@article{lee_kwon_aylor_marchuk_2022, title={A cross-species approach using an in vivo evaluation platform in mice demonstrates that sequence variation in human RABEP2 modulates ischemic stroke outcomes}, volume={109}, ISSN={["1537-6605"]}, DOI={10.1016/j.ajhg.2022.09.003}, abstractNote={Ischemic stroke, caused by vessel blockage, results in cerebral infarction, the death of brain tissue. Previously, quantitative trait locus (QTL) mapping of cerebral infarct volume and collateral vessel number identified a single, strong genetic locus regulating both phenotypes. Additional studies identified RAB GTPase-binding effector protein 2 (Rabep2) as the casual gene. However, there is yet no evidence that variation in the human ortholog of this gene plays any role in ischemic stroke outcomes. We established an in vivo evaluation platform in mice by using adeno-associated virus (AAV) gene replacement and verified that both mouse and human RABEP2 rescue the mouse Rabep2 knockout ischemic stroke volume and collateral vessel phenotypes. Importantly, this cross-species complementation enabled us to experimentally investigate the functional effects of coding sequence variation in human RABEP2. We chose four coding variants from the human population that are predicted by multiple in silico algorithms to be damaging to RABEP2 function. In vitro and in vivo analyses verify that all four led to decreased collateral vessel connections and increased infarct volume. Thus, there are naturally occurring loss-of-function alleles. This cross-species approach will expand the number of targets for therapeutics development for ischemic stroke.}, number={10}, journal={AMERICAN JOURNAL OF HUMAN GENETICS}, author={Lee, Han Kyu and Kwon, Do Hoon and Aylor, David L. and Marchuk, Douglas A.}, year={2022}, month={Oct}, pages={1814–1827} }
 @article{witchey_doyle_fredenburg_st armour_horman_odenkirk_aylor_baker_patisaul_2022, title={Impacts of Gestational FireMaster 550 (FM 550) Exposure on the Neonatal Cortex are Sex Specific and Largely Attributable to the Organophosphate Esters}, volume={9}, ISSN={["1423-0194"]}, DOI={10.1159/000526959}, abstractNote={<b><i>Introduction:</i></b> Flame retardants (FRs) are common bodily and environmental pollutants, creating concern about their potential toxicity. We and others have found that the commercial mixture FireMaster® 550 (FM 550) or its individual brominated (BFR) and organophosphate ester (OPFR) components are potential developmental neurotoxicants. Using Wistar rats, we previously reported that developmental exposure to FM 550 or its component classes produced sex- and compound-specific effects on adult socioemotional behaviors. The underlying mechanisms driving the behavioral phenotypes are unknown. <b><i>Methods:</i></b> To further mechanistic understanding, here we conducted transcriptomics in parallel with a novel lipidomics approach using cortical tissues from newborn siblings of the rats in the published behavioral study. Inclusion of lipid composition is significant because it is rarely examined in developmental neurotoxicity studies. Pups were gestationally exposed via oral dosing to the dam to FM 550 or the BFR or OPFR components at environmentally relevant doses. <b><i>Results:</i></b> The neonatal cortex was highly sexually dimorphic in lipid and transcriptome composition, and males were more significantly impacted by FR exposure. Multiple adverse modes of action for the BFRs and OPFRs on neurodevelopment were identified, with the OPFRs being more disruptive than the BFRs via multiple mechanisms including dysregulation of mitochondrial function and disruption of cholinergic and glutamatergic systems. Disrupted mitochondrial function by environmental factors has been linked to a higher risk of autism spectrum disorders and neurodegenerative disorders. Impacted lipid classes included ceramides, sphingomyelins, and triacylglycerides. Robust ceramide upregulation in the OPFR females could suggest a heightened risk of brain metabolic disease. <b><i>Conclusions:</i></b> This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern. }, journal={NEUROENDOCRINOLOGY}, author={Witchey, S. K. and Doyle, M. G. and Fredenburg, J. D. and St Armour, G. and Horman, B. and Odenkirk, M. T. and Aylor, D. L. and Baker, E. S. and Patisaul, H. B.}, year={2022}, month={Sep} }
 @article{lee_wetzel-strong_aylor_marchuk_2021, title={A Neuroprotective Locus Modulates Ischemic Stroke Infarction Independent of Collateral Vessel Anatomy}, volume={15}, ISSN={["1662-453X"]}, DOI={10.3389/fnins.2021.705160}, abstractNote={Although studies with inbred strains of mice have shown that infarct size is largely determined by the extent of collateral vessel connections between arteries in the brain that enable reperfusion of the ischemic territory, we have identified strain pairs that do not vary in this vascular phenotype, but which nonetheless exhibit large differences in infarct size. In this study we performed quantitative trait locus (QTL) mapping in mice from an intercross between two such strains, WSB/EiJ (WSB) and C57BL/6J (B6). This QTL mapping revealed only one neuroprotective locus on Chromosome 8 (Chr 8) that co-localizes with a neuroprotective locus we mapped previously from F2 progeny between C3H/HeJ (C3H) and B6. The allele-specific phenotypic effect on infarct volume at the genetic region identified by these two independent mappings was in the opposite direction of the parental strain phenotype; namely, the B6 allele conferred increased susceptibility to ischemic infarction. Through two reciprocal congenic mouse lines with either the C3H or B6 background at the Chr 8 locus, we verified the neuroprotective effects of this genetic region that modulates infarct volume without any effect on the collateral vasculature. Additionally, we surveyed non-synonymous coding SNPs and performed RNA-sequencing analysis to identify potential candidate genes within the genetic interval. Through these approaches, we suggest new genes for future mechanistic studies of infarction following ischemic stroke, which may represent novel gene/protein targets for therapeutic development.}, journal={FRONTIERS IN NEUROSCIENCE}, author={Lee, Han Kyu and Wetzel-Strong, Sarah E. and Aylor, David L. and Marchuk, Douglas A.}, year={2021}, month={Aug} }
 @article{widmayer_handel_aylor_2020, title={Age and Genetic Background Modify Hybrid Male Sterility in House Mice}, volume={216}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.120.303474}, abstractNote={Abstract
               Hybrid male sterility (HMS) contributes to reproductive isolation commonly observed among house mouse (Mus musculus) subspecies, both in the wild and in laboratory crosses. Incompatibilities involving specific Prdm9 alleles and certain Chromosome (Chr) X genotypes are known determinants of fertility and HMS, and previous work in the field has demonstrated that genetic background modifies these two major loci. We constructed hybrids that have identical genotypes at Prdm9 and identical X chromosomes, but differ widely across the rest of the genome. In each case, we crossed female PWK/PhJ mice representative of the M. m. musculus subspecies to males from a classical inbred strain representative of M. m. domesticus: 129S1/SvImJ, A/J, C57BL/6J, or DBA/2J. We detected three distinct trajectories of fertility among the hybrids using breeding experiments. The PWK129S1 males were always infertile. PWKDBA2 males were fertile, despite their genotypes at the major HMS loci. We also observed age-dependent changes in fertility parameters across multiple genetic backgrounds. The PWKB6 and PWKAJ males were always infertile before 12 weeks and after 35 weeks. However, some PWKB6 and PWKAJ males were transiently fertile between 12 and 35 weeks. This observation could resolve previous contradictory reports about the fertility of PWKB6. Taken together, these results point to multiple segregating HMS modifier alleles, some of which have age-related modes of action. The ultimate identification of these alleles and their age-related mechanisms will advance understanding both of the genetic architecture of HMS and of how reproductive barriers are maintained between house mouse subspecies.}, number={2}, journal={GENETICS}, author={Widmayer, Samuel J. and Handel, Mary Ann and Aylor, David L.}, year={2020}, month={Oct}, pages={585–597} }
 @article{garbutt_konganti_konneker_hillhouse_phelps_jones_aylor_threadgill_2020, title={Derivation of stable embryonic stem cell-like, but transcriptionally heterogenous, induced pluripotent stem cells from non-permissive mouse strains}, volume={31}, ISSN={["1432-1777"]}, DOI={10.1007/s00335-020-09849-x}, abstractNote={Genetic background is known to play a role in the ability to derive pluripotent, embryonic stem cells (ESC), a trait referred to as permissiveness. Previously we demonstrated that induced pluripotent stem cells (iPSC) can be readily derived from non-permissive mouse strains by addition of serum-based media supplemented with GSK3B and MEK inhibitors, termed 2iS media, 3 days into reprogramming. Here, we describe the derivation of second type of iPSC colony from non-permissive mouse strains that can be stably maintained independently of 2iS media. The resulting cells display transcriptional heterogeneity similar to that observed in ESC from permissive genetic backgrounds derived in conventional serum containing media supplemented with leukemia inhibitor factor. However, unlike previous studies that report exclusive subpopulations, we observe both exclusive and simultaneous expression of naive and primed cell surface markers. Herein, we explore shifts in pluripotency in the presence of 2iS and characterize heterogenous subpopulations to determine their pluripotent state and role in heterogenous iPSCs derived from the non-permissive NOD/ShiLtJ strain. We conclude that heterogeneity is a naturally occurring, necessary quality of stem cells that allows for the maintenance of pluripotency. This study further demonstrates the efficacy of the 2iS reprogramming technique. It is also the first study to derive stable ESC-like stem cells from the non-permissive NOD/ShiLtJ and WSB/EiJ strains, enabling easier and broader research possibilities into pluripotency for these and similar non-permissive mouse strains and species.}, number={9-12}, journal={MAMMALIAN GENOME}, publisher={Springer Science and Business Media LLC}, author={Garbutt, Tiffany A. and Konganti, Kranti and Konneker, Thomas and Hillhouse, Andrew and Phelps, Drake and Jones, Alexis and Aylor, David and Threadgill, David W.}, year={2020}, month={Dec}, pages={263–286} }
 @article{lee_widmayer_huang_aylor_marchuk_2019, title={Novel Neuroprotective Loci Modulating Ischemic Stroke Volume in Wild-Derived Inbred Mouse Strains}, volume={213}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.119.302555}, abstractNote={Abstract
               To identify genes involved in cerebral infarction, we have employed a forward genetic approach in inbred mouse strains, using quantitative trait loci (QTL) mapping for cerebral infarct volume after middle cerebral artery occlusion. We had previously observed that infarct volume is inversely correlated with cerebral collateral vessel density in most strains. In this study, we expanded the pool of allelic variation among classical inbred mouse strains by utilizing the eight founder strains of the Collaborative Cross and found a wild-derived strain, WSB/EiJ, that breaks this general rule that collateral vessel density inversely correlates with infarct volume. WSB/EiJ and another wild-derived strain, CAST/EiJ, show the highest collateral vessel densities of any inbred strain, but infarct volume of WSB/EiJ mice is 8.7-fold larger than that of CAST/EiJ mice. QTL mapping between these strains identified four new neuroprotective loci modulating cerebral infarct volume while not affecting collateral vessel phenotypes. To identify causative variants in genes, we surveyed nonsynonymous coding SNPs between CAST/EiJ and WSB/EiJ and found 96 genes harboring coding SNPs predicted to be damaging and mapping within one of the four intervals. In addition, we performed RNA-sequencing for brain tissue of CAST/EiJ and WSB/EiJ mice and identified 79 candidate genes mapping in one of the four intervals showing strain-specific differences in expression. The identification of the genes underlying these neuroprotective loci will provide new understanding of genetic risk factors of ischemic stroke, which may provide novel targets for future therapeutic intervention of human ischemic stroke.}, number={3}, journal={GENETICS}, author={Lee, Han Kyu and Widmayer, Samuel J. and Huang, Min-Nung and Aylor, David L. and Marchuk, Douglas A.}, year={2019}, month={Nov}, pages={1079–1092} }
 @article{patisaul_fenton_aylor_2018, title={Animal models of endocrine disruption}, volume={32}, ISSN={1521-690X}, url={http://dx.doi.org/10.1016/j.beem.2018.03.011}, DOI={10.1016/j.beem.2018.03.011}, abstractNote={Endocrine disrupting chemicals (EDCs) are compounds that alter the structure and function of the endocrine system and may be contributing to disorders of the reproductive, metabolic, neuroendocrine and other complex systems. Typically, these outcomes cannot be modeled in cell-based or other simple systems necessitating the use of animal testing. Appropriate animal model selection is required to effectively recapitulate the human experience, including relevant dosing and windows of exposure, and ensure translational utility and reproducibility. While classical toxicology heavily relies on inbred rats and mice, and focuses on apical endpoints such as tumor formation or birth defects, EDC researchers have used a greater diversity of species to effectively model more subtle but significant outcomes such as changes in pubertal timing, mammary gland development, and social behaviors. Advances in genomics, neuroimaging and other tools are making a wider range of animal models more widely available to EDC researchers.}, number={3}, journal={Best Practice & Research Clinical Endocrinology & Metabolism}, publisher={Elsevier BV}, author={Patisaul, Heather B. and Fenton, Suzanne E. and Aylor, David}, year={2018}, month={Jun}, pages={283–297} }
 @article{garbutt_konneker_konganti_hillhouse_swift-haire_jones_phelps_aylor_threadgill_2018, title={Permissiveness to form pluripotent stem cells may be an evolutionarily derived characteristic in Mus muscuius}, volume={8}, ISSN={["2045-2322"]}, url={https://doi.org/10.1038/s41598-018-32116-8}, DOI={10.1038/s41598-018-32116-8}, abstractNote={AbstractMus musculus is the only known species from which embryonic stem cells (ESC) can be isolated under conditions requiring only leukemia inhibitory factor (LIF). Other species are non-permissive in LIF media, and form developmentally primed epiblast stem cells (EpiSC) similar to cells derived from post-implantation, egg cylinders. To evaluate whether non-permissiveness extends to induced pluripotent stem cells (iPSC), we derived iPSC from the eight founder strains of the mouse Collaborative Cross. Two strains, NOD/ShiLtJ and the WSB/EiJ, were non-permissive, consistent with the previous classification of NOD/ShiLtJ as non-permissive to ESC derivation. We determined non-permissiveness is recessive, and that non-permissive genomes do not compliment. We overcame iPSC non-permissiveness by using GSK3B and MEK inhibitors with serum, a technique we termed 2iS reprogramming. Although used for ESC derivation, GSK3B and MEK inhibitors have not been used during iPSC reprogramming because they inhibit survival of progenitor differentiated cells. iPSC derived in 2iS are more transcriptionally similar to ESC than EpiSC, indicating that 2iS reprogramming acts to overcome genetic background constraints. Finally, of species tested for ESC or iPSC derivation, only some M. musculus strains are permissive under LIF culture conditions suggesting that this is an evolutionarily derived characteristic in the M. musculus lineage.}, journal={SCIENTIFIC REPORTS}, author={Garbutt, Tiffany A. and Konneker, Thomas I and Konganti, Kranti and Hillhouse, Andrew E. and Swift-Haire, Francis and Jones, Alexis and Phelps, Drake and Aylor, David L. and Threadgill, David W.}, year={2018}, month={Oct} }
 @article{venkatratnam_house_konganti_mckenney_threadgill_chiu_aylor_wright_rusyn_2018, title={Population-based dose-response analysis of liver transcriptional response to trichloroethylene in mouse}, volume={29}, ISSN={["1432-1777"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85040693289&partnerID=MN8TOARS}, DOI={10.1007/s00335-018-9734-y}, abstractNote={Studies of gene expression are common in toxicology and provide important clues to mechanistic understanding of adverse effects of chemicals. Most prior studies have been performed in a single strain or cell line; however, gene expression is heavily influenced by the genetic background, and these genotype-expression differences may be key drivers of inter-individual variation in response to chemical toxicity. In this study, we hypothesized that the genetically diverse Collaborative Cross mouse population can be used to gain insight and suggest mechanistic hypotheses for the dose- and genetic background-dependent effects of chemical exposure. This hypothesis was tested using a model liver toxicant trichloroethylene (TCE). Liver transcriptional responses to TCE exposure were evaluated 24 h after dosing. Transcriptomic dose–responses were examined for both TCE and its major oxidative metabolite trichloroacetic acid (TCA). As expected, peroxisome- and fatty acid metabolism-related pathways were among the most dose–responsive enriched pathways in all strains. However, nearly half of the TCE-induced liver transcriptional perturbation was strain-dependent, with abundant evidence of strain/dose interaction, including in the peroxisomal signaling-associated pathways. These effects were highly concordant between the administered TCE dose and liver levels of TCA. Dose–response analysis of gene expression at the pathway level yielded points of departure similar to those derived from the traditional toxicology studies for both non-cancer and cancer effects. Mapping of expression–genotype–dose relationships revealed some significant associations; however, the effects of TCE on gene expression in liver appear to be highly polygenic traits that are challenging to positionally map. This study highlights the usefulness of mouse population-based studies in assessing inter-individual variation in toxicological responses, but cautions that genetic mapping may be challenging because of the complexity in gene exposure–dose relationships.}, number={1-2}, journal={MAMMALIAN GENOME}, author={Venkatratnam, Abhishek and House, John S. and Konganti, Kranti and McKenney, Connor and Threadgill, David W. and Chiu, Weihsueh A. and Aylor, David L. and Wright, Fred A. and Rusyn, Ivan}, year={2018}, month={Feb}, pages={168–181} }
 @article{wang_pehrsson_purushotham_li_zhuo_zhang_lawson_province_krapp_lan_et al._2018, title={The NIEHS TaRGET II Consortium and environmental epigenomics}, volume={36}, ISSN={1087-0156 1546-1696}, url={http://dx.doi.org/10.1038/NBT.4099}, DOI={10.1038/NBT.4099}, number={3}, journal={Nature Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Wang, Ting and Pehrsson, Erica C and Purushotham, Deepak and Li, Daofeng and Zhuo, Xiaoyu and Zhang, Bo and Lawson, Heather A and Province, Michael A and Krapp, Christopher and Lan, Yemin and et al.}, year={2018}, month={Mar}, pages={225–227} }
 @misc{wang_pehrsson_purushotham_li_zhuo_zhang_lawson_province_krapp_lan_et al._2018, title={The NIEHS TaRGET II Consortium and environmental epigenomics}, volume={36}, number={3}, journal={Nature Biotechnology}, author={Wang, T. and Pehrsson, E. C. and Purushotham, D. and Li, D. F. and Zhuo, X. Y. and Zhang, B. and Lawson, H. A. and Province, M. A. and Krapp, C. and Lan, Y. M. and et al.}, year={2018}, pages={225–227} }
 @article{venkatratnam_furuya_kosyk_gold_bodnar_konganti_threadgill_gillespie_aylor_wright_et al._2017, title={Editor's Highlight: Collaborative Cross Mouse Population Enables Refinements to Characterization of the Variability in Toxicokinetics of Trichloroethylene and Provides Genetic Evidence for the Role of PPAR Pathway in Its Oxidative Metabolism}, volume={158}, ISSN={["1096-0929"]}, DOI={10.1093/toxsci/kfx065}, abstractNote={Background
Trichloroethylene (TCE) is a known carcinogen in humans and rodents. Previous studies of inter-strain variability in TCE metabolism were conducted in multi-strain panels of classical inbred mice with limited genetic diversity to identify gene-environment interactions associated with chemical exposure.


Objectives
To evaluate inter-strain variability in TCE metabolism and identify genetic determinants that are associated with TCE metabolism and effects using Collaborative Cross (CC), a large panel of genetically diverse strains of mice.


Methods
We administered a single oral dose of 0, 24, 80, 240, or 800 mg/kg of TCE to mice from 50 CC strains, and collected organs 24 h post-dosing. Levels of trichloroacetic acid (TCA), a major oxidative metabolite of TCE were measured in multiple tissues. Protein expression and activity levels of TCE-metabolizing enzymes were evaluated in the liver. Liver transcript levels of known genes perturbed by TCE exposure were also quantified. Genetic association mapping was performed on the acquired phenotypes.


Results
TCA levels varied in a dose- and strain-dependent manner in liver, kidney, and serum. The variability in TCA levels among strains did not correlate with expression or activity of a number of enzymes known to be involved in TCE oxidation. Peroxisome proliferator-activated receptor alpha (PPARα)-responsive genes were found to be associated with strain-specific differences in TCE metabolism.


Conclusions
This study shows that CC mouse population is a valuable tool to quantitatively evaluate inter-individual variability in chemical metabolism and to identify genes and pathways that may underpin population differences.}, number={1}, journal={TOXICOLOGICAL SCIENCES}, author={Venkatratnam, Abhishek and Furuya, Shinji and Kosyk, Oksana and Gold, Avram and Bodnar, Wanda and Konganti, Kranti and Threadgill, David W. and Gillespie, Kevin M. and Aylor, David L. and Wright, Fred A. and et al.}, year={2017}, month={Jul}, pages={48–62} }
 @article{shorter_odet_aylor_pan_kao_fu_morgan_greenstein_bell_stevans_et al._2017, title={Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross}, volume={206}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.116.199596}, abstractNote={Abstract
               The goal of the Collaborative Cross (CC) project was to generate and distribute over 1000 independent mouse recombinant inbred strains derived from eight inbred founders. With inbreeding nearly complete, we estimated the extinction rate among CC lines at a remarkable 95%, which is substantially higher than in the derivation of other mouse recombinant inbred populations. Here, we report genome-wide allele frequencies in 347 extinct CC lines. Contrary to expectations, autosomes had equal allelic contributions from the eight founders, but chromosome X had significantly lower allelic contributions from the two inbred founders with underrepresented subspecific origins (PWK/PhJ and CAST/EiJ). By comparing extinct CC lines to living CC strains, we conclude that a complex genetic architecture is driving extinction, and selection pressures are different on the autosomes and chromosome X. Male infertility played a large role in extinction as 47% of extinct lines had males that were infertile. Males from extinct lines had high variability in reproductive organ size, low sperm counts, low sperm motility, and a high rate of vacuolization of seminiferous tubules. We performed QTL mapping and identified nine genomic regions associated with male fertility and reproductive phenotypes. Many of the allelic effects in the QTL were driven by the two founders with underrepresented subspecific origins, including a QTL on chromosome X for infertility that was driven by the PWK/PhJ haplotype. We also performed the first example of cross validation using complementary CC resources to verify the effect of sperm curvilinear velocity from the PWK/PhJ haplotype on chromosome 2 in an independent population across multiple generations. While selection typically constrains the examination of reproductive traits toward the more fertile alleles, the CC extinct lines provided a unique opportunity to study the genetic architecture of fertility in a widely genetically variable population. We hypothesize that incompatibilities between alleles with different subspecific origins is a key driver of infertility. These results help clarify the factors that drove strain extinction in the CC, reveal the genetic regions associated with poor fertility in the CC, and serve as a resource to further study mammalian infertility.}, number={2}, journal={GENETICS}, author={Shorter, John R. and Odet, Fanny and Aylor, David L. and Pan, Wenqi and Kao, Chia-Yu and Fu, Chen-Ping and Morgan, Andrew P. and Greenstein, Seth and Bell, Timothy A. and Stevans, Alicia M. and et al.}, year={2017}, month={Jun}, pages={557–572} }
 @article{hunter_robinson_aylor_singh_2016, title={Genetic Background, Maternal Age, and Interaction Effects Mediate Rates of Crossing Over in Drosophila melanogaster Females}, volume={6}, ISSN={["2160-1836"]}, DOI={10.1534/g3.116.027631}, abstractNote={AbstractMeiotic recombination is a genetic process that is critical for proper chromosome segregation in many organisms. Despite being fundamental for organismal fitness, rates of crossing over vary greatly between taxa. Both genetic and environmental factors contribute to phenotypic variation in crossover frequency, as do genotype–environment interactions. Here, we test the hypothesis that maternal age influences rates of crossing over in a genotypic-specific manner. Using classical genetic techniques, we estimated rates of crossing over for individual Drosophila melanogaster females from five strains over their lifetime from a single mating event. We find that both age and genetic background significantly contribute to observed variation in recombination frequency, as do genotype–age interactions. We further find differences in the effect of age on recombination frequency in the two genomic regions surveyed. Our results highlight the complexity of recombination rate variation and reveal a new role of genotype by maternal age interactions in mediating recombination rate.}, number={5}, journal={G3-GENES GENOMES GENETICS}, author={Hunter, Chad M. and Robinson, Matthew C. and Aylor, David L. and Singh, Nadia D.}, year={2016}, month={May}, pages={1409–1416} }
 @article{didion_morgan_clayshulte_mcmullan_yadgary_petkov_bell_gatti_crowley_hua_et al._2015, title={A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2}, volume={11}, ISSN={["1553-7404"]}, DOI={10.1371/journal.pgen.1004850}, abstractNote={Significant departures from expected Mendelian inheritance ratios (transmission ratio distortion, TRD) are frequently observed in both experimental crosses and natural populations. TRD on mouse Chromosome (Chr) 2 has been reported in multiple experimental crosses, including the Collaborative Cross (CC). Among the eight CC founder inbred strains, we found that Chr 2 TRD was exclusive to females that were heterozygous for the WSB/EiJ allele within a 9.3 Mb region (Chr 2 76.9 – 86.2 Mb). A copy number gain of a 127 kb-long DNA segment (designated as responder to drive, R2d) emerged as the strongest candidate for the causative allele. We mapped R2d sequences to two loci within the candidate interval. R2d1 is located near the proximal boundary, and contains a single copy of R2d in all strains tested. R2d2 maps to a 900 kb interval, and the number of R2d copies varies from zero in classical strains (including the mouse reference genome) to more than 30 in wild-derived strains. Using real-time PCR assays for the copy number, we identified a mutation (R2d2WSBdel1) that eliminates the majority of the R2d2WSB copies without apparent alterations of the surrounding WSB/EiJ haplotype. In a three-generation pedigree segregating for R2d2WSBdel1, the mutation is transmitted to the progeny and Mendelian segregation is restored in females heterozygous for R2d2WSBdel1, thus providing direct evidence that the copy number gain is causal for maternal TRD. We found that transmission ratios in R2d2WSB heterozygous females vary between Mendelian segregation and complete distortion depending on the genetic background, and that TRD is under genetic control of unlinked distorter loci. Although the R2d2WSB transmission ratio was inversely correlated with average litter size, several independent lines of evidence support the contention that female meiotic drive is the cause of the distortion. We discuss the implications and potential applications of this novel meiotic drive system.}, number={2}, journal={PLOS GENETICS}, author={Didion, John P. and Morgan, Andrew P. and Clayshulte, Amelia M. -F. and Mcmullan, Rachel C. and Yadgary, Liran and Petkov, Petko M. and Bell, Timothy A. and Gatti, Daniel M. and Crowley, James J. and Hua, Kunjie and et al.}, year={2015}, month={Feb} }
 @article{crowley_zhabotynsky_sun_huang_pakatci_kim_wang_morgan_calaway_aylor_et al._2015, title={Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance}, volume={47}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/NG.3222}, DOI={10.1038/NG.3222}, abstractNote={Fernando Pardo-Manuel de Villena and colleagues generate a 3 × 3 diallel cross of three inbred mouse lines and examine gene expression in multiple tissues. They identify allelic imbalance favoring the expression of the paternal allele across the genome. Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression across multiple tissues in a three-way diallel. Greater than 80% of mouse genes have cis regulatory variation. Effects from these variants influence complex traits and usually extend to the human ortholog. Further, we estimate that at least one in every thousand SNPs creates a cis regulatory effect. We also observe two types of parent-of-origin effects, including classical imprinting and a new global allelic imbalance in expression favoring the paternal allele. We conclude that, as with humans, pervasive regulatory variation influences complex genetic traits in mice and provide a new resource toward understanding the genetic control of transcription in mammals.}, number={4}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Crowley, James J and Zhabotynsky, Vasyl and Sun, Wei and Huang, Shunping and Pakatci, Isa Kemal and Kim, Yunjung and Wang, Jeremy R and Morgan, Andrew P and Calaway, John D and Aylor, David L and et al.}, year={2015}, month={Mar}, pages={353–360} }
 @article{crowley_zhabotynsky_sun_huang_pakatci_kim_wang_morgan_calaway_aylor_et al._2015, title={Erratum: Corrigendum: Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance}, volume={47}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/NG0615-690A}, DOI={10.1038/NG0615-690A}, abstractNote={Nat. Genet. 47, 353–360 (2015); published online 2 March 2015; corrected after print 16 April 2015 In the version of this article initially published, an accession number was not provided for RNA-seq data sets. The RNA-seq data sets that passed quality control are available at the Sequence Read Archive (SRA) under accession SRP056236.}, number={6}, journal={Nature Genetics}, publisher={Springer Nature}, author={Crowley, James J and Zhabotynsky, Vasyl and Sun, Wei and Huang, Shunping and Pakatci, Isa Kemal and Kim, Yunjung and Wang, Jeremy R and Morgan, Andrew P and Calaway, John D and Aylor, David L and et al.}, year={2015}, month={May}, pages={690–690} }
 @article{rebuli_camacho_adonay_reif_aylor_patisaul_2015, title={Impact of Low-Dose Oral Exposure to Bisphenol A (BPA) on Juvenile and Adult Rat Exploratory and Anxiety Behavior: A CLARITY-BPA Consortium Study}, volume={148}, ISSN={["1096-0929"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84952932385&partnerID=MN8TOARS}, DOI={10.1093/toxsci/kfv163}, abstractNote={Bisphenol A (BPA) is a high volume production chemical and has been identified as an endocrine disruptor, prompting concern that developmental exposure could impact brain development and behavior. Rodent and human studies suggest that early life BPA exposure may result in an anxious, hyperactive phenotype but results are conflicting and data from studies using multiple doses below the no-observed-adverse-effect level are limited. To address this, the present studies were conducted as part of the CLARITY-BPA (Consortium Linking Academic and Regulatory Insights on BPA Toxicity) program. The impact of perinatal BPA exposure (2.5, 25, or 2500 µg/kg body weight (bw)/day) on behaviors related to anxiety and exploratory activity was assessed in juvenile (prepubertal) and adult NCTR Sprague-Dawley rats of both sexes. Ethinyl estradiol (0.5 µg/kg bw/day) was used as a reference estrogen. Exposure spanned gestation and lactation with dams gavaged from gestational day 6 until birth and then the offspring gavaged directly through weaning (n = 12/sex/group). Behavioral assessments included open field, elevated plus maze, and zero maze. Anticipated sex differences in behavior were statistically identified or suggested in most cases. No consistent effects of BPA were observed for any endpoint, in either sex, at either age compared to vehicle controls; however, significant differences between BPA-exposed and ethinyl estradiol-exposed groups were identified for some endpoints. Limitations of this study are discussed and include suboptimal statistical power and low concordance across behavioral tasks. These data do not indicate BPA-related effects on anxiety or exploratory activity in these developmentally exposed rats.}, number={2}, journal={TOXICOLOGICAL SCIENCES}, author={Rebuli, Meghan E. and Camacho, Luisa and Adonay, Maria E. and Reif, David M. and Aylor, David L. and Patisaul, Heather B.}, year={2015}, month={Dec}, pages={341–354} }
 @article{odet_pan_bell_goodson_stevans_yun_aylor_kao_mcmillan_villena_et al._2015, title={The Founder Strains of the Collaborative Cross Express a Complex Combination of Advantageous and Deleterious Traits for Male Reproduction}, volume={5}, ISSN={["2160-1836"]}, DOI={10.1534/g3.115.020172}, abstractNote={Abstract
               Surveys of inbred strains of mice are standard approaches to determine the heritability and range of phenotypic variation for biomedical traits. In addition, they may lead to the identification of novel phenotypes and models of human disease. Surprisingly, male reproductive phenotypes are among the least-represented traits in the Mouse Phenome Database. Here we report the results of a broad survey of the eight founder inbred strains of both the Collaborative Cross (CC) and the Diversity Outbred populations, two new mouse resources that are being used as platforms for systems genetics and sources of mouse models of human diseases. Our survey includes representatives of the three main subspecies of the house mice and a mix of classical and wild-derived inbred strains. In addition to standard staples of male reproductive phenotyping such as reproductive organ weights, sperm counts, and sperm morphology, our survey includes sperm motility and the first detailed survey of testis histology. As expected for such a broad survey, heritability varies widely among traits. We conclude that although all eight inbred strains are fertile, most display a mix of advantageous and deleterious male reproductive traits. The CAST/EiJ strain is an outlier, with an unusual combination of deleterious male reproductive traits including low sperm counts, high levels of morphologically abnormal sperm, and poor motility. In contrast, sperm from the PWK/PhJ and WSB/EiJ strains had the greatest percentages of normal morphology and vigorous motility. Finally, we report an abnormal testis phenotype that is highly heritable and restricted to the WSB/EiJ strain. This phenotype is characterized by the presence of a large, but variable, number of vacuoles in at least 10% of the seminiferous tubules. The onset of the phenotype between 2 and 3 wk of age is temporally correlated with the formation of the blood-testis barrier. We speculate that this phenotype may play a role in high rates of extinction in the CC project and in the phenotypes associated with speciation in genetic crosses that use the WSB/EiJ strain as representative of the Mus muculus domesticus subspecies.}, number={12}, journal={G3-GENES GENOMES GENETICS}, author={Odet, Fanny and Pan, Wenqi and Bell, Timothy A. and Goodson, Summer G. and Stevans, Alicia M. and Yun, Zianing and Aylor, David L. and Kao, Chia-Yu and McMillan, Leonard and Villena, Fernando Pardo-Manuel and et al.}, year={2015}, month={Dec}, pages={2671–2683} }
 @article{rutledge_aylor_carpenter_peck_chines_ostrowski_chesler_churchill_villena_kelada_2014, title={Genetic Regulation of Zfp30, CXCL1, and Neutrophilic Inflammation in Murine Lung}, volume={198}, ISSN={["1943-2631"]}, DOI={10.1534/genetics.114.168138}, abstractNote={AbstractAllergic asthma is a complex disease characterized in part by granulocytic inflammation of the airways. In addition to eosinophils, neutrophils (PMN) are also present, particularly in cases of severe asthma. We sought to identify the genetic determinants of neutrophilic inflammation in a mouse model of house dust mite (HDM)-induced asthma. We applied an HDM model of allergic asthma to the eight founder strains of the Collaborative Cross (CC) and 151 incipient lines of the CC (preCC). Lung lavage fluid was analyzed for PMN count and the concentration of CXCL1, a hallmark PMN chemokine. PMN and CXCL1 were strongly correlated in preCC mice. We used quantitative trait locus (QTL) mapping to identify three variants affecting PMN, one of which colocalized with a QTL for CXCL1 on chromosome (Chr) 7. We used lung eQTL data to implicate a variant in the gene Zfp30 in the CXCL1/PMN response. This genetic variant regulates both CXCL1 and PMN by altering Zfp30 expression, and we model the relationships between the QTL and these three endophenotypes. We show that Zfp30 is expressed in airway epithelia in the normal mouse lung and that altering Zfp30 expression in vitro affects CXCL1 responses to an immune stimulus. Our results provide strong evidence that Zfp30 is a novel regulator of neutrophilic airway inflammation.}, number={2}, journal={GENETICS}, author={Rutledge, Holly and Aylor, David L. and Carpenter, Danielle E. and Peck, Bailey C. and Chines, Peter and Ostrowski, Lawrence E. and Chesler, Elissa J. and Churchill, Gary A. and Villena, Fernando Pardo-Manuel and Kelada, Samir N. P.}, year={2014}, month={Oct}, pages={735–U376} }
 @article{kelada_carpenter_aylor_chines_rutledge_chesler_churchill_villena_schwartz_collins_2014, title={Integrative Genetic Analysis of Allergic Inflammation in the Murine Lung}, volume={51}, ISSN={["1535-4989"]}, DOI={10.1165/rcmb.2013-0501oc}, abstractNote={Airway allergen exposure induces inflammation among individuals with atopy that is characterized by altered airway gene expression, elevated levels of T helper type 2 cytokines, mucus hypersecretion, and airflow obstruction. To identify the genetic determinants of the airway allergen response, we employed a systems genetics approach. We applied a house dust mite mouse model of allergic airway disease to 151 incipient lines of the Collaborative Cross, a new mouse genetic reference population, and measured serum IgE, airway eosinophilia, and gene expression in the lung. Allergen-induced serum IgE and airway eosinophilia were not correlated. We detected quantitative trait loci (QTL) for airway eosinophilia on chromosome (Chr) 11 (71.802-87.098 megabases [Mb]) and allergen-induced IgE on Chr 4 (13.950-31.660 Mb). More than 4,500 genes expressed in the lung had gene expression QTL (eQTL), the majority of which were located near the gene itself. However, we also detected approximately 1,700 trans-eQTL, and many of these trans-eQTL clustered into two regions on Chr 2. We show that one of these loci (at 147.6 Mb) is associated with the expression of more than 100 genes, and, using bioinformatics resources, fine-map this locus to a 53 kb-long interval. We also use the gene expression and eQTL data to identify a candidate gene, Tlcd2, for the eosinophil QTL. Our results demonstrate that hallmark allergic airway disease phenotypes are associated with distinct genetic loci on Chrs 4 and 11, and that gene expression in the allergically inflamed lung is controlled by both cis and trans regulatory factors.}, number={3}, journal={AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY}, author={Kelada, Samir N. P. and Carpenter, Danielle E. and Aylor, David L. and Chines, Peter and Rutledge, Holly and Chesler, Elissa J. and Churchill, Gary A. and Villena, Fernando Pardo-Manuel and Schwartz, David A. and Collins, Francis S.}, year={2014}, month={Sep}, pages={436–445} }
 @article{xiao_ciavatta_aylor_hu_de villena_falk_jennette_2013, title={Genetically Determined Severity of Anti-Myeloperoxidase Glomerulonephritis}, volume={182}, ISSN={0002-9440}, url={http://dx.doi.org/10.1016/j.ajpath.2012.12.006}, DOI={10.1016/j.ajpath.2012.12.006}, abstractNote={Myeloperoxidase (MPO) is a target antigen for antineutrophil cytoplasmic autoantibodies (ANCA). There is evidence that MPO-ANCA cause necrotizing and crescentic glomerulonephritis (NCGN) and vasculitis. NCGN severity varies among patients with ANCA disease, and genetic factors influence disease severity. The role of genetics in MPO-ANCA NCGN severity was investigated using 13 inbred mouse strains, F1 and F2 hybrids, bone marrow chimeras, and neutrophil function assays. Mouse strains include founders of the Collaborative Cross. Intravenous injection of anti-MPO IgG induced glomerular crescents in >60% of glomeruli in 129S6/SvEv and CAST/EiJ mice, but <1% in A/J, DBA/1J, DBA/2J, NOD/LtJ, and PWK/PhJ mice. C57BL6J, 129S1/SvImJ, LP/J, WSB/EiJ, NZO/HILtJ, and C3H mice had intermediate severity. High-density genotypes at 542,190 single nucleotide polymorphisms were used to identify candidate loci for disease severity by identifying genomic regions that are different between 129S6/SvEv and 129S1/SvImJ mice, which are genetically similar but phenotypically distinct. C57BL/6 × 129S6 F2 mice were genotyped at 76 SNPs to capture quantitative trait loci for disease severity. The absence of a dominant quantitative trait locus suggests that differences in severity are the result of multiple gene interactions. In vivo studies using bone marrow chimeric mice and in vitro studies of neutrophil activation by anti-MPO IgG indicated that severity of NCGN is mediated by genetically determined differences in the function of neutrophils. Myeloperoxidase (MPO) is a target antigen for antineutrophil cytoplasmic autoantibodies (ANCA). There is evidence that MPO-ANCA cause necrotizing and crescentic glomerulonephritis (NCGN) and vasculitis. NCGN severity varies among patients with ANCA disease, and genetic factors influence disease severity. The role of genetics in MPO-ANCA NCGN severity was investigated using 13 inbred mouse strains, F1 and F2 hybrids, bone marrow chimeras, and neutrophil function assays. Mouse strains include founders of the Collaborative Cross. Intravenous injection of anti-MPO IgG induced glomerular crescents in >60% of glomeruli in 129S6/SvEv and CAST/EiJ mice, but <1% in A/J, DBA/1J, DBA/2J, NOD/LtJ, and PWK/PhJ mice. C57BL6J, 129S1/SvImJ, LP/J, WSB/EiJ, NZO/HILtJ, and C3H mice had intermediate severity. High-density genotypes at 542,190 single nucleotide polymorphisms were used to identify candidate loci for disease severity by identifying genomic regions that are different between 129S6/SvEv and 129S1/SvImJ mice, which are genetically similar but phenotypically distinct. C57BL/6 × 129S6 F2 mice were genotyped at 76 SNPs to capture quantitative trait loci for disease severity. The absence of a dominant quantitative trait locus suggests that differences in severity are the result of multiple gene interactions. In vivo studies using bone marrow chimeric mice and in vitro studies of neutrophil activation by anti-MPO IgG indicated that severity of NCGN is mediated by genetically determined differences in the function of neutrophils. Anti-neutrophil cytoplasmic autoantibodies (ANCA), including ANCA specific for myeloperoxidase (MPO-ANCA), are associated with systemic vasculitis and pauci-immune necrotizing crescentic glomerulonephritis (NCGN), and there is strong evidence that MPO-ANCA are pathogenic.1Falk R.J. Jennette J.C. ANCA disease: where is this field going?.J Am Soc Nephrol. 2010; 21: 745-752Crossref PubMed Scopus (94) Google Scholar NCGN is induced in mice by injecting anti-MPO IgG,2Xiao H. Heeringa P. Hu P. Liu Z. Zhao M. Aratani Y. Maeda N. Falk R.J. Jennette J.C. Antineutrophil cytoplasmic autoantibodies specific for myeloperoxidase cause glomerulonephritis and vasculitis in mice.J Clin Invest. 2002; 110: 955-963Crossref PubMed Scopus (1011) Google Scholar, 3Xiao H. Heeringa P. Liu Z. Huugen D. Hu P. Falk R.J. Jennette J.C. A major role for neutrophils in anti-myeloperoxidase antibody induced necrotizing and crescentic glomerulonephritis.Am J Pathol. 2005; 167: 39-45Abstract Full Text Full Text PDF PubMed Scopus (273) Google Scholar, 4Xiao H. Schreiber A. Heeringa P. Falk R.J. Jennette J.C. Alternative complement pathway in the pathogenesis of disease mediated by antineutrophil cytoplasmic autoantibodies.Am J Pathol. 2007; 170: 52-64Abstract Full Text Full Text PDF PubMed Scopus (431) Google Scholar, 5Jennette J.C. Xiao H. Falk R. Gasim A.M. Experimental models of vasculitis and glomerulonephritis induced by antineutrophil cytoplasmic autoantibodies.Contrib Nephrol. 2011; 169: 211-220Crossref PubMed Scopus (52) Google Scholar and is mediated by neutrophils, enhanced by neutrophil priming, modulated by Fc gamma receptor engagement, and requires alternative complement pathway activation.2Xiao H. Heeringa P. Hu P. Liu Z. Zhao M. Aratani Y. Maeda N. Falk R.J. Jennette J.C. Antineutrophil cytoplasmic autoantibodies specific for myeloperoxidase cause glomerulonephritis and vasculitis in mice.J Clin Invest. 2002; 110: 955-963Crossref PubMed Scopus (1011) Google Scholar, 3Xiao H. Heeringa P. Liu Z. Huugen D. Hu P. Falk R.J. Jennette J.C. A major role for neutrophils in anti-myeloperoxidase antibody induced necrotizing and crescentic glomerulonephritis.Am J Pathol. 2005; 167: 39-45Abstract Full Text Full Text PDF PubMed Scopus (273) Google Scholar, 4Xiao H. Schreiber A. Heeringa P. Falk R.J. Jennette J.C. Alternative complement pathway in the pathogenesis of disease mediated by antineutrophil cytoplasmic autoantibodies.Am J Pathol. 2007; 170: 52-64Abstract Full Text Full Text PDF PubMed Scopus (431) Google Scholar, 5Jennette J.C. Xiao H. Falk R. Gasim A.M. Experimental models of vasculitis and glomerulonephritis induced by antineutrophil cytoplasmic autoantibodies.Contrib Nephrol. 2011; 169: 211-220Crossref PubMed Scopus (52) Google Scholar, 6Schreiber A. Xiao H. Falk R.J. Jennette J.C. Bone marrow-derived cells are sufficient and necessary targets to mediate glomerulonephritis and vasculitis induced by anti-myeloperoxidase antibodies.J Am Soc Nephrol. 2006; 17: 3355-3364Crossref PubMed Scopus (92) Google Scholar, 7Schreiber A. Xiao H. Jennette J.C. Schneider W. Luft F.C. Kettritz R. C5a receptor mediates neutrophil activation and ANCA-induced glomerulonephritis.J Am Soc Nephrol. 2009; 20: 289-298Crossref PubMed Scopus (308) Google Scholar Patients with ANCA disease have varied NCGN severity, ranging from 100% to <5% crescents (average, 50%),8Jennette J.C. Rapidly progressive and crescentic glomerulonephritis.Kidney Int. 2003; 63: 1164-1172Crossref PubMed Scopus (326) Google Scholar and a minority of patients have systemic small vessel vasculitis with no glomerulonephritis.1Falk R.J. Jennette J.C. ANCA disease: where is this field going?.J Am Soc Nephrol. 2010; 21: 745-752Crossref PubMed Scopus (94) Google Scholar Evidence for genetic influence on ANCA-associated disease includes familial occurrences,9Hay E.M. Beaman M. Ralston A.J. Ackrill P. Bernstein R.M. Holt P.J. Wegener's granulomatosis occurring in siblings.Br J Rheumatol. 1991; 30: 144-145Crossref PubMed Scopus (28) Google Scholar, 10Muniain M.A. Moreno J.C. Gonzalez Campora R. Wegener's granulomatosis in two sisters.Ann Rheum Dis. 1986; 45: 417-421Crossref PubMed Scopus (32) Google Scholar, 11Nowack R. Lehmann H. Flores-Suarez L.F. Nanhou A. van der Woude F.J. Familial occurrence of systemic vasculitis and rapidly progressive glomerulonephritis.Am J Kidney Dis. 1999; 34: 364-373Abstract Full Text Full Text PDF PubMed Scopus (41) Google Scholar, 12Brener Z. Cohen L. Goldberg S.J. Kaufman A.M. ANCA-associated vasculitis in Greek siblings with chronic exposure to silica.Am J Kidney Dis. 2001; 38: E28Abstract Full Text Full Text PDF PubMed Scopus (19) Google Scholar, 13Manganelli P. Giacosa R. Fietta P. Zanetti A. Neri T.M. Familial vasculitides: churg-Strauss syndrome and Wegener's granulomatosis in 2 first-degree relatives.J Rheumatol. 2003; 30: 618-621PubMed Google Scholar greater frequency in first-degree relatives,14Knight A. Sandin S. Askling J. Risks and relative risks of Wegener's granulomatosis among close relatives of patients with the disease.Arthritis Rheum. 2008; 58: 302-307Crossref PubMed Scopus (57) Google Scholar differences in racial incidence,14Knight A. Sandin S. Askling J. Risks and relative risks of Wegener's granulomatosis among close relatives of patients with the disease.Arthritis Rheum. 2008; 58: 302-307Crossref PubMed Scopus (57) Google Scholar, 15O'Donnell J.L. Stevanovic V.R. Frampton C. Stamp L.K. Chapman P.T. Wegener's granulomatosis in New Zealand: evidence for a latitude dependent incidence gradient.Intern Med J. 2007; 37: 242-246Crossref PubMed Scopus (63) Google Scholar, 16Mahr A. Guillevin L. Poissonnet M. Ayme S. Prevalences of polyarteritis nodosa, microscopic polyangiitis, Wegener's granulomatosis, and Churg-Strauss syndrome in a French urban multiethnic population in 2000: a capture-recapture estimate.Arthritis Rheum. 2004; 51: 92-99Crossref PubMed Scopus (395) Google Scholar, 17Hogan S.L. Falk R.J. Chin H. Cai J. Jennette C.E. Jennette J.C. Nachman P.H. Predictors of relapse and treatment resistance in antineutrophil cytoplasmic antibody-associated small-vessel vasculitis.Ann Intern Med. 2005; 143: 621-631Crossref PubMed Scopus (373) Google Scholar association between disease severity and polymorphisms in genes that influence immune responses and inflammation,18Spencer S.J. Burns A. Gaskin G. Pusey C.D. Rees A.J. HLA class II specificities in vasculitis with antibodies to neutrophil cytoplasmic antigens.Kidney Int. 1992; 41: 1059-1063Crossref PubMed Scopus (88) Google Scholar, 19Esnault V.L. Testa A. Audrain M. Rogé C. Barrier J.H. Sesboüé R. Martin J.P. Lesavre P. Alpha 1-antitrypsin genetic polymorphism in ANCA positive systemic vasculitis.Kidney Int. 1993; 43: 1329-1332Crossref PubMed Scopus (202) Google Scholar, 20Griffith M.E. Lovegrove J.U. Gaskin G. Whitehouse D.B. Pusey C.D. C-antineutrophil cytoplasmic antibody positivity in vasculitis patients is associated with the Z allele of alpha-1-antitrypsin, and P-antineutrophil cytoplasmic antibody positivity with the S allele.Nephrol Dial Transplant. 1996; 11: 438-443Crossref PubMed Google Scholar, 21Jagiello P. Gencik M. Arning L. Wieczorek S. Kunstmann E. Csernok E. Gross W.L. Epplen J.T. New genomic region for Wegener's granulomatosis as revealed by an extended association screen with 202 apoptosis-related genes.Hum Genet. 2004; 114: 468-477Crossref PubMed Scopus (120) Google Scholar, 22Heckmann M. Holle J.U. Arning L. Knaup S. Hellmich B. Nothnagel M. Jagiello P. Gross W.L. Epplen J.T. Wieczorek S. The Wegener's granulomatosis quantitative trait locus on chromosome 6p21.3 as characterised by tagSNP genotyping.Ann Rheum Dis. 2008; 67: 972-979Crossref PubMed Scopus (74) Google Scholar, 23Carr E.J. Clatworthy M.R. Lowe C.E. Todd J.A. Wong A. Vyse T.J. Kamesh L. Watts R.A. Lyons P.A. Smith K.G. 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Lyons P.A. Rees A.J. Smith K.G. The contribution of genetic variation and infection to the pathogenesis of ANCA associated systemic vasculitis.Arthritis Res Ther. 2010; 12: 202Crossref PubMed Scopus (59) Google Scholar, 28Cao Y. Schmitz J.L. Yang J. Hogan S.L. Bunch D. Hu Y. Jennette C.E. Berg E.A. Arnett Jr., F.C. Jennette J.C. Falk R.J. Preston G.A. DRB1*15 allele is a risk factor for PR3-ANCA disease in African Americans.J Am Soc Nephrol. 2011; 122: 1161-1167Crossref Scopus (84) Google Scholar and a genome-wide association study that indicates genetically determined differences between disease associated with MPO-ANCA versus proteinase 3–specific ANCA (PR3-ANCA).29Lyons P.A. Rayner T.F. Trivedi S. Holle J.U. Watts R.A. Jayne D.R. et al.Genetically distinct subsets within ANCA-associated vasculitis.N Engl J Med. 2012; 367: 214-223Crossref PubMed Scopus (704) Google Scholar Intravenous injection of anti-MPO IgG into C57BL/6 (B6) mice induces NCGN with crescent formation in approximately 5% to 10% of glomeruli in 100% of mice.2Xiao H. Heeringa P. Hu P. Liu Z. Zhao M. Aratani Y. Maeda N. Falk R.J. Jennette J.C. Antineutrophil cytoplasmic autoantibodies specific for myeloperoxidase cause glomerulonephritis and vasculitis in mice.J Clin Invest. 2002; 110: 955-963Crossref PubMed Scopus (1011) Google Scholar, 3Xiao H. Heeringa P. Liu Z. Huugen D. Hu P. Falk R.J. Jennette J.C. A major role for neutrophils in anti-myeloperoxidase antibody induced necrotizing and crescentic glomerulonephritis.Am J Pathol. 2005; 167: 39-45Abstract Full Text Full Text PDF PubMed Scopus (273) Google Scholar, 4Xiao H. Schreiber A. Heeringa P. Falk R.J. Jennette J.C. Alternative complement pathway in the pathogenesis of disease mediated by antineutrophil cytoplasmic autoantibodies.Am J Pathol. 2007; 170: 52-64Abstract Full Text Full Text PDF PubMed Scopus (431) Google Scholar, 5Jennette J.C. Xiao H. Falk R. Gasim A.M. Experimental models of vasculitis and glomerulonephritis induced by antineutrophil cytoplasmic autoantibodies.Contrib Nephrol. 2011; 169: 211-220Crossref PubMed Scopus (52) Google Scholar, 6Schreiber A. Xiao H. Falk R.J. Jennette J.C. Bone marrow-derived cells are sufficient and necessary targets to mediate glomerulonephritis and vasculitis induced by anti-myeloperoxidase antibodies.J Am Soc Nephrol. 2006; 17: 3355-3364Crossref PubMed Scopus (92) Google Scholar, 7Schreiber A. Xiao H. Jennette J.C. Schneider W. Luft F.C. Kettritz R. C5a receptor mediates neutrophil activation and ANCA-induced glomerulonephritis.J Am Soc Nephrol. 2009; 20: 289-298Crossref PubMed Scopus (308) Google Scholar To investigate the effect of genetic backgrounds on disease severity, anti-MPO IgG was injected into 12 additional mouse strains, which demonstrated substantial differences in disease susceptibility and severity. High-density genotyping was used to identify candidate loci for disease severity by identifying genomic regions that are different between genetically similar, but phenotypically distinct, sister strains. F2 mice from a cross between low-severity B6 mice and high-severity 129S6/SvEv (129S6) mice were genotyped to identify quantitative trait loci (QTL) for disease severity. In vivo studies using bone marrow (BM) chimeric mice and in vitro studies of neutrophil activation by anti-MPO IgG demonstrated that NCGN severity is mediated by genetically determined differences in neutrophil function. C57B6/6J (B6), 129S6/SvEv (129S6), 129S1/SvImJ (129S1), LP/J (LP), WSB/EiJ (WSB), NZO/H1LtJ (NZO), PWK/PhJ (PWK), NOD/LtJ (NOD), DBA1, DBA2, AJ, C3H, and CAST/Ei (CAST), C57BL/6J (B6) and LP/J (LP) mice were purchased from Jackson Laboratories (Bar Harbor, ME). 129S6/SvEv (129S6), 129S1, Rag2 knockout with B6.SJL background (Rag2−/−B6), and Rag2 knockout with 129S6/SvEv background (Rag2−/−129S6) mice were purchased from Taconic Farms (Germantown, NY). NOD/LtJ, NZO/H1LtJ, PWK/PhJ, and WSB/EiJ were obtained from the University of North Carolina Department of Genetics. MPO knockout (Mpo−/−) mice were initially generated by Aratani and colleagues.30Aratani Y. Koyama H. Nyui S. Suzuki K. Kura F. Maeda N. Severe impairment in early host defense against Candida albicans in mice deficient in myeloperoxidase.Infect Immun. 1999; 67: 1828-1836Crossref PubMed Google Scholar B6, 129S1, NOD, NZO, PWK, WSB, CAST, and A/J strains are founders of the Collaborative Cross31Churchill G.A. Airey D.C. Allayee H. Angel J.M. Attie A.D. Beatty J. et al.The Collaborative Cross, a community resource for the genetic analysis of complex traits.Nat Genet. 2004; 36: 1133-1137Crossref PubMed Scopus (838) Google Scholar, 32Aylor D.L. Valdar W. Foulds-Mathes W. Buus R.J. Verdugo R.A. Baric R.S. et al.Genetic analysis of complex traits in the emerging Collaborative Cross.Genome Research. 2011; 21: 1213-1222Crossref PubMed Scopus (267) Google Scholar and capture 90% of the genetic diversity among laboratory mice. F1 mice were generated by B6 backcross with 129S6 mice, and 100 F2 mice were generated by (B6X129S6) F1 intercross. Mice were maintained by University of North Carolina Division of Laboratory Animal Medicine in adherence to the 2011 NIH Guide for Care and Use of Laboratory Animals. Purification of native mouse MPO and immunization of Mpo−/− mice were performed as described.2Xiao H. Heeringa P. Hu P. Liu Z. Zhao M. Aratani Y. Maeda N. Falk R.J. Jennette J.C. Antineutrophil cytoplasmic autoantibodies specific for myeloperoxidase cause glomerulonephritis and vasculitis in mice.J Clin Invest. 2002; 110: 955-963Crossref PubMed Scopus (1011) Google Scholar Mpo−/− mice 8 to 10 weeks old were immunized intraperitoneally with 20 μg of purified murine MPO in complete Freund's adjuvant and boosted twice with 10 μg of MPO in incomplete Freund's adjuvant. Anti-MPO was monitored by enzyme-linked immunosorbent assay. Anti-MPO IgG was isolated from serum of Mpo−/− mice immunized with MPO by 50% ammonium sulfate precipitation and protein G affinity chromatography.2Xiao H. Heeringa P. Hu P. Liu Z. Zhao M. Aratani Y. Maeda N. Falk R.J. Jennette J.C. Antineutrophil cytoplasmic autoantibodies specific for myeloperoxidase cause glomerulonephritis and vasculitis in mice.J Clin Invest. 2002; 110: 955-963Crossref PubMed Scopus (1011) Google Scholar Purity of antibodies was confirmed by SDS-PAGE electrophoresis, and protein concentrations determined by Coomassie protein assay (Pierce, Rockford, IL). Mice were injected intravenously with 50 μg/g bodyweight mouse anti-mouse MPO IgG.2Xiao H. Heeringa P. Hu P. Liu Z. Zhao M. Aratani Y. Maeda N. Falk R.J. Jennette J.C. Antineutrophil cytoplasmic autoantibodies specific for myeloperoxidase cause glomerulonephritis and vasculitis in mice.J Clin Invest. 2002; 110: 955-963Crossref PubMed Scopus (1011) Google Scholar After 6 days, mice were sacrificed and kidneys examined by light microscopy for NCGN. For BM transplantation experiments, 6 weeks after BM transfer, Rag2−/− mice were injected intravenously with 50 μg/g body weight of anti-MPO IgG and sacrificed 6 days later. Kidneys were collected at the time of sacrifice and fixed in 10% formalin, embedded in paraffin, sectioned at 4 μm, stained with H&E and periodic acid Schiff, and then evaluated by light microscopy. The extent of glomerular crescents and necrosis were expressed as mean % glomeruli with crescents or necrosis by counting all glomeruli in cross sections of both kidneys, which averaged approximately 80 per mouse. Glomerular leukocytes in kidneys from BM chimeric mice were evaluated by immunohistochemistry on paraffin sections. BM cells were harvested from femurs and tibia of B6 and 129S6 mice, and erythrocytes removed by hypotonic lysis.7Schreiber A. Xiao H. Jennette J.C. Schneider W. Luft F.C. Kettritz R. C5a receptor mediates neutrophil activation and ANCA-induced glomerulonephritis.J Am Soc Nephrol. 2009; 20: 289-298Crossref PubMed Scopus (308) Google Scholar Age-matched Rag2−/−B6 and Rag2−/−129S6 recipient mice were kept under sterile conditions and given acidified water with 0.2% neomycin at least 1 week before irradiation. Recipients were lethally γ-irradiated with 900 rad, and 12 to 24 hours later were reconstituted intravenously with 1.5 × 107 donor BM cells: 129/S6 donor cells into Rag2−/−B6 recipients (129S6 → Rag2−/−B6 chimeras), B6 donor cells into Rag2−/−129S6 recipients (B6 → Rag2−/−129S6 chimeras). Successful transplantation was confirmed by flow cytometry measuring CD45.1 and CD45.2 (BD Pharmingen, San Jose, CA), which distinguish leukocytes from recipients and donors. Superoxide dismutase (SOD)-inhibitable reduction of ferricytochrome C was used to measure neutrophil oxidative activity. Neutrophils were suspended at 1 × 107 in HBSS buffer and pretreated with 5 μg/mL cytochalasin B for 15 minutes at 4°C. Neutrophils (5 × 105, in HBSS) were prewarmed with 50 μmol/L ferricytochrome with or without 300 U/mL SOD for 15 minutes at 37°C and then primed with 2 ng/mL tumor necrosis factor-alpha (TNF-α) for 15 minutes at 37°C. Primed neutrophils were incubated with 250 μg/mL anti-mouse MPO IgG at 37°C, and absorption of samples was scanned at 550 nm every 5 minutes for 60 minutes using a Microplate Autoreader (Molecular Devices, Sunnyvale, CA). Genetic variation among mouse strains was determined by comparing publically available high-density genotypes at 542,190 single nucleotide polymorphisms (SNPs) using a mouse diversity array.33Beck J.A. Lloyd S. Hafezparast M. Lennon-Pierce M. Eppig J.T. Festing M.F. Fisher E.M. Genealogies of mouse inbred strains.Nat Genet. 2000; 24: 23-25Crossref PubMed Scopus (664) Google Scholar, 34Simpson E.M. Linder C.C. Sargent E.E. Davisson M.T. Mobraaten L.E. Sharp J.J. Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice.Nat Genet. 1997; 16: 19-27Crossref PubMed Scopus (607) Google Scholar, 35Threadgill D.W. Yee D. Matin A. Nadeau J.H. Magnuson T. Genealogy of the 129 inbred strains: 129/SvJ is a contaminated inbred strain.Mamm Genome. 1997; 8: 390-393Crossref PubMed Scopus (188) Google Scholar, 36Yang H. Ding Y. Hutchins L.N. Szatkiewicz J. Bell T.A. Paigen B.J. Graber J.H. de Villena F.P. Churchill G.A. A customized and versatile high-density genotyping array for the mouse.Nat Methods. 2009; 6: 663-666Crossref PubMed Scopus (205) Google Scholar Genomic clustering of identical genotypes was performed to identify regions identical by descent (IBD). IBD was performed by counting the number of identical SNPs in 100 SNP windows. Windows with 98% genotype similarity were declared IBD.36Yang H. Ding Y. Hutchins L.N. Szatkiewicz J. Bell T.A. Paigen B.J. Graber J.H. de Villena F.P. Churchill G.A. A customized and versatile high-density genotyping array for the mouse.Nat Methods. 2009; 6: 663-666Crossref PubMed Scopus (205) Google Scholar B6 × 129S6 F2 intercross was used to associate genetic variants with NCGN phenotypes. Genomic DNA was isolated from tails with a proteinase K/SDS lysis solution followed by phenol-chloroform extraction. Ninety-nine female F2 mice were genotyped at 76 SNPs using Sequenom iPEX MassARRAY (Sequenom, San Diego, CA) (1 of 108 samples was inadequate). The genetic map was estimated using the R/qtl est.map function (R software; http://www.r-project.org/)37Broman K.W. Wu H. Sen S. Churchill G.A. QTL mapping in experimental crosses.Bioinformatics. 2003; 19: 889-890Crossref PubMed Scopus (2356) Google Scholar, 38Sen S. Johannes F. Broman K.W. Selective genotyping and phenotyping strategies in a complex trait context.Genetics. 2009; 181: 1613-1626Crossref PubMed Scopus (21) Google Scholar assuming genotyping error of 0.001. Single-QTL interval mapping (IM) was performed using the R/qtl scanone function on % crescents and log % crescents. Log % crescents was distributed normally and IM was performed using a normal model. % crescents was mapped with a nonparametric IM model. A two-QTL model was used for log % crescents using the R/qtl scantwo function. Thresholds for both single- and two-QTL models were determined by 1000 permutations.39Churchill G.A. Doerge R.W. Empirical threshold values for quantitative trait mapping.Genetics. 1994; 138: 963-971Crossref PubMed Google Scholar Tukey's multiple comparison test was used for evaluating differences in mean percent crescents between groups. Mean % crescents induced by anti-MPO varied from 0% to >60% in 13 mouse strains including 8 Collaborative Cross founders that include 90% of the genetic diversity among laboratory mice31Churchill G.A. Airey D.C. Allayee H. Angel J.M. Attie A.D. Beatty J. et al.The Collaborative Cross, a community resource for the genetic analysis of complex traits.Nat Genet. 2004; 36: 1133-1137Crossref PubMed Scopus (838) Google Scholar, 32Aylor D.L. Valdar W. Foulds-Mathes W. Buus R.J. Verdugo R.A. Baric R.S. et al.Genetic analysis of complex traits in the emerging Collaborative Cross.Genome Research. 2011; 21: 1213-1222Crossref PubMed Scopus (267) Google Scholar (Table 1 and Figures 1 and 2). 129S6/SvEv (129S6) mice had 47 to 90% (mean 63.7%) compared to 4 to 23% in B6 (mean 9.5%) (P < 0.001). 129S1 mice developed an average of 21% crescents, which was a significant reduction (P < 0.001) compared to 129S6. LP/J mice were included because they share ancestry with 129 mice33Beck J.A. Lloyd S. Hafezparast M. Lennon-Pierce M. Eppig J.T. Festing M.F. Fisher E.M. Genealogies of mouse inbred strains.Nat Genet. 2000; 24: 23-25Crossref PubMed Scopus (664) Google Scholar and were found to have severity similar to 129S1 rather than 129S6. DBA1, DBA2, and C3H were included because they have susceptibility to vasculitis in other models. As shown in Figure 2 and Table 1, anti-MPO IgG induced NCGN in WSB and C3H mice, similar to B6 mice. CAST mice developed severe NCGN similar to 129S6. NZO mice developed <5% crescents. Only a minority of PWK and DBA1 mice developed crescents, affecting <1% of glomeruli. NOD, AJ, and DBA2 mice were resistant to NCGN induction.Table 1Anti-MPO IgG–Induced Glomerular Lesions in Different Strains of MiceStrainsMouse numbers, nMice with crescents, nMean % crescents when presentMice with necrosis, nMean % necrosis when presentB627279.5274.0129S6242463.7∗P < 0.001 versus B6 and 129S1 mice.2422.4∗P < 0.001 versus B6 and 129S1 mice.129S1222221.1†P > 0.4 versus LP mice.217.3†P > 0.4 versus LP mice.LP8819.885.9WSB449.042.8NZO442.842.8PWK510.70NANOD40NA0NADBA1520.90NADBA250NA0NAAJ40NA0NAC3H555.242.3CAST5561.2535.6NA, not applicable; no crescents or necrosis was observed.∗ P < 0.001 versus B6 and 129S1 mice.† P > 0.4 versus LP mice. Open table in a new tab Figure 2Severity of NCGN in 13 strains of mice and in B6 × 129S6 F1 and F2 mice, represented as the % of glomeruli with crescents. The two groups of B6 mice received different antibody preparations.View Large Image Figure ViewerDownload Hi-res image Download (PPT) NA, not applicable; no crescents or necrosis was observed. 129S6 and 129S1 have a significantly different fraction of glomeruli affected but are closely related, with most genetic differences clustered.34Simpson E.M. Linder C.C. Sargent E.E. Davisson M.T. Mobraaten L.E. Sharp J.J. Genetic variation among 129 substrains and its importance for targeted mutagenesis in mice.Nat Genet. 1997; 16: 19-27Crossref PubMed Scopus (607) Google Scholar, 35Threadgill D.W. Yee D. Matin A. Nadeau J.H. Magnuson T. Genealogy of the 129 inbred strains: 129/SvJ is a contaminated inbred strain.Mamm Genome. 1997; 8: 390-393Crossref PubMed Scopus (188) Google Scholar High-density genotypes were compared between 129S6 and 129S1 strains (Table 2 and 3). B6 and LP strains were also evaluated. The mouse diversity array36Yang H. Ding Y. Hutchins L.N. Szatkiewicz J. Bell T.A. Paigen B.J. Graber J.H. de Villena F.P. Churchill G.A. A customized and versatile high-density genotyping array for the mouse.Nat Methods. 2009; 6: 663-666Crossref PubMed Scopus (205) Google Scholar, 40Yang H. Wang J.R. Didion J.P. Buus R.J. Bell T.A. Welsh C.E. Bonhomme F. Yu A.H. Nachman M.W. Pialek J. Tucker P. Boursot P. McMillan L. Churchill G.A. de Villena F.P. Subspecific origin and haplotype diversity in the laboratory mouse.Nat Genet. 2011; 43: 648-655Crossref PubMed Scopus (332) Google Scholar used for genotyping contains 542,190 SNPs. Of these, 137,378 SNPs (25.34%) segregated among the four strains. B6 differs from the other three strains at over 20% of SNPs, LP differs from 129 at 7% to 8%, and the 129 substrains differ from each other at <1% (Table 3).Table 2SNP Genotypes in IBD and Non-IBD Regions between 129S1 and 129S6IBDNon-IDBTotal mismatches4604048Fraction of mismatches10.20%89.80%Fraction of genome96.69%3.31%Frequency of mismatches0.09%22.85% Open table in a new tab Table 3Comparative Genotype Analysis Using the Mouse Diversity Array129S6 vs B6129S6 vs 129 S1129S6 vs LP/J129S1 vs LP/J129S1 vs B6B6 vs LP/JGenome wide Number of mismatches115,069450841,94938,908114,567116,926 Percentage of mismatches21.22%0.83%7.74%7.18%21.13%21.57% Percentage of matches78.78%99.17%92.26%92.82%78.87%78.43% Percentage of IBD∗The fraction of the genome that was defined as identical by descent (IBD) between any two strains was determined by calculating the percentage of those two genomes with 98% or greater identity over windows of 100 SNPs.27.42%96.69%72.16%74.43%28.04%27.99%129S6 and 129S1 non-IBD†The regions of the genome that were non-IBD between 129 S6 and 129 S1 contained 17,713 SNPs of the Mouse Diversity Array. Pairwise genotype comparisons of the four inbred mouse strains were performed at these 17,713 SNPs to assess the genetic relatedness within the 129 S6 and 129 S1 non-IBD regions. Number of mismatches407540483931110036413481 Percentage of mismatches23.01%22.85%}, number={4}, journal={The American Journal of Pathology}, publisher={Elsevier BV}, author={Xiao, Hong and Ciavatta, Dominic and Aylor, David L. and Hu, Peiqi and de Villena, Fernando Pardo-Manuel and Falk, Ronald J. and Jennette, J. Charles}, year={2013}, month={Apr}, pages={1219–1226} }
 @article{phillippi_xie_miller_bell_zhang_lenarcic_aylor_krovi_threadgill_pardo-manuel de villena_et al._2013, title={Using the emerging Collaborative Cross to probe the immune system}, volume={15}, ISSN={1466-4879 1476-5470}, url={http://dx.doi.org/10.1038/GENE.2013.59}, DOI={10.1038/GENE.2013.59}, abstractNote={The Collaborative Cross (CC) is an emerging panel of recombinant inbred (RI) mouse strains. Each strain is genetically distinct but all descended from the same eight inbred founders. In 66 strains from incipient lines of the CC (pre-CC), as well as the 8 CC founders and some of their F1 offspring, we examined subsets of lymphocytes and antigen-presenting cells. We found significant variation among the founders, with even greater diversity in the pre-CC. Genome-wide association using inferred haplotypes detected highly significant loci controlling B-to-T cell ratio, CD8 T-cell numbers, CD11c and CD23 expression. Comparison of overall strain effects in the CC founders with strain effects at QTL in the pre-CC revealed sharp contrasts in the genetic architecture of two traits with significant loci: variation in CD23 can be explained largely by additive genetics at one locus, whereas variation in B-to-T ratio has a more complex etiology. For CD23, we found a strong QTL whose confidence interval contained the CD23 structural gene Fcer2a. Our data on the pre-CC demonstrate the utility of the CC for studying immunophenotypes and the value of integrating founder, CC and F1 data. The extreme immunophenotypes observed could have pleiotropic effects in other CC experiments.}, number={1}, journal={Genes & Immunity}, publisher={Springer Science and Business Media LLC}, author={Phillippi, J and Xie, Y and Miller, D R and Bell, T A and Zhang, Z and Lenarcic, A B and Aylor, D L and Krovi, S H and Threadgill, D W and Pardo-Manuel de Villena, F and et al.}, year={2013}, month={Nov}, pages={38–46} }
 @article{mathes_aylor_miller_churchill_chesler_villena_threadgill_pomp_2011, title={Architecture of energy balance traits in emerging lines of the Collaborative Cross}, volume={300}, ISSN={["1522-1555"]}, DOI={10.1152/ajpendo.00707.2010}, abstractNote={The potential utility of the Collaborative Cross (CC) mouse resource was evaluated to better understand complex traits related to energy balance. A primary focus was to examine if genetic diversity in emerging CC lines (pre-CC) would translate into equivalent phenotypic diversity. Second, we mapped quantitative trait loci (QTL) for 15 metabolism- and exercise-related phenotypes in this population. We evaluated metabolic and voluntary exercise traits in 176 pre-CC lines, revealing phenotypic variation often exceeding that seen across the eight founder strains from which the pre-CC was derived. Many phenotypic correlations existing within the founder strains were no longer significant in the pre-CC population, potentially representing reduced linkage disequilibrium (LD) of regions harboring multiple genes with effects on energy balance or disruption of genetic structure of extant inbred strains with substantial shared ancestry. QTL mapping revealed five significant and eight suggestive QTL for body weight (Chr 4, 7.54 Mb; CI 3.32–10.34 Mb; Bwq14), body composition, wheel running (Chr 16, 33.2 Mb; CI 32.5–38.3 Mb), body weight change in response to exercise (1: Chr 6, 77.7Mb; CI 72.2–83.4 Mb and 2: Chr 6, 42.8 Mb; CI 39.4–48.1 Mb), and food intake during exercise (Chr 12, 85.1 Mb; CI 82.9–89.0 Mb). Some QTL overlapped with previously mapped QTL for similar traits, whereas other QTL appear to represent novel loci. These results suggest that the CC will be a powerful, high-precision tool for examining the genetic architecture of complex traits such as those involved in regulation of energy balance.}, number={6}, journal={AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM}, author={Mathes, Wendy Foulds and Aylor, David L. and Miller, Darla R. and Churchill, Gary A. and Chesler, Elissa J. and Villena, Fernando Pardo-Manuel and Threadgill, David W. and Pomp, Daniel}, year={2011}, month={Jun}, pages={E1124–E1134} }
 @article{aylor_zeng_2008, title={From classical genetics to quantitative genetics to systems biology: Modeling epistasis}, volume={4}, number={3}, journal={PLoS Genetics}, author={Aylor, D. L. and Zeng, Z. B.}, year={2008} }
 @article{zou_aylor_zeng_2007, title={eQTL Viewer: visualizing how sequence variation affects genome-wide transcription}, volume={8}, number={7}, journal={BMC Bioinformatics}, author={Zou, W. and Aylor, D. L. and Zeng, Z. B.}, year={2007} }