on the tribes Achlyodini Burmeister, 1878 and Carcharodini Verity, 1940 reveals many incon­sistencies between the resulting phylogeny and the current classification. These problems are corrected by proposing new taxa, changing the ranks of others, or synonymizing them, and transferring species between genera. As a result, five subtribes, one genus, 20 subgenera, and one species are proposed as new: Cyclo­semiina Grishin, new subtribe (type genus Cyclosemia Mabille, 1878), Ilianina Grishin, new subtribe (type genus Iliana E. Bell, 1937), Nisoniadina Grishin, new subtribe (type genus Nisoniades Hübner, [1819]), …

Genetic And Environmental Drivers Of Migratory Behavior In Western Burrowing Owls And Implications For Conservation And Management, Kelly Barr, Christen M. Bossu, Rachel A. Bay, Eric C. Anderson, Jim Belthoff, Lynne A. Trulio, Debra Chromczak, Colleen L. Wisinski, Thomas B. Smith, Kristen C. Ruegg

Biology Faculty Publications and Presentations

Migration is driven by a combination of environmental and genetic factors, but many questions remain about those drivers. Potential interactions between genetic and environmental variants associated with different migratory phenotypes are rarely the focus of study. We pair low coverage whole genome resequencing with a de novo genome assembly to examine population structure, inbreeding, and the environmental factors associated with genetic differentiation between migratory and resident breeding phenotypes in a species of conservation concern, the western burrowing owl (Athene cunicularia hypugaea). Our analyses reveal a dichotomy in gene flow depending on whether the population is resident or migratory, …

Demographic History Shapes North American Gray Wolf Genomic Diversity And Informs Species' Conservation, Bridgett M. Vonholdt, Daniel R. Stahler, Kristin Brzeski, Marco Musiani, Rolf O. Peterson, Michael Phillips, John Stephenson, Kent Laudon, Erin Meredith, John A. Vucetich, Jennifer A. Leonard, Robert K. Wayne

Michigan Tech Publications, Part 2

Effective population size estimates are critical information needed for evolutionary predictions and conservation decisions. This is particularly true for species with social factors that restrict access to breeding or experience repeated fluctuations in population size across generations. We investigated the genomic estimates of effective population size along with diversity, subdivision, and inbreeding from 162,109 minimally filtered and 81,595 statistically neutral and unlinked SNPs genotyped in 437 grey wolf samples from North America collected between 1986 and 2021. We found genetic structure across North America, represented by three distinct demographic histories of western, central, and eastern regions of the continent. Further, …

A Haplotype-Resolved Chromosome-Scale Genome For Quercus Rubra L. Provides Insights Into The Genetics Of Adaptive Traits For Red Oak Species, Beant Kapoor, Jerry Jenkins, Jeremy Schmutz, Tatyana Zhebentyayeva, Carsten Kulheim, Mark Coggeshall, Chris Heim, Jesse R. Lasky, Laura Leites, Nurul Islam-Faridi, Jeanne Romero-Severson, Victoria L. Deleo, Sarah M. Lucas, Desanka Lazic, Oliver Gailing, John Carlson, Margaret Staton

Michigan Tech Publications, Part 2

Northern red oak (Quercus rubra L.) is an ecologically and economically important forest tree native to North America. We present a chromosome-scale genome of Q. rubra generated by the combination of PacBio sequences and chromatin conformation capture (Hi-C) scaffolding. This is the first reference genome from the red oak clade (section Lobatae). The Q. rubra assembly spans 739 Mb with 95.27% of the genome in 12 chromosomes and 33,333 protein-coding genes. Comparisons to the genomes of Quercus lobata and Quercus mongolica revealed high collinearity, with intrachromosomal structural variants present. Orthologous gene family analysis with other tree species revealed that gene …

Multivariate Adaptive Shrinkage Improves Cross-Population Transcriptome Prediction And Association Studies In Underrepresented Populations, Daniel Araujo, Chris Nguyen, Xiaowei Hu, Anna V. Mikhaylova, Christopher R. Gignoux, Kristin Ardlie, Kent D. Taylor, Peter Durda, Yongmei Liu, George Papanicolaou, Michael H. Cho, Stephen S. Rich, Jerome I. Rotter, Nhlbi Topmed Consortium, Hae Kyung Im, Ani Manichaikul, Heather Wheeler

Biology: Faculty Publications and Other Works

Transcriptome prediction models built with data from European-descent individuals are less accurate when applied to different populations because of differences in linkage disequilibrium patterns and allele frequencies. We hypothesized that methods that leverage shared regulatory effects across different conditions, in this case, across different populations, may improve cross-population transcriptome prediction. To test this hypothesis, we made transcriptome prediction models for use in transcriptome-wide association studies (TWASs) using different methods (elastic net, joint-tissue imputation [JTI], matrix expression quantitative trait loci [Matrix eQTL], multivariate adaptive shrinkage in R [MASHR], and transcriptome-integrated genetic association resource [TIGAR]) and tested their out-of-sample transcriptome prediction accuracy …

Phylogenomics Reveals The History Of Host Use In Mosquitoes, John Soghigian, Charles Sither, Silvia Andrade Justi, Gen Morinaga, Brian K. Cassel, Christopher J. Vitek, Todd Livdahl, Siyang Xia, Andrea Gloria-Soria, Jeffrey R. Powell

School of Integrative Biological and Chemical Sciences Faculty Publications and Presentations

Mosquitoes have profoundly affected human history and continue to threaten human health through the transmission of a diverse array of pathogens. The phylogeny of mosquitoes has remained poorly characterized due to difficulty in taxonomic sampling and limited availability of genomic data beyond the most important vector species. Here, we used phylogenomic analysis of 709 single copy ortholog groups from 256 mosquito species to produce a strongly supported phylogeny that resolves the position of the major disease vector species and the major mosquito lineages. Our analyses support an origin of mosquitoes in the early Triassic (217 MYA [highest posterior density region: …

Butterfly Classification And Species Discovery Using Genomics, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Genomic sequencing of worldwide butterfly fauna followed by phylogenetic analysis of protein-coding genes informs butterfly classification throughout the taxonomic hierarchy, from families to species. As a rule, we attribute the same taxonomic rank to more prominent clades of comparable divergence (that is, at the same level in the tree). For species delimitation, we use criteria based on relative genetic differentiation and the extent of gene exchange between populations. We analyze the current taxonomic classification of butterflies in the light of genomic phylogenies and encounter clades that correspond to yet unnamed taxa. As a result, 11 tribes, 33 subtribes, 2 genera, …

Targeted Sequencing Of The Panicum Miliaceum Gene Space And Genotyping Of Variant Sites From Population Genetics Studies, Combined In A Single Assay, As A Tool For Broomcorn Millet Assisted Breeding, Gabriele Magris, Serena Foria, Silvano Ciani, Dipak K. Santra, Ombretta Polenghi, Virna Cerne, Michele Morgante, Gabriele Di Gaspero

Department of Agronomy and Horticulture: Faculty Publications

Broomcorn millet (Panicum miliaceum L.) is a prehistorical cereal, today cultivated as a minor crop with low yields but with a renewed interest for its high water use effciency and gluten-free grains. To reverse the downward trend in broomcorn millet cultivation, the crop needs genetic improvement and creation of novel genetic variation to increase productivity. In order to facilitate genomics-assisted breeding, we designed a reduced representation genome-sequencing assay that investigates 1.8% of the nuclear DNA in a targeted and reproducible way, with an intensity of genomic sampling that is a direct function of local recombination rate. We used this …

Genomic Analysis Of Clostridioides Difficile Recovered From Horses In Western Australia, Natasza M. R. Hain-Saunders, Daniel R. Knight, Mieghan Bruce, David Byrne, Thomas V. Riley

Research outputs 2022 to 2026

Clostridioides difficile poses an ongoing threat as a cause of gastrointestinal disease in humans and animals. Traditionally considered a human healthcare-related disease, increases in community-associated C. difficile infection (CDI) and growing evidence of inter-species transmission suggest a wider perspective is required for CDI control. In horses, C. difficile is a major cause of diarrhoea and life-threatening colitis. This study aimed to better understand the epidemiology of CDI in Australian horses and provide insights into the relationships between horse, human and environmental strains. A total of 752 faecal samples from 387 Western Australian horses were collected. C. difficile was isolated from …

Tumor Biology And Immune Infiltration Define Primary Liver Cancer Subsets Linked To Overall Survival After Immunotherapy, Anuradha Budhu, Erica C Pehrsson, Aiwu He, Lipika Goyal, Robin Kate Kelley, Hien Dang, Changqing Xie, Cecilia Monge, Mayank Tandon, Lichun Ma, Mahler Revsine, Laura Kuhlman, Karen Zhang, Islam Baiev, Ryan Lamm, Keyur Patel, David E Kleiner, Stephen M Hewitt, Bao Tran, Jyoti Shetty, Xiaolin Wu, Yongmei Zhao, Tsai-Wei Shen, Sulbha Choudhari, Yuliya Kriga, Kris Ylaya, Andrew C Warner, Elijah F Edmondson, Marshonna Forgues, Tim F Greten, Xin Wei Wang

Kimmel Cancer Center Faculty Papers

Primary liver cancer is a rising cause of cancer deaths in the US. Although immunotherapy with immune checkpoint inhibitors induces a potent response in a subset of patients, response rates vary among individuals. Predicting which patients will respond to immune checkpoint inhibitors is of great interest in the field. In a retrospective arm of the National Cancer Institute Cancers of the Liver: Accelerating Research of Immunotherapy by a Transdisciplinary Network (NCI-CLARITY) study, we use archived formalin-fixed, paraffin-embedded samples to profile the transcriptome and genomic alterations among 86 hepatocellular carcinoma and cholangiocarcinoma patients prior to and following immune checkpoint inhibitor treatment. …

Integrative Molecular Analysis Of Dna Methylation Dynamics Unveils Molecules With Prognostic Potential In Breast Cancer, Rashid Mehmood, Alanoud Alsaleh, Muzamil Y. Want, Ijaz Ahmad, Sami Siraj, Muhammad Ishtiaq, Faizah A. Alshehri, Muhammad Naseem, Noriko Yasuhara

All Works

DNA methylation acts as a major epigenetic modification in mammals, characterized by the transfer of a methyl group to a cytosine. DNA methylation plays a pivotal role in regulating normal development, and misregulation in cells leads to an abnormal phenotype as is seen in several cancers. Any mutations or expression anomalies of genes encoding regulators of DNA methylation may lead to abnormal expression of critical molecules. A comprehensive genomic study encompassing all the genes related to DNA methylation regulation in relation to breast cancer is lacking. We used genomic and transcriptomic datasets from the Cancer Genome Atlas (TGCA) Pan-Cancer Atlas, …

A Taxonomic List Of The Old World Genera In The Subfamily Hesperiinae (Hesperiidae) Arranged Into Tribes, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

A taxonomic list of valid genera in the subfamily Hesperiinae from the Old World assigned to tribes is provided. This list is based on phylogenetic analysis of genomic sequence data complemented by morphological considerations. As a result, there are no incertae sedis non-fossil genera in the family Hesperiidae.

Protocol To Identify The Core Gene Supported By An Essential Gene In E. Coli Bacteria Using A Genome-Wide Suppressor Screen, Isao Masuda, Ya-Ming Hou

Department of Biochemistry and Molecular Biology Faculty Papers

We describe here a genome-wide screening approach to identify the most critical core reaction among a network of many that are supported by an essential gene to establish cell viability. We describe steps for maintenance plasmid construction, knockout cell construction, and phenotype validation. We then detail isolation of suppressors, whole-genome sequencing analysis, and reconstruction of CRISPR mutants. We focus on E. coli trmD, which encodes an essential methyl transferase that synthesizes m1G37 on the 3'-side of the tRNA anticodon. For complete details on the use and execution of this protocol, please refer to Masuda et al. (2022).

Additional Taxonomic Refinements Suggested By Genomic Analysis Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Paul A. Opler, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Comparative analyses of genomic data reveal further insights into the phylogeny and taxonomic classification of butterflies presented here. As a result, 2 new subgenera and 2 new species of Hesperiidae are described: Borna Grishin, subgen. n. (type species Godmania borincona Watson, 1937) and Lilla Grishin, subgen. n. (type species Choranthus lilliae Bell, 1931) of Choranthus Scudder, 1872, Cecropterus (Murgaria) markwalkeri Grishin, sp. n. (type locality in Mexico: Sonora), and Hedone yunga Grishin, sp. n. (type locality in Bolivia: Yungas, La Paz). The lectotype is designated for Aethilla toxeus Plötz, 1882. The type locality of Dion uza (Hewitson, 1877) is likely …

Thirteen New Species Of Butterflies (Lepidoptera: Hesperiidae) From Texas, Jing Zhang, Qian Cong, Nick V. Grishin

Insecta Mundi

Analyses of whole genomic shotgun datasets, COI barcodes, morphology, and historical literature suggest that the following 13 butterfly species from the family Hesperiidae (Lepidoptera: Papilionoidea) in Texas, USA are distinct from their closest named relatives and therefore are described as new (type localities are given in parenthesis): Spicauda atelis Grishin, new species (Hidalgo Co., Mission), Urbanus (Urbanus) rickardi Grishin, new species (Hidalgo Co., nr. Madero), Urbanus (Urbanus) oplerorum Grishin, new spe­cies (Hidalgo Co., Mission/Madero), Telegonus tsongae Grishin, new species (Starr Co., Roma), Autochton caballo Grishin, new species (Hidalgo Co., 6 mi W of Hidalgo), Epargyreus fractigutta …

Comparative Genomic Analysis Of 31 Phytophthora Genomes Reveals Genome Plasticity And Horizontal Gene Transfer, Brent A. Kronmiller, Nicolas Feau, Danyu Shen, Javier F. Tabima, Shahin S. Ali, Andrew D. Armitage, Felipe Arredondo, Bryan A. Bailey, Stephanie R. Bollmann, Angela Dale, Richard J. Harrison, Kelly Hrywkiw, Takao Kasuga, Rebecca Mcdougal, Charlotte F. Nellist, Preeti Panda, Sucheta Tripathy, Nari M. Williams, Wenwu Ye, Yuanchao Wang, Richard C. Hamelin, Niklaus Grünwald

Biology

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. …

Genomic Analyses Of Gray Fox Lineages Suggest Ancient Divergence And Secondary Contact In The Southern Great Plains, Elizabeth M. Kierepka, Sophie Preckler-Quisquater, Dawn M. Reding, Antoinette Piaggio, Seth P.D. Riley, Benjamin N. Sacks

USDA Wildlife Services: Staff Publications

The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that …

Multi-Ancestry Genome-Wide Association Analyses Improve Resolution Of Genes And Pathways Influencing Lung Function And Chronic Obstructive Pulmonary Disease Risk, Nick Shrine, Abril G. Izquierdo, Jing Chen, Richard Packer, Robert J. Hall, Anna L. Guyatt, Chiara Batini, Rebecca J. Thompson, Chandan Puvuluri, Vidhi Malik, Brian D. Hobbs, Matthew Moll, Wonji Kim, Ruth Tal-Singer, Per Bakke, Katherine A. Fawcett, Catherine John, Kayesha Coley, Noemi Nicole Piga, Sinjini Sikdar, Martin D. Tobin, Et Al.

Mathematics & Statistics Faculty Publications

Lung-function impairment underlies chronic obstructive pulmonary disease (COPD) and predicts mortality. In the largest multi-ancestry genome-wide association meta-analysis of lung function to date, comprising 580,869 participants, we identified 1,020 independent association signals implicating 559 genes supported by ≥2 criteria from a systematic variant-to-gene mapping framework. These genes were enriched in 29 pathways. Individual variants showed heterogeneity across ancestries, age and smoking groups, and collectively as a genetic risk score showed strong association with COPD across ancestry groups. We undertook phenome-wide association studies for selected associated variants as well as trait and pathway-specific genetic risk scores to infer possible consequences of …

Development Of Competency-Based Online Genomic Medicine Training (Cogent)., Susanne B Haga, Wendy K Chung, Luis A Cubano, Timothy B Curry, Philip E Empey, Geoffrey S Ginsburg, Kara Mangold, Christina Y Miyake, Siddharth K Prakash, Laura B Ramsey, Robb Rowley, Carolyn R Rohrer Vitek, Todd C Skaar, Julia Wynn, Teri A Manolio

Journal Articles

The fields of genetics and genomics have greatly expanded across medicine through the development of new technologies that have revealed genetic contributions to a wide array of traits and diseases. Thus, the development of widely available educational resources for all healthcare providers is essential to ensure the timely and appropriate utilization of genetics and genomics patient care. In 2020, the National Human Genome Research Institute released a call for new proposals to develop accessible, sustainable online education for health providers. This paper describes the efforts of the six teams awarded to reach the goal of providing genetic and genomic training …

Extrachromosomal Dna (Ecdna): An Origin Of Tumor Heterogeneity, Genomic Remodeling, And Drug Resistance., Lauren T Pecorino, Roel G W Verhaak, Anton Henssen, Paul S Mischel

Faculty Research 2022

The genome of cancer cells contains circular extrachromosomal DNA (ecDNA) elements not found in normal cells. Analysis of clinical samples reveal they are common in most cancers and their presence indicates poor prognosis. They often contain enhancers and driver oncogenes that are highly expressed. The circular ecDNA topology leads to an open chromatin conformation and generates new gene regulatory interactions, including with distal enhancers. The absence of centromeres leads to random distribution of ecDNAs during cell division and genes encoded on them are transmitted in a non-mendelian manner. ecDNA can integrate into and exit from chromosomal DNA. The numbers of …

Taxonomic Assessment Of Two Wild House Mouse Subspecies Using Whole-Genome Sequencing., Raman Akinyanju Lawal, Verity L Mathis, Mary Barter, Jeremy R. Charette, Alexis Garretson, Beth L Dumont

Faculty Research 2022

The house mouse species complex (Mus musculus) is comprised of three primary subspecies. A large number of secondary subspecies have also been suggested on the basis of divergent morphology and molecular variation at limited numbers of markers. While the phylogenetic relationships among the primary M. musculus subspecies are well-defined, relationships among secondary subspecies and between secondary and primary subspecies remain less clear. Here, we integrate de novo genome sequencing of museum-stored specimens of house mice from one secondary subspecies (M. m. bactrianus) and publicly available genome sequences of house mice previously characterized as M. m. helgolandicus, with whole genome sequences …

Adding Gene Transcripts Into Genomic Prediction Improves Accuracy And Reveals Sampling Time Dependence., Bruno C Perez, Marco C A M Bink, Karen L. Svenson, Gary Churchill, Mario P L Calus

Faculty Research 2022

Recent developments allowed generating multiple high-quality 'omics' data that could increase the predictive performance of genomic prediction for phenotypes and genetic merit in animals and plants. Here, we have assessed the performance of parametric and nonparametric models that leverage transcriptomics in genomic prediction for 13 complex traits recorded in 478 animals from an outbred mouse population. Parametric models were implemented using the best linear unbiased prediction, while nonparametric models were implemented using the gradient boosting machine algorithm. We also propose a new model named GTCBLUP that aims to remove between-omics-layer covariance from predictors, whereas its counterpart GTBLUP does not do …