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1.  Congenital abnormalities of the urogenital tract: the clue is in the cord? 
BMJ Case Reports  2014;2014:bcr2014208172.
Congenital abnormalities of the female urogenital tract are not uncommon, with an estimated incidence of 2–4% across the female population. Within this population, up to 40% will have associated renal tract abnormalities. A previously well 12-year-old girl presented to the emergency department with abdominal pain, vomiting and a palpable pelvic mass. Ultrasound and MR scans were performed. The imaging revealed a didelphys uterus, an obstructed hemivagina and ipsilateral renal agenesis, characteristic of Herlyn-Werner-Wunderlich syndrome. The patient was noted at birth to have a single umbilical artery, which is associated with an increased risk of congenital abnormalities and useful information for the early identification of abnormalities that have implications for renal function and future fertility.
PMCID: PMC4256657  PMID: 25465462
2.  Individual surgeon mortality rates: can outliers be detected? A national utility analysis 
BMJ Open  2016;6(10):e012471.
There is controversy on the proposed benefits of publishing mortality rates for individual surgeons. In some procedures, analysis at the level of an individual surgeon may lack statistical power. The aim was to determine the likelihood that variation in surgeon performance will be detected using published outcome data.
A national analysis surgeon-level mortality rates to calculate the level of power for the reported mortality rate across multiple surgical procedures.
The UK from 2010 to 2014.
Surgeons who performed colon cancer resection, oesophagectomy or gastrectomy, elective aortic aneurysm repair, hip replacement, bariatric surgery or thyroidectomy.
The likelihood of detecting an individual with a 30-day, 90-day or in-patient mortality rate of up to 5 times the national mean or median (as available). This was represented using a novel heat-map approach.
Overall mortality rates for the procedures ranged from 0.07% to 4.5% and mean/median surgeon volume was between 23 and 75 cases. The national median case volume for colorectal (n=55) and upper gastrointestinal (n=23) cancer resections provides around 20% power to detect a mortality rate of 3 times the national median, while, for hip replacement, this is a rate 5 times the national average. At the mortality rates reported for thyroid (0.08%) and bariatric (0.07%) procedures, it is unlikely a surgeon would perform a sufficient number of procedures in his/her entire career to stand a good chance of detecting a mortality rate 5 times the national average.
At present, surgeons with increased mortality rates are unlikely to be detected. Performance within an expected mortality rate range cannot be considered reliable evidence of acceptable performance. Alternative approaches should focus on commonly occurring meaningful outcome measures, with infrequent events analysed predominately at the hospital level.
PMCID: PMC5093625  PMID: 27799243
SURGERY; Patient safety; Patient outcome assessment; Surgeons/standards; Operative/mortailty
3.  Sex differences and hormonal effects on gut microbiota composition in mice 
Gut Microbes  2016;7(4):313-322.
We previously reported quantitation of gut microbiota in a panel of 89 different inbred strains of mice, and we now examine the question of sex differences in microbiota composition. When the total population of 689 mice was examined together, several taxa exhibited significant differences in abundance between sexes but a larger number of differences were observed at the single strain level, suggesting that sex differences can be obscured by host genetics and environmental factors. We also examined a subset of mice on chow and high fat diets and observed sex-by-diet interactions. We further investigated the sex differences using gonadectomized and hormone treated mice from 3 different inbred strains. Principal coordinate analysis with unweighted UniFrac distances revealed very clear effects of gonadectomy and hormone replacement on microbiota composition in all 3 strains. Moreover, bile acid analyses showed gender-specific differences as well as effects of gonodectomy, providing one possible mechanism mediating sex differences in microbiota composition.
PMCID: PMC4988450  PMID: 27355107
genetics; gut microbiota interactions; hormones; inbred strains; sex-by-diet interactions; sex differences
4.  Determining Surgical Complications in the Overweight (DISCOVER): a multicentre observational cohort study to evaluate the role of obesity as a risk factor for postoperative complications in general surgery 
BMJ Open  2015;5(7):e008811.
Obesity is increasingly prevalent among patients undergoing surgery. Conflicting evidence exists regarding the impact of obesity on postoperative complications. This multicentre study aims to determine whether obesity is associated with increased postoperative complications following general surgery.
Methods and analysis
This prospective, multicentre cohort study will be performed utilising a collaborative methodology. Consecutive adults undergoing open or laparoscopic, elective or emergency, gastrointestinal, bariatric or hepatobiliary surgery will be included. Day case patients will be excluded. The primary end point will be the overall 30-day major complication rate (Clavien-Dindo grade III–V complications). Data will be collected to risk-adjust outcomes for potential confounding factors, such as preoperative cardiac risk. This study will be disseminated through structured medical student networks using established collaborative methodology. The study will be powered to detect a two-percentage point increase in the major postoperative complication rate in obese versus non-obese patients.
Ethics and dissemination
Following appropriate assessment, an exemption from full ethics committee review has been received, and the study will be registered as a clinical audit or service evaluation at each participating hospital. Dissemination will take place through national and local research collaborative networks.
PMCID: PMC4513439  PMID: 26195471
5.  Cost-effectiveness of malaria diagnosis using rapid diagnostic tests compared to microscopy or clinical symptoms alone in Afghanistan 
Malaria Journal  2015;14:217.
Improving access to parasitological diagnosis of malaria is a central strategy for control and elimination of the disease. Malaria rapid diagnostic tests (RDTs) are relatively easy to perform and could be used in primary level clinics to increase coverage of diagnostics and improve treatment of malaria.
A cost-effectiveness analysis was undertaken of RDT-based diagnosis in public health sector facilities in Afghanistan comparing the societal and health sector costs of RDTs versus microscopy and RDTs versus clinical diagnosis in low and moderate transmission areas. The effect measure was ‘appropriate treatment for malaria’ defined using a reference diagnosis. Effects were obtained from a recent trial of RDTs in 22 public health centres with cost data collected directly from health centres and from patients enrolled in the trial. Decision models were used to compare the cost of RDT diagnosis versus the current diagnostic method in use at the clinic per appropriately treated case (incremental cost-effectiveness ratio, ICER).
RDT diagnosis of Plasmodium vivax and Plasmodium falciparum malaria in patients with uncomplicated febrile illness had higher effectiveness and lower cost compared to microscopy and was cost-effective across the moderate and low transmission settings. RDTs remained cost-effective when microscopy was used for other clinical purposes. In the low transmission setting, RDTs were much more effective than clinical diagnosis (65.2% (212/325) vs 12.5% (40/321)) but at an additional cost (ICER) of US$4.5 per appropriately treated patient including a health sector cost (ICER) of US$2.5 and household cost of US$2.0. Sensitivity analysis, which varied drug costs, indicated that RDTs would remain cost-effective if artemisinin combination therapy was used for treating both P. vivax and P. falciparum. Cost-effectiveness of microscopy relative to RDT is further reduced if the former is used exclusively for malaria diagnosis. In the health service setting of Afghanistan, RDTs are a cost-effective intervention compared to microscopy.
RDTs remain cost-effective across a range of drug costs and if microscopy is used for a range of diagnostic services. RDTs have significant advantages over clinical diagnosis with minor increases in the cost of service provision.
Trial Registration
The trial was registered at under identifier NCT00935688.
Electronic supplementary material
The online version of this article (doi:10.1186/s12936-015-0696-1) contains supplementary material, which is available to authorized users.
PMCID: PMC4450447  PMID: 26016871
Cost-effectiveness analysis; Malaria; Rapid diagnostic test; Microscopy diagnosis; Clinical diagnosis; Plasmodium vivax; Plasmodium falciparum; Afghanistan
6.  Allele-specific expression and eQTL analysis in mouse adipose tissue 
BMC Genomics  2014;15(1):471.
The simplest definition of cis-eQTLs versus trans, refers to genetic variants that affect expression in an allele specific manner, with implications on underlying mechanism. Yet, due to technical limitations of expression microarrays, the vast majority of eQTL studies performed in the last decade used a genomic distance based definition as a surrogate for cis, therefore exploring local rather than cis-eQTLs.
In this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific.
We suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-471) contains supplementary material, which is available to authorized users.
PMCID: PMC4089026  PMID: 24927774
Cis; Trans; eQTL; Allele Specific Expression; Adipose; RNA-seq; DNase I hypersensitivity; DBA/2J; C57BL/6J
8.  Genetic Control of Obesity and Gut Microbiota Composition in Response to High-Fat, High-Sucrose Diet in Mice 
Cell metabolism  2013;17(1):141-152.
Obesity is a highly heritable disease driven by complex interactions between genetic and environmental factors. Human genome-wide association studies (GWAS) have identified a number of loci contributing to obesity; however, a major limitation of these studies is the inability to assess environmental interactions common to obesity. Using a systems genetics approach, we measured obesity traits, global gene expression, and gut microbiota composition in response to a high-fat/high-sucrose (HF/HS) diet of more than 100 inbred strains of mice. Here we show that HF/HS feeding promotes robust, strain-specific changes in obesity that is not accounted for by food intake and provide evidence for a genetically determined set-point for obesity. GWAS analysis identified 11 genome-wide significant loci associated with obesity traits, several of which overlap with loci identified in human studies. We also show strong relationships between genotype and gut microbiota plasticity during HF/HS feeding and identify gut microbial phylotypes associated with obesity.
PMCID: PMC3545283  PMID: 23312289
9.  The Systems Genetics Resource: A Web Application to Mine Global Data for Complex Disease Traits 
The Systems Genetics Resource (SGR) ( is a new open-access web application and database that contains genotypes and clinical and intermediate phenotypes from both human and mouse studies. The mouse data include studies using crosses between specific inbred strains and studies using the Hybrid Mouse Diversity Panel. SGR is designed to assist researchers studying genes and pathways contributing to complex disease traits, including obesity, diabetes, atherosclerosis, heart failure, osteoporosis, and lipoprotein metabolism. Over the next few years, we hope to add data relevant to deafness, addiction, hepatic steatosis, toxin responses, and vascular injury. The intermediate phenotypes include expression array data for a variety of tissues and cultured cells, metabolite levels, and protein levels. Pre-computed tables of genetic loci controlling intermediate and clinical phenotypes, as well as phenotype correlations, are accessed via a user-friendly web interface. The web site includes detailed protocols for all of the studies. Data from published studies are freely available; unpublished studies have restricted access during their embargo period.
PMCID: PMC3657633  PMID: 23730305
database; genomics; systems biology; data integration; web services; data analysis
10.  Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits 
We have developed an association-based approach using classical inbred strains of mice in which we correct for population structure, which is very extensive in mice, using an efficient mixed-model algorithm. Our approach includes inbred parental strains as well as recombinant inbred strains in order to capture loci with effect sizes typical of complex traits in mice (in the range of 5 % of total trait variance). Over the last few years, we have typed the hybrid mouse diversity panel (HMDP) strains for a variety of clinical traits as well as intermediate phenotypes and have shown that the HMDP has sufficient power to map genes for highly complex traits with resolution that is in most cases less than a megabase. In this essay, we review our experience with the HMDP, describe various ongoing projects, and discuss how the HMDP may fit into the larger picture of common diseases and different approaches.
PMCID: PMC3586763  PMID: 22892838
11.  ABCC6 Localizes to the Mitochondria-Associated Membrane 
Circulation research  2012;111(5):516-520.
Mutations of the orphan transporter ABCC6 (ATP-binding cassette, subfamily C, member 6) cause the connective tissue disorder pseudoxanthoma elasticum. ABCC6 was thought to be located on the plasma membrane of liver and kidney cells.
Mouse systems genetics and bioinformatics suggested that ABCC6 deficiency affects mitochondrial gene expression. We therefore tested whether ABCC6 associates with mitochondria.
Methods and Results
We found ABCC6 in crude mitochondrial fractions and subsequently pinpointed its localization to the purified mitochondria-associated membrane fraction. Cell-surface biotinylation in hepatocytes confirmed that ABCC6 is intracellular. Abcc6-knockout mice demonstrated mitochondrial abnormalities and decreased respiration reserve capacity.
Our finding that ABCC6 localizes to the mitochondria-associated membrane has implications for its mechanism of action in normal and diseased states.
PMCID: PMC3540978  PMID: 22811557
PXE; vascular calcification; ABCC6/MRP6; MAM; mitochondria; cardiovascular disease
12.  Applying perceptual and adaptive learning techniques for teaching introductory histopathology 
Medical students are expected to master the ability to interpret histopathologic images, a difficult and time-consuming process. A major problem is the issue of transferring information learned from one example of a particular pathology to a new example. Recent advances in cognitive science have identified new approaches to address this problem.
We adapted a new approach for enhancing pattern recognition of basic pathologic processes in skin histopathology images that utilizes perceptual learning techniques, allowing learners to see relevant structure in novel cases along with adaptive learning algorithms that space and sequence different categories (e.g. diagnoses) that appear during a learning session based on each learner's accuracy and response time (RT). We developed a perceptual and adaptive learning module (PALM) that utilized 261 unique images of cell injury, inflammation, neoplasia, or normal histology at low and high magnification. Accuracy and RT were tracked and integrated into a “Score” that reflected students rapid recognition of the pathologies and pre- and post-tests were given to assess the effectiveness.
Accuracy, RT and Scores significantly improved from the pre- to post-test with Scores showing much greater improvement than accuracy alone. Delayed post-tests with previously unseen cases, given after 6-7 weeks, showed a decline in accuracy relative to the post-test for 1st-year students, but not significantly so for 2nd-year students. However, the delayed post-test scores maintained a significant and large improvement relative to those of the pre-test for both 1st and 2nd year students suggesting good retention of pattern recognition. Student evaluations were very favorable.
A web-based learning module based on the principles of cognitive science showed an evidence for improved recognition of histopathology patterns by medical students.
PMCID: PMC3908489  PMID: 24524000
Cognitive science; dermatology; medical education; pathology; perceptual learning
13.  Abcc6 deficiency causes increased infarct size and apoptosis in a mouse cardiac ischemia-reperfusion (I/R) model 
ABCC6 genetic deficiency underlies Pseudoxanthoma elasticum (PXE) in humans, characterized by ectopic calcification, and early cardiac disease. The spectrum of PXE has been noted in Abcc6 deficient mice, including dystrophic cardiac calcification. We tested the role of Abcc6 in response to cardiac ischemia-reperfusion (I/R) injury.
Methods and results
To determine the role of Abcc6 in cardio-protection we induced ischemic injury in mice in vivo by occluding the left anterior descending artery (30min) followed by reperfusion (48hrs). Infarct size was increased in Abcc6 deficient mice compared to wild type controls. Additionally, an Abcc6 transgene significantly reduced infarct size on the background of a naturally occurring Abcc6 deficiency. There were no differences in cardiac calcification following I/R, but increased cardiac apoptosis was noted in Abcc6 deficient mice. Previous studies have implicated the BMP signaling pathway in directing calcification, and here we show the BMP responsive transcription factors, pSmad1/5/8 were increased in hearts of Abcc6 mice. Consistent with this finding, BMP4 and BMP9 were increased, and ALK2 and Endoglin were down-regulated in cardiac extracts from Abcc6 deficient mice versus controls.
These data identify Abcc6 as a novel modulator of cardiac myocyte survival after I/R. This cardio-protective mechanism may involve inhibition of the BMP signaling pathway, which modulates apoptosis.
PMCID: PMC3227394  PMID: 21979437
ABCC6; Pseudoxanthoma elasticum; BMP signaling; apoptosis; cardiac ischemia-reperfusion (I/R)
14.  Cost analysis of school-based intermittent screening and treatment of malaria in Kenya 
Malaria Journal  2011;10:273.
The control of malaria in schools is receiving increasing attention, but there remains currently no consensus as to the optimal intervention strategy. This paper analyses the costs of intermittent screening and treatment (IST) of malaria in schools, implemented as part of a cluster-randomized controlled trial on the Kenyan coast.
Financial and economic costs were estimated using an ingredients approach whereby all resources required in the delivery of IST are quantified and valued. Sensitivity analysis was conducted to investigate how programme variation affects costs and to identify potential cost savings in the future implementation of IST.
The estimated financial cost of IST per child screened is US$ 6.61 (economic cost US$ 6.24). Key contributors to cost were salary costs (36%) and malaria rapid diagnostic tests (RDT) (22%). Almost half (47%) of the intervention cost comprises redeployment of existing resources including health worker time and use of hospital vehicles. Sensitivity analysis identified changes to intervention delivery that can reduce programme costs by 40%, including use of alternative RDTs and removal of supervised treatment. Cost-effectiveness is also likely to be highly sensitive to the proportion of children found to be RDT-positive.
In the current context, school-based IST is a relatively expensive malaria intervention, but reducing the complexity of delivery can result in considerable savings in the cost of intervention.
(Costs are reported in US$ 2010).
PMCID: PMC3187739  PMID: 21933376
15.  Mouse Genome-Wide Association and Systems Genetics Identify Asxl2 As a Regulator of Bone Mineral Density and Osteoclastogenesis 
PLoS Genetics  2011;7(4):e1002038.
Significant advances have been made in the discovery of genes affecting bone mineral density (BMD); however, our understanding of its genetic basis remains incomplete. In the current study, genome-wide association (GWA) and co-expression network analysis were used in the recently described Hybrid Mouse Diversity Panel (HMDP) to identify and functionally characterize novel BMD genes. In the HMDP, a GWA of total body, spinal, and femoral BMD revealed four significant associations (−log10P>5.39) affecting at least one BMD trait on chromosomes (Chrs.) 7, 11, 12, and 17. The associations implicated a total of 163 genes with each association harboring between 14 and 112 genes. This list was reduced to 26 functional candidates by identifying those genes that were regulated by local eQTL in bone or harbored potentially functional non-synonymous (NS) SNPs. This analysis revealed that the most significant BMD SNP on Chr. 12 was a NS SNP in the additional sex combs like-2 (Asxl2) gene that was predicted to be functional. The involvement of Asxl2 in the regulation of bone mass was confirmed by the observation that Asxl2 knockout mice had reduced BMD. To begin to unravel the mechanism through which Asxl2 influenced BMD, a gene co-expression network was created using cortical bone gene expression microarray data from the HMDP strains. Asxl2 was identified as a member of a co-expression module enriched for genes involved in the differentiation of myeloid cells. In bone, osteoclasts are bone-resorbing cells of myeloid origin, suggesting that Asxl2 may play a role in osteoclast differentiation. In agreement, the knockdown of Asxl2 in bone marrow macrophages impaired their ability to form osteoclasts. This study identifies a new regulator of BMD and osteoclastogenesis and highlights the power of GWA and systems genetics in the mouse for dissecting complex genetic traits.
Author Summary
Osteoporosis is a disease of weak and fracture-prone bones. The characteristic of bone that is most predictive of fractures is low bone mineral density (BMD), a trait primarily controlled by genetics. In recent years, significant advances have been made in the discovery of genes affecting BMD; however, our understanding of its genetic basis is still primitive. In this study, we used genome-wide association in the mouse to identify additional sex combs like-2 (Asxl2) as a novel BMD gene. In confirmation of our genetic analysis, mice deficient in Asxl2 had reduced BMD. To evaluate its function in bone, the expression levels of Asxl2 and tens of thousands of other genes were measured in bone in a large number of inbred mouse strains. Asxl2 demonstrated a pattern of expression indicative of genes that play a critical role in osteoclasts, the cells that are responsible for bone resorption. Further study of Asxl2 may reveal novel therapeutic targets for the treatment and prevention of osteoporosis.
PMCID: PMC3072371  PMID: 21490954
16.  Upstream transcription factor 1 influences plasma lipid and metabolic traits in mice 
Human Molecular Genetics  2009;19(4):597-608.
Upstream transcription factor 1 (USF1) has been associated with familial combined hyperlipidemia, the metabolic syndrome, and related conditions, but the mechanisms involved are unknown. In this study, we report validation of Usf1 as a causal gene of cholesterol homeostasis, insulin sensitivity and body composition in mouse models using several complementary approaches and identify associated pathways and gene expression network modules. Over-expression of human USF1 in both transgenic mice and mice with transient liver-specific over-expression influenced metabolic trait phenotypes, including obesity, total cholesterol level, LDL/VLDL cholesterol and glucose/insulin ratio. Additional analyses of trait and hepatic gene expression data from an F2 population derived from C57BL/6J and C3H/HeJ strains in which there is a naturally occurring variation in Usf1 expression supported a causal role for Usf1 for relevant metabolic traits. Gene network and pathway analyses of the liver gene expression signatures in the F2 population and the hepatic over-expression model suggested the involvement of Usf1 in immune responses and metabolism, including an Igfbp2-centered module. In all three mouse model settings, notable sex specificity was observed, consistent with human studies showing differences in association with USF1 gene polymorphisms between sexes.
PMCID: PMC2807368  PMID: 19995791
17.  Variations in DNA elucidate molecular networks that cause disease 
Nature  2008;452(7186):429-435.
Identifying variations in DNA that increase susceptibility to disease is one of the primary aims of genetic studies using a forward genetics approach. However, identification of disease-susceptibility genes by means of such studies provides limited functional information on how genes lead to disease. In fact, in most cases there is an absence of functional information altogether, preventing a definitive identification of the susceptibility gene or genes. Here we develop an alternative to the classic forward genetics approach for dissecting complex disease traits where, instead of identifying susceptibility genes directly affected by variations in DNA, we identify gene networks that are perturbed by susceptibility loci and that in turn lead to disease. Application of this method to liver and adipose gene expression data generated from a segregating mouse population results in the identification of a macrophage-enriched network supported as having a causal relationship with disease traits associated with metabolic syndrome. Three genes in this network, lipoprotein lipase (Lpl), lactamase β (Lactb) and protein phosphatase 1-like (Ppm1l), are validated as previously unknown obesity genes, strengthening the association between this network and metabolic disease traits. Our analysis provides direct experimental support that complex traits such as obesity are emergent properties of molecular networks that are modulated by complex genetic loci and environmental factors.
PMCID: PMC2841398  PMID: 18344982
18.  An integrative genomics approach to infer causal associations between gene expression and disease 
Nature genetics  2005;37(7):710-717.
A key goal of biomedical research is to elucidate the complex network of gene interactions underlying complex traits such as common human diseases. Here we detail a multistep procedure for identifying potential key drivers of complex traits that integrates DNA-variation and gene-expression data with other complex trait data in segregating mouse populations. Ordering gene expression traits relative to one another and relative to other complex traits is achieved by systematically testing whether variations in DNA that lead to variations in relative transcript abundances statistically support an independent, causative or reactive function relative to the complex traits under consideration. We show that this approach can predict transcriptional responses to single gene–perturbation experiments using gene-expression data in the context of a segregating mouse population. We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity.
PMCID: PMC2841396  PMID: 15965475
19.  Validation of Candidate Causal Genes for Abdominal Obesity Which Affect Shared Metabolic Pathways and Networks 
Nature genetics  2009;41(4):415-423.
A major task in dissecting the genetics of complex traits is to identify causal genes for disease phenotypes. We previously developed a method to infer causal relationships among genes through the integration of DNA variation, gene transcription, and phenotypic information. Here we validated our method through the characterization of transgenic and knockout mouse models of candidate genes that were predicted to be causal for abdominal obesity. Perturbation of eight out of the nine genes, with Gas7, Me1 and Gpx3 being novel, resulted in significant changes in obesity related traits. Liver expression signatures revealed alterations in common metabolic pathways and networks contributing to abdominal obesity and overlapped with a macrophage-enriched metabolic network module that is highly associated with metabolic traits in mice and humans. Integration of gene expression in the design and analysis of traditional F2 intercross studies allows high confidence prediction of causal genes and identification of involved pathways and networks.
PMCID: PMC2837947  PMID: 19270708
20.  Disruption of the Aortic Elastic Lamina and Medial Calcification Share Genetic Determinants in Mice 
Disruption of the elastic lamina, as an early indicator of aneurysm formation, and vascular calcification frequently occur together in atherosclerotic lesions of humans.
Methods and Results
We now report evidence of shared genetic basis for disruption of the elastic lamina (medial disruption) and medial calcification in an F2 mouse intercross between C57BL/6J and C3H/HeJ on a hyperlipidemic apolipoprotein E (ApoE−/−) null background. We identified 3 quantitative trait loci (QTLs) on chromosomes 6, 13, and 18, which are common to both traits, and 2 additional QTLs for medial calcification on chromosomes 3 and 7. Medial disruption, including severe disruptions leading to aneurysm formation, and medial calcification were highly correlated and occurred concomitantly in the cross. The chromosome 18 locus showed a striking male sex-specificity for both traits. To identify candidate genes, we integrated data from microarray analysis, genetic segregation, and clinical traits. The chromosome 7 locus contains the Abcc6 gene, known to mediate myocardial calcification. Using transgenic complementation, we show that Abcc6 also contributes to aortic medial calcification.
Our data indicate that calcification, though possibly contributory, does not always lead to medial disruption and that in addition to aneurysm formation, medial disruption may be the precursor to calcification.
PMCID: PMC2836127  PMID: 20031637
aneurysm vascular calcification; Abcc6; Alox5; genetics; gene expression
21.  An integrative genetics approach to identify candidategenes regulating bone density: combining linkage, gene expression and association 
Numerous quantitative trait loci (QTL) affecting bone traits have been identified in the mouse; however, few of the underlying genes have been discovered. To improve the process of transitioning from QTL to gene we describe an integrative genetics approach, which combines linkage analysis, expression QTL (eQTL) mapping, causality modeling and genetic association in outbred mice. In C57BL/6J X C3H/HeJ (BXH) F2 mice, nine QTL regulating femoral bone mineral density (BMD) were identified. To select candidate genes from within each QTL region, microarray gene expression profiles from individual F2 mice were used to identify 148 genes whose expression was correlated with BMD and regulated by local eQTL. Many of the genes that were the most highly correlated with BMD have been previously shown to modulate bone mass or skeletal development. Candidates were further prioritized by determining if their expression was predicted to underlie variation in BMD. Using network edge orienting (NEO), a causality modeling algorithm, 18 of the 148 candidates were predicted to be causally related to differences in BMD. To fine-map QTL, markers in outbred MF1 mice were tested for association with BMD. Three chromosome 11 SNPs were identified that were associated with BMD within the Bmd11 QTL. Finally, our approach provides strong support for Wnt9a, Rasd1 or both underlying Bmd11. Integration of multiple genetic and genomic data sets can substantially improve the efficiency of QTL fine-mapping and candidate gene identification.
PMCID: PMC2661539  PMID: 18767929
Quantitative trait locus; bone mineral density; integrative genetics; genetic association; causality
22.  Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice 
Mammalian Genome  2006;17(6):466-479.
The millions of common DNA variations that occur in the human population, or among inbred strains of mice and rats, perturb the expression (transcript levels) of a large fraction of the genes expressed in a particular tissue. The hundreds or thousands of common cis-acting variations that occur in the population may in turn affect the expression of thousands of other genes by affecting transcription factors, signaling molecules, RNA processing, and other processes that act in trans. The levels of transcripts are conveniently quantitated using expression arrays, and the cis- and trans-acting loci can be mapped using quantitative trait locus (QTL) analysis, in the same manner as loci for physiologic or clinical traits. Thousands of such expression QTL (eQTL) have been mapped in various crosses in mice, as well as other experimental organisms, and less detailed maps have been produced in studies of cells from human pedigrees. Such an integrative genetics approach (sometimes referred to as “genetical genomics”) is proving useful for identifying genes and pathways that contribute to complex clinical traits. The coincidence of clinical trait QTL and eQTL can help in the prioritization of positional candidate genes. More importantly, mathematical modeling of correlations between levels of transcripts and clinical traits in genetic crosses can allow prediction of causal interactions and the identification of “key driver” genes. An important objective of such studies will be to model biological networks in physiologic processes. When combined with high-density single nucleotide polymorphism (SNP) mapping, it should be feasible to identify genes that contribute to transcript levels using association analysis in outbred populations. In this review we discuss the basic concepts and applications of this integrative genomic approach to cardiovascular and metabolic diseases.
PMCID: PMC2679634  PMID: 16783628
23.  Concept, Design and Implementation of a Cardiovascular Gene-Centric 50 K SNP Array for Large-Scale Genomic Association Studies 
PLoS ONE  2008;3(10):e3583.
A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a “cosmopolitan” tagging approach to capture the genetic diversity across ∼2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.
PMCID: PMC2571995  PMID: 18974833
24.  High-Resolution Mapping of Gene Expression Using Association in an Outbred Mouse Stock 
PLoS Genetics  2008;4(8):e1000149.
Quantitative trait locus (QTL) analysis is a powerful tool for mapping genes for complex traits in mice, but its utility is limited by poor resolution. A promising mapping approach is association analysis in outbred stocks or different inbred strains. As a proof of concept for the association approach, we applied whole-genome association analysis to hepatic gene expression traits in an outbred mouse population, the MF1 stock, and replicated expression QTL (eQTL) identified in previous studies of F2 intercross mice. We found that the mapping resolution of these eQTL was significantly greater in the outbred population. Through an example, we also showed how this precise mapping can be used to resolve previously identified loci (in intercross studies), which affect many different transcript levels (known as eQTL “hotspots”), into distinct regions. Our results also highlight the importance of correcting for population structure in whole-genome association studies in the outbred stock.
Author Summary
In rodents, as in humans, traits such as obesity or diabetes are under the influence of many genes spread throughout the genome. Using linkage analysis, the locations of the major contributing genes can be mapped only to very large regions of chromosomes, usually encompassing hundreds of genes. This has made it difficult to identify the underlying genes and mutations. Another approach, analogous to genome-wide association in human populations, is to use association analyses among outbred stocks of mice. In this proof-of-principle article, we make use of common variations that locally perturb gene expression to demonstrate the greatly improved mapping resolution of association in mice. Our results indicate that association analyses in mice are a powerful approach to the dissection of complex traits and their underlying molecular networks.
PMCID: PMC2483929  PMID: 18688273
25.  Mapping the Genetic Architecture of Gene Expression in Human Liver 
PLoS Biology  2008;6(5):e107.
Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process.
Author Summary
Genome-wide association studies seek to identify regions of the genome in which changes in DNA in a given population are correlated with disease, drug response, or other phenotypes of interest. However, changes in DNA that associate with traits like common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in the higher-order disease traits. Therefore, identifying molecular phenotypes that vary in response to changes in DNA that also associate with changes in disease traits can provide the functional information necessary to not only identify and validate the susceptibility genes directly affected by changes in DNA, but to understand as well the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. To enable this type of approach we profiled the expression levels of 39,280 transcripts and genotyped 782,476 SNPs in 427 human liver samples, identifying thousands of DNA variants that strongly associated with liver gene expression. These relationships were then leveraged by integrating them with genotypic and expression data from other human and mouse populations, leading to the direct identification of candidate susceptibility genes corresponding to genetic loci identified as key drivers of disease. Our analysis is able to provide much needed functional support for these candidate susceptibility genes.
Identifying changes in DNA that associate with changes in gene expression in human tissues elucidates the genetic architecture of gene expression in human populations and enables the direct identification of functionally supported candidate susceptibility genes in genomic regions associated with disease.
PMCID: PMC2365981  PMID: 18462017

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