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1.  eMERGEing progress in genomics—the first seven years 
Frontiers in Genetics  2014;5:184.
The electronic MEdical Records & GEnomics (eMERGE) network was established in 2007 by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) in part to explore the utility of electronic medical records (EMRs) in genome science. The initial focus was on discovery primarily using the genome-wide association paradigm, but more recently, the network has begun evaluating mechanisms to implement new genomic information coupled to clinical decision support into EMRs. Herein, we describe this evolution including the development of the individual and merged eMERGE genomic datasets, the contribution the network has made toward genomic discovery and human health, and the steps taken toward the next generation genotype-phenotype association studies and clinical implementation.
doi:10.3389/fgene.2014.00184
PMCID: PMC4060012  PMID: 24987407
biobanks; genome-wide association studies; pharmacogenomics; electronic medical records
2.  Genetic-based prediction of disease traits: prediction is very difficult, especially about the future† 
Frontiers in Genetics  2014;5:162.
Translation of results from genetic findings to inform medical practice is a highly anticipated goal of human genetics. The aim of this paper is to review and discuss the role of genetics in medically-relevant prediction. Germline genetics presages disease onset and therefore can contribute prognostic signals that augment laboratory tests and clinical features. As such, the impact of genetic-based predictive models on clinical decisions and therapy choice could be profound. However, given that (i) medical traits result from a complex interplay between genetic and environmental factors, (ii) the underlying genetic architectures for susceptibility to common diseases are not well-understood, and (iii) replicable susceptibility alleles, in combination, account for only a moderate amount of disease heritability, there are substantial challenges to constructing and implementing genetic risk prediction models with high utility. In spite of these challenges, concerted progress has continued in this area with an ongoing accumulation of studies that identify disease predisposing genotypes. Several statistical approaches with the aim of predicting disease have been published. Here we summarize the current state of disease susceptibility mapping and pharmacogenetics efforts for risk prediction, describe methods used to construct and evaluate genetic-based predictive models, and discuss applications.
doi:10.3389/fgene.2014.00162
PMCID: PMC4040440  PMID: 24917882
predictive model; genetic risk; human genetics; prognosis; clinical utility
3.  Novel pathways in the pathobiology of human abdominal aortic aneurysms 
Objectives
Abdominal aortic aneurysm (AAA), a dilatation of the infrarenal aorta, typically affects males > 65 years. The pathobiological mechanisms of human AAA are poorly understood. The goal of this study was to identify novel pathways involved in the development of AAAs.
Methods
A custom-designed “AAA-chip” was used to assay 43 of the differentially expressed genes identified in a previously published microarray study between AAA (n = 15) and control (n = 15) infrarenal abdominal aorta. Protein analyses were performed on selected genes.
Results
Altogether 38 of the 43 genes on the “AAA-chip” showed significantly different expression. Novel validated genes in AAA pathobiology included ADCY7, ARL4C, BLNK, FOSB, GATM, LYZ, MFGE8, PRUNE2, PTPRC, SMTN, TMODI and TPM2. These genes represent a wide range of biological functions, such as calcium signaling, development and differentiation, as well as cell adhesion not previously implicated in AAA pathobiology. Protein analyses for GATM, CD4, CXCR4, BLNK, PLEK, LYZ, FOSB, DUSP6, ITGA5 and PTPRC confirmed the mRNA findings.
Conclusion
The results provide new directions for future research into AAA pathogenesis to study the role of novel genes confirmed here. New treatments and diagnostic tools for AAA could potentially be identified by studying these novel pathways.
doi:10.1159/000339303
PMCID: PMC3782105  PMID: 22797469
gene expression; vascular biology; aorta; abdominal aortic aneurysm
4.  Update on Abdominal Aortic Aneurysm Research: From Clinical to Genetic Studies 
Scientifica  2014;2014:564734.
An abdominal aortic aneurysm (AAA) is a dilatation of the abdominal aorta with a diameter of at least 3.0 cm. AAAs are often asymptomatic and are discovered as incidental findings in imaging studies or when the AAA ruptures leading to a medical emergency. AAAs are more common in males than females, in individuals of European ancestry, and in those over 65 years of age. Smoking is the most important environmental risk factor. In addition, a positive family history of AAA increases the person's risk for AAA. Interestingly, diabetes has been shown to be a protective factor for AAA in many large studies. Hallmarks of AAA pathogenesis include inflammation, vascular smooth muscle cell apoptosis, extracellular matrix degradation, and oxidative stress. Autoimmunity may also play a role in AAA development and progression. In this Outlook paper, we summarize our recent studies on AAA including clinical studies related to surgical repair of AAA and genetic risk factor and large-scale gene expression studies. We conclude with a discussion on our research projects using large data sets available through electronic medical records and biobanks.
doi:10.1155/2014/564734
PMCID: PMC4009235  PMID: 24834361
5.  Mechanistic Phenotypes: An Aggregative Phenotyping Strategy to Identify Disease Mechanisms Using GWAS Data 
PLoS ONE  2013;8(12):e81503.
A single mutation can alter cellular and global homeostatic mechanisms and give rise to multiple clinical diseases. We hypothesized that these disease mechanisms could be identified using low minor allele frequency (MAF<0.1) non-synonymous SNPs (nsSNPs) associated with “mechanistic phenotypes”, comprised of collections of related diagnoses. We studied two mechanistic phenotypes: (1) thrombosis, evaluated in a population of 1,655 African Americans; and (2) four groupings of cancer diagnoses, evaluated in 3,009 white European Americans. We tested associations between nsSNPs represented on GWAS platforms and mechanistic phenotypes ascertained from electronic medical records (EMRs), and sought enrichment in functional ontologies across the top-ranked associations. We used a two-step analytic approach whereby nsSNPs were first sorted by the strength of their association with a phenotype. We tested associations using two reverse genetic models and standard additive and recessive models. In the second step, we employed a hypothesis-free ontological enrichment analysis using the sorted nsSNPs to identify functional mechanisms underlying the diagnoses comprising the mechanistic phenotypes. The thrombosis phenotype was solely associated with ontologies related to blood coagulation (Fisher's p = 0.0001, FDR p = 0.03), driven by the F5, P2RY12 and F2RL2 genes. For the cancer phenotypes, the reverse genetics models were enriched in DNA repair functions (p = 2×10−5, FDR p = 0.03) (POLG/FANCI, SLX4/FANCP, XRCC1, BRCA1, FANCA, CHD1L) while the additive model showed enrichment related to chromatid segregation (p = 4×10−6, FDR p = 0.005) (KIF25, PINX1). We were able to replicate nsSNP associations for POLG/FANCI, BRCA1, FANCA and CHD1L in independent data sets. Mechanism-oriented phenotyping using collections of EMR-derived diagnoses can elucidate fundamental disease mechanisms.
doi:10.1371/journal.pone.0081503
PMCID: PMC3861317  PMID: 24349080
6.  Identification, basic characterization and evolutionary analysis of differentially spliced mRNA isoforms of human YAP1 gene 
Gene  2012;509(2):215-222.
The YAP1 gene encodes a potent new oncogene and stem cell factor. However, in some cancers, the YAP1 gene plays a role of tumor suppressor. At present, the gene and its products are intensely studied and its cDNAs are used as transgenes in cellular and animal models. Here, we report 4 new potential mRNA splicing isoforms of the YAP1 gene, bringing the total number of isoforms to 8. We detected all 8 YAP1 isoforms in a panel of human tissues and evaluated the expression of the longest isoform of YAP1 (YAP1-2δ) using Real Time PCR. All YAP1 isoforms are barely detectable in human leukocytes compared to fair levels of expression found in other human tissues. We analyzed the structure of the genomic region that gave rise to alternatively spliced YAP1 transcripts in different metazoans. We found that YAP1 isoforms, which utilize exon 6 emerged in evolution with the appearance of amniotes. Interestingly, 6 YAP1 isoforms, which contain the exon 5 extension, exon 6 or both would have their leucine zipper region disrupted in the predicted protein product, compared to the intact leucine zipper found in two YAP1 (α) isoforms. This observation has direct functional ramifications for YAP1 signaling. We also propose a normalized nomenclature for the mRNA splice variants of YAP1 gene, which should aid in the characterization of signaling differences among the potential protein products of the YAP1 gene.
doi:10.1016/j.gene.2012.08.025
PMCID: PMC3455135  PMID: 22939869
Alternative splicing; WW domains; Leucine Zipper; Quantitative RT-PCR
7.  The Electronic Medical Records and Genomics (eMERGE) Network: Past, Present and Future 
The Electronic Medical Records and Genomics (eMERGE) Network is a National Human Genome Research Institute (NHGRI)-funded consortium engaged in the development of methods and best-practices for utilizing the Electronic Medical Record (EMR) as a tool for genomic research. Now in its sixth year, its second funding cycle and comprising nine research groups and a coordinating center, the network has played a major role in validating the concept that clinical data derived from EMRs can be used successfully for genomic research. Current work is advancing knowledge in multiple disciplines at the intersection of genomics and healthcare informatics, particularly electronic phenotyping, genome-wide association studies, genomic medicine implementation and the ethical and regulatory issues associated with genomics research and returning results to study participants. Here we describe the evolution, accomplishments, opportunities and challenges of the network since its inception as a five-group consortium focused on genotype-phenotype associations for genomic discovery to its current form as a nine-group consortium pivoting towards implementation of genomic medicine.
doi:10.1038/gim.2013.72
PMCID: PMC3795928  PMID: 23743551
electronic medical records; personalized medicine; genome-wide association studies; genetics and genomics; collaborative research
8.  WT1 marker is not sufficient for distinguishing between melanoma and melanocytic nevi 
Journal of cutaneous pathology  2009;36(10):1077-1082.
Background
The heterogeneous histological features of melanoma may often overlap with melanocytic nevi. For this reason, pathologists have sought after immunohistochemistry to assist with difficult cases. Recently, Wilms’ tumor 1 protein (WT1) has been suggested to differentiate between melanoma and melanocytic nevi.
Objective
Our objective was to determine whether immunohistochemistry analysis of WT1 expression is a reliable tool in differentiating cutaneous melanoma from melanocytic nevi.
Methods
Forty-five melanoma and 43 melanocytic nevi were immunostained with anti-WT1 monoclonal antibody (clone 6F-H2).
Results
Forty of the 45 cutaneous melanoma (89%) and 22 of the 43 melanocytic nevi (51%) stained (> 10% cells) for WT1. The highest sensitivity for WT1 was expressed by nodular melanoma (19/20), superficial spreading melanoma (8/10) and Spitz nevi (9/11). At the threshold of above 75% WT1-stained cells, the specificity for melanoma was 95% but the sensitivity was only 31%. At the threshold of 10%, the sensitivity increased to 89% but the specificity decreased to only 49%. Finally, at the threshold of 25% and 50%, the sensitivity and specificity were 71%, 61% and 64%, 77%, respectively.
Conclusions
Our data suggest that melanoma is associated with increased WT1 expression. However, as a single immunostaining marker, WT1 is not sufficient for distinguishing melanoma from melanocytic nevi.
doi:10.1111/j.1600-0560.2009.01224.x
PMCID: PMC3776411  PMID: 19615003
9.  Role of Complement Cascade in Abdominal Aortic Aneurysms 
Objective
The goal of this study was to investigate the role of complement cascade genes in the pathobiology of human abdominal aortic aneurysms (AAAs).
Methods and Results
Results of a genome-wide microarray expression profiling revealed 3,274 differentially expressed genes between aneurysmal and control aortic tissue. Interestingly, 13 genes in the complement cascade were significantly differentially expressed between AAA and the controls. In silico analysis of the promoters of the 13 complement cascade genes showed enrichment for transcription factor binding sites for STAT5A. Chromatin-immunoprecipitation experiments demonstrated binding of transcription factor STAT5A to the promoters of the majority of the complement cascade genes. Immunohistochemical analysis showed strong staining for C2 in AAA tissues.
Conclusions
These results provide strong evidence that the complement cascade plays a role in human AAA. Based on our microarray studies, the pathway is activated in AAA, particularly via the lectin and classical pathways. The overrepresented binding sites of transcription factor STAT5A in the complement cascade gene promoters suggest a role for STAT5A in the coordinated regulation of complement cascade gene expression.
doi:10.1161/ATVBAHA.111.227652
PMCID: PMC3712630  PMID: 21493888
Abdominal aortic aneurysm; complement cascade; genetic association study; STAT5; chromatin immunoprecipitation
10.  Identification of Fetal and Maternal Single Nucleotide Polymorphisms in Candidate Genes That Predispose to Spontaneous Preterm Labor with Intact Membranes 
Objective
To determine whether maternal/fetal SNPs in candidate genes are associated with spontaneous preterm labor/delivery.
Study Design
A genetic association study was conducted in 223 mothers and 179 fetuses [preterm labor with intact membranes who delivered <37 weeks (PTB)], and 599 mothers and 628 fetuses (normal pregnancy): 190 candidate genes and 775 SNPs were studied. Single locus/haplotype association analyses were performed; FDR was used to correct for multiple testing (q*=0.15)].
Results
1) The strongest single locus associations with PTB were IL6R (fetus: p=0.000148) and TIMP2 (mother: p=0.000197), remaining significant after correction for multiple comparisons; 2) Global haplotype analysis indicated an association between a fetal DNA variant in IGF2 and maternal COL4A3 (global p=0.004 and 0.007, respectively).
Conclusion
A SNP involved in controlling fetal inflammation (IL6R) and DNA variants in maternal genes encoding for proteins involved in extracellular matrix biology approximately doubled the risk of PTB.
doi:10.1016/j.ajog.2010.03.026
PMCID: PMC3604889  PMID: 20452482
Chorioamnionitis; DNA variants; extracellular matrix; genetic association study; genomics; genotype; haplotype; high dimensional biology; IL-6; parturition; prematurity; SNP
11.  MicroRNA expression signature in human abdominal aortic aneurysms 
BMC Medical Genomics  2012;5:25.
Background
Abdominal aortic aneurysm (AAA) is a dilatation of the aorta affecting most frequently elderly men. Histologically AAAs are characterized by inflammation, vascular smooth muscle cell apoptosis, and extracellular matrix degradation. The mechanisms of AAA formation, progression, and rupture are currently poorly understood. A previous mRNA expression study revealed a large number of differentially expressed genes between AAA and non-aneurysmal control aortas. MicroRNAs (miRNAs), small non-coding RNAs that are post-transcriptional regulators of gene expression, could provide a mechanism for the differential expression of genes in AAA.
Methods
To determine differences in miRNA levels between AAA (n = 5) and control (n = 5) infrarenal aortic tissues, a microarray study was carried out. Results were adjusted using Benjamini-Hochberg correction (adjusted p < 0.05). Real-time quantitative RT-PCR (qRT-PCR) assays with an independent set of 36 AAA and seven control tissues were used for validation. Potential gene targets were retrieved from miRNA target prediction databases Pictar, TargetScan, and MiRTarget2. Networks from the target gene set were generated and examined using the network analysis programs, CytoScape® and Ingenuity Pathway Core Analysis®.
Results
A microarray study identified eight miRNAs with significantly different expression levels between AAA and controls (adjusted p < 0.05). Real-time qRT-PCR assays validated the findings for five of the eight miRNAs. A total of 222 predicted miRNA target genes known to be differentially expressed in AAA based on a prior mRNA microarray study were identified. Bioinformatic analyses revealed that several target genes are involved in apoptosis and activation of T cells.
Conclusions
Our genome-wide approach revealed several differentially expressed miRNAs in human AAA tissue suggesting that miRNAs play a role in AAA pathogenesis.
doi:10.1186/1755-8794-5-25
PMCID: PMC3507654  PMID: 22704053
Apoptosis; Microarray analysis; Vascular biology; miRNA-mRNA analysis; Network analysis
12.  Genes and Abdominal Aortic Aneurysm 
Annals of vascular surgery  2010;25(3):388-412.
Abdominal aortic aneurysm (AAA) is a multifactorial disease with a strong genetic component. Since first candidate gene studies were published 20 years ago, nearly 100 genetic association studies using single nucleotide polymorphisms (SNPs) in biologically relevant genes have been reported on AAA. The studies investigated SNPs in genes of the extracellular matrix, the cardiovascular system, the immune system, and signaling pathways. Very few studies were large enough to draw firm conclusions and very few results could be replicated in another sample set. The more recent unbiased approaches are family-based DNA linkage studies and genome-wide genetic association studies, which have the potential of identifying the genetic basis for AAA, if appropriately powered and well-characterized large AAA cohorts are used. SNPs associated with AAA have already been identified in these large multicenter studies. One significant association was of a variant in a gene called CNTN3 which is located on chromosome 3p12.3. Two follow-up studies, however, could not replicate the association. Two other SNPs, which are located on chromosome 9p21 and 9q33 were replicated in other samples. The two genes with the strongest supporting evidence of contribution to the genetic risk for AAA are the CDKN2BAS gene, also known as ANRIL, which encodes an antisense RNA that regulates expression of the cyclin-dependent kinase inhibitors CDKN2A and CDKN2B, and DAB2IP, which encodes an inhibitor of cell growth and survival. Functional studies are now needed to establish the mechanisms by which these genes contribute to AAA pathogenesis.
doi:10.1016/j.avsg.2010.09.004
PMCID: PMC3058859  PMID: 21146954
13.  A genetic association study of maternal and fetal candidate genes that predispose to preterm prelabor rupture of membranes (PROM) 
American journal of obstetrics and gynecology  2010;203(4):361.e1-361.e30.
Objective
To determine whether maternal/fetal SNPs in candidate genes are associated with preterm prelabor rupture of membranes (pPROM).
Study Design
A case-control study was conducted in patients with pPROM (225 mothers and 155 fetuses) and 599 mothers and 628 fetuses with a normal pregnancy; 190 candidate genes and 775 SNPs were studied. Single locus/haplotype association analyses were performed; FDR was used to correct for multiple testing (q*=0.15)].
Results
1) A SNP in TIMP2 in mothers was significantly associated with pPROM(OR=2.12 95% CI [1.47-3.07], p = 0.000068), and this association remained significant after correction for multiple comparisons; 2) Haplotypes for COL4A3 in the mother were associated with pPROM (global p = 0.003); 3) Multilocus analysis identified a three locus model, which included maternal SNPs in COL1A2, DEFA5, and EDN1.
Conclusion
DNA variants in a maternal gene involved in extracellular matrix metabolism doubled the risk of pPROM.
doi:10.1016/j.ajog.2010.05.026
PMCID: PMC2989662  PMID: 20673868
Chorioamnionitis; DNA variants; extracellular matrix; genetic association study; genomics; genotype; haplotype; high dimensional biology; MMP; parturition; pPROM; prematurity; SNP
14.  Polymorphisms in Maternal and Fetal Genes Encoding for Proteins Involved in Extracellular Matrix Metabolism Alter the Risk for Small-for-Gestational-Age 
OBJECTIVE
To examine the association between maternal and fetal genetic variants and small-for-gestational-age (SGA).
METHODS
A case-control study was conducted in patients with SGA neonates (530 maternal and 436 fetal) and controls (599 maternal and 628 fetal); 190 candidate genes and 775 SNPs were studied. Single locus, multilocus and haplotype association analyses were performed on maternal and fetal data with logistic regression, multifactor dimensionality reduction (MDR) analysis, and haplotype-based association with 2 and 3 marker sliding windows, respectively. Ingenuity Pathway Analysis (IPA) software was used to assess pathways that associate with SGA.
RESULTS
The most significant single locus association in maternal data was with a SNP in tissue inhibitor of metalloproteinase 2 (TIMP2) (rs2277698 OR = 1.71 95% CI [1.26-2.32], p = 0.0006) while in the fetus it was with a SNP in fibronectin 1 isoform 3 preproprotein (FN1) (rs3796123, OR = 1.46 95% CI [1.20-1.78], p = 0.0001). Both SNPs were adjusted for potential confounders (maternal body mass index and fetal sex). Haplotype analyses resulted in associations in alpha 1 type I collagen preproprotein (COL1A1, rs1007086-rs2141279-rs17639446, global p = 0.006) in mothers and FN1 (rs2304573-rs1250204-rs1250215, global p = 0.045) in fetuses. Multilocus analyses with MDR identified a two SNP model with maternal variants collagen type V alpha 2 (COL5A2) and plasminogen activator urokinase (PLAU) predicting SGA outcome correctly 59% of the time (p = 0.035).
CONCLUSIONS
Genetic variants in extracellular matrix related genes showed significant single locus association with SGA. These data are consistent with other studies that have observed elevated circulating fibronectin concentrations in association with increased risk of SGA. The present study supports the hypothesis that DNA variants can partially explain risk of SGA in a cohort of Hispanic women.
doi:10.3109/14767058.2010.497572
PMCID: PMC3104673  PMID: 20617897
DNA variants; extracellular matrix; genetic association study; genomics; genotype; haplotype; high dimensional biology; SNP; intrauterine growth restriction; genetic epidemiology; complex disease
15.  Regional expression of HOXA4 along the aorta and its potential role in human abdominal aortic aneurysms 
BMC Physiology  2011;11:9.
Background
The infrarenal abdominal aorta exhibits increased disease susceptibility relative to other aortic regions. Allograft studies exchanging thoracic and abdominal segments showed that regional susceptibility is maintained regardless of location, suggesting substantial roles for embryological origin, tissue composition and site-specific gene expression.
Results
We analyzed gene expression with microarrays in baboon aortas, and found that members of the HOX gene family exhibited spatial expression differences. HOXA4 was chosen for further study, since it had decreased expression in the abdominal compared to the thoracic aorta. Western blot analysis from 24 human aortas demonstrated significantly higher HOXA4 protein levels in thoracic compared to abdominal tissues (P < 0.001). Immunohistochemical staining for HOXA4 showed nuclear and perinuclear staining in endothelial and smooth muscle cells in aorta. The HOXA4 transcript levels were significantly decreased in human abdominal aortic aneurysms (AAAs) compared to age-matched non-aneurysmal controls (P < 0.00004). Cultured human aortic endothelial and smooth muscle cells stimulated with INF-γ (an important inflammatory cytokine in AAA pathogenesis) showed decreased levels of HOXA4 protein (P < 0.0007).
Conclusions
Our results demonstrated spatial variation in expression of HOXA4 in human aortas that persisted into adulthood and that downregulation of HOXA4 expression was associated with AAAs, an important aortic disease of the ageing population.
doi:10.1186/1472-6793-11-9
PMCID: PMC3125234  PMID: 21627813
16.  Binding Sites for Ets Family of Transcription Factors Dominate the Promoter Regions of Differentially Expressed Genes in Abdominal Aortic Aneurysms 
Background
Previously, we identified 3,274 distinct differentially expressed genes in abdominal aortic aneurysm (AAA) tissue compared to non-aneurysmal controls. As transcriptional control is responsible for these expression changes, we sought to find common transcriptional elements in the promoter regions of the differentially expressed genes.
Methods and Results
We analyzed the up- and downregulated gene sets with Whole Genome rVISTA to determine the transcription factor binding sites (TFBSs) overrepresented in the 5 kb promoter regions of the 3,274 genes. The downregulated gene set yielded 144 TFBSs that were overrepresented in the subset when compared to the entire genome. In contrast, the upregulated gene set yielded only 13 distinct overrepresented TFBSs. Interestingly, as classified by TRANSFAC®, 8 of the 13 transcription factors (TFs) binding to these regions belong to the ETS family. Additionally, NFKB and its subunits p50 and p65 showed enrichment. Immunohistochemical analyses in 10 of the TFs from the upregulated analysis showed 9 to be present in AAA tissue. Based on Gene Ontology analysis of biological process categories of the upregulated target genes of enriched TFs, 10 TFs had enrichment in immune system process among their target genes.
Conclusions
Our genome-wide analysis provides further evidence of ETS and NFKB involvement in AAA. Additionally, our results provide novel insight for future studies aiming to dissect the pathogenesis of AAA and have uncovered potential therapeutic targets for AAA prevention.
doi:10.1161/CIRCGENETICS.108.843854
PMCID: PMC3089770  PMID: 20031636
Aneurysm; Aorta; Genomics; Transcription Factors
17.  Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19 
BMC Medical Genetics  2011;12:14.
Background
Abdominal aortic aneurysm (AAA) is a complex disorder with multiple genetic risk factors. Using affected relative pair linkage analysis, we previously identified an AAA susceptibility locus on chromosome 19q13. This locus has been designated as the AAA1 susceptibility locus in the Online Mendelian Inheritance in Man (OMIM) database.
Methods
Nine candidate genes were selected from the AAA1 locus based on their function, as well as mRNA expression levels in the aorta. A sample of 394 cases and 419 controls was genotyped for 41 SNPs located in or around the selected nine candidate genes using the Illumina GoldenGate platform. Single marker and haplotype analyses were performed. Three genes (CEBPG, PEPD and CD22) were selected for DNA sequencing based on the association study results, and exonic regions were analyzed. Immunohistochemical staining of aortic tissue sections from AAA and control individuals was carried out for the CD22 and PEPD proteins with specific antibodies.
Results
Several SNPs were nominally associated with AAA (p < 0.05). The SNPs with most significant p-values were located near the CCAAT enhancer binding protein (CEBPG), peptidase D (PEPD), and CD22. Haplotype analysis found a nominally associated 5-SNP haplotype in the CEBPG/PEPD locus, as well as a nominally associated 2-SNP haplotype in the CD22 locus. DNA sequencing of the coding regions revealed no variation in CEBPG. Seven sequence variants were identified in PEPD, including three not present in the NCBI SNP (dbSNP) database. Sequencing of all 14 exons of CD22 identified 20 sequence variants, five of which were in the coding region and six were in the 3'-untranslated region. Five variants were not present in dbSNP. Immunohistochemical staining for CD22 revealed protein expression in lymphocytes present in the aneurysmal aortic wall only and no detectable expression in control aorta. PEPD protein was expressed in fibroblasts and myofibroblasts in the media-adventitia border in both aneurysmal and non-aneurysmal tissue samples.
Conclusions
Association testing of the functional positional candidate genes on the AAA1 locus on chromosome 19q13 demonstrated nominal association in three genes. PEPD and CD22 were considered the most promising candidate genes for altering AAA risk, based on gene function, association evidence, gene expression, and protein expression.
doi:10.1186/1471-2350-12-14
PMCID: PMC3037298  PMID: 21247474
18.  Mitochondrial MnSOD mRNA expression in human chorioamniotic membranes and its association with labor, inflammation and infection 
Objective
Human parturition is characterized by the activation of genes involved in acute inflammatory in the fetal membranes. Manganese superoxide dismutase (MnSOD) is a mitochondrial enzyme that scavenges reactive oxygen species (ROS). MnSOD is up-regulated in sites of inflammation and has an important role in the down-regulation of acute inflammatory processes. Therefore, the aim of this study was to determine the differences in MnSOD mRNA expression in the fetal membranes in patients with term and preterm labor as well as in acute chorioamnionitis.
Study design
Fetal membranes were obtained from patients in the following groups: 1) term not in labor (n=29); 2) term in labor (n=29); 3) spontaneous preterm labor with intact mebranes (n=16); 4) PTL with histological chorioamnionitis (n=12); 5) preterm prelabor rupture of membranes (PPROM; n=17); and 6) PPROM with histological chorioamnionitis (n=21). MnSOD mRNA expression in the membranes was determined by quantitative real-time RT-PCR.
Results
1) MnSOD mRNA expression was higher in the fetal membranes of patients at term in labor than those not in labor (2.4-fold; p=0.02); 2) the amount of MnSOD mRNA in the fetal membranes was higher in PTL than in term labor or in PPROM (7.2-fold, p=0.03; 3.2-fold, p=0.03, respectively); 3) MnSOD mRNA expression was higher when histological chorioamnionitis was present both among patients with PPROM (3.8-fold, p=0.02) and with PTL (5.4-fold, p=0.02) than in patients with these conditions without histological chorioamnionitis; 4) expression of MnSOD mRNA was higher in PTL with chorioamnionitis than in PPROM with chorioamnionitis (4.3-fold, p=0.03);
Conclusion
The increase in MnSOD mRNA expression by fetal membranes in term labor and in histological chorioamnionitis in PTL and PPROM suggests that the fetus deploys anti-oxidant mechanisms to constrain the inflammatory processes in the chorioamniotic membranes.
doi:10.3109/14767050903019676
PMCID: PMC2823267  PMID: 19900038
fetal gender; gene expression; preterm delivery; preterm labor; preterm prelabor rupture of the membranes; reactive oxygen species; scavenger
19.  Diagnostic Markers of Ovarian Cancer by High-Throughput Antigen Cloning and Detection on Arrays 
Cancer research  2006;66(2):1181-1190.
A noninvasive screening test would significantly facilitate early detection of epithelial ovarian cancer. This study used a combination of high-throughput selection and array-based serologic detection of many antigens indicative of the presence of cancer, thereby using the immune system as a biosensor. This high-throughput selection involved biopanning of an ovarian cancer phage display library using serum immunoglobulins from an ovarian cancer patient as bait. Protein macroarrays containing 480 of these selected antigen clones revealed 65 clones that interacted with immunoglobulins in sera from 32 ovarian cancer patients but not with sera from 25 healthy women or 14 patients having other benign or malignant gynecologic diseases. Sequence analysis data of these 65 clones revealed 62 different antigens. Among the markers, we identified some known antigens, including RCAS1, signal recognition protein-19, AHNAK-related sequence, nuclear autoantogenic sperm protein, Nijmegen breakage syndrome 1 (Nibrin), ribosomal protein L4, Homo sapiens KIAA0419 gene product, eukaryotic initiation factor 5A, and casein kinase II, as well as many previously uncharacterized antigenic gene products. Using these 65 antigens on protein microarrays, we trained neural networks on two-color fluorescent detection of serum IgG binding and found an average sensitivity and specificity of 55% and 98%, respectively. In addition, the top 6 of the most specific clones resulted in an average sensitivity and specificity of 32% and 94%, respectively. This global approach to antigenic profiling, epitomics, has applications to cancer and autoimmune diseases for diagnostic and therapeutic studies. Further work with larger panels of antigens should provide a comprehensive set of markers with sufficient sensitivity and specificity suitable for clinical testing in high-risk populations.
doi:10.1158/0008-5472.CAN-04-2962
PMCID: PMC2546578  PMID: 16424057
20.  Analytical approaches to detect maternal/fetal genotype incompatibilities that increase risk of pre-eclampsia 
BMC Medical Genetics  2008;9:60.
Background
In utero interactions between incompatible maternal and fetal genotypes are a potential mechanism for the onset or progression of pregnancy related diseases such as pre-eclampsia (PE). However, the optimal analytical approach and study design for evaluating incompatible maternal/offspring genotype combinations is unclear.
Methods
Using simulation, we estimated the type I error and power of incompatible maternal/offspring genotype models for two analytical approaches: logistic regression used with case-control mother/offspring pairs and the log-linear regression used with case-parent triads. We evaluated a real dataset consisting of maternal/offspring pairs with and without PE for incompatibility effects using the optimal analysis based on the results of the simulation study.
Results
We identified a single coding scheme for the incompatibility effect that was equally or more powerful than all of the alternative analysis models evaluated, regardless of the true underlying model for the incompatibility effect. In addition, the log-linear regression was more powerful than the logistic regression when the heritability was low, and more robust to adjustment for maternal or fetal effects. For the PE data, this analysis revealed three genes, lymphotoxin alpha (LTA), von Willebrand factor (VWF), and alpha 2 chain of type IV collagen (COL4A2) with possible incompatibility effects.
Conclusion
The incompatibility model should be evaluated for complications of pregnancy, such as PE, where the genotypes of two individuals may contribute to the presence of disease.
doi:10.1186/1471-2350-9-60
PMCID: PMC2474585  PMID: 18598365
21.  Human spontaneous labor without histologic chorioamnionitis is characterized by an acute inflammation gene expression signature 
OBJECTIVE
The purpose of this study was to identify which biological processes may be involved in normal labor.
STUDY DESIGN
Transcriptional profiles for chorioamniotic membranes (n=24) and blood (n=20) were generated from patients at term with no labor (TNL) and in labor (TIL).
RESULTS
Expression of 197 transcripts (P≤0.02) differentiated TIL and TNL chorioamniotic membrane samples. Gene Ontology analysis indicated that TIL samples had increased expression of multiple chemokines and transcripts associated with neutrophil and monocyte recruitment. Microarray results were verified using quantitative real-time RT-PCR with independent samples. Transcriptional profiles from blood RNA revealed no Gene Ontology category enrichment of discriminant probe sets.
CONCLUSION
Labor induces gene expression changes consistent with localized inflammation, despite the absence of histologically detectable inflammation.
doi:10.1016/j.ajog.2005.08.057
PMCID: PMC1800883  PMID: 16890549
chorioamniotic membrane; blood, transcriptional profile; microarray; acute inflammation; parturition; chorioamnionitis; chemokines; cytokines
22.  The life-time prevalence of abdominal aortic aneurysms among siblings of aneurysm patients is eight-fold higher than among siblings of spouses; an analysis of 187 aneurysm families in Nova Scotia, Canada 
Background
Abdominal aortic aneurysms (AAAs) are frequently familial. The aim of this study was to compare the prevalence of AAA among the siblings of AAA patients to that in the spouses’ siblings.
Methods
The siblings of 375 AAA patients and the siblings of the spouses of the AAA patients were included in this study and offered ultrasonography screening for AAA. Participants were asked to complete a questionnaire to collect demographic and general health information. Statistical analysis was carried out using Fisher’s exact test. Odds ratios and 95% confidence intervals were also calculated.
Results
Abdominal ultrasonography examination was carried out for 309 individuals. The results indicated that 11 of 98 (11.2%) brothers of AAA patients, 4 of 147 (2.7%) sisters, and none of the 64 siblings of the spouses of the AAA patients were found to have an AAA. Combining the information from the ultrasonography screening and medical records on already known cases of AAA in these families, altogether 29.0% (44/152) of the brothers of AAA patients, 11.1% (20/181) of the sisters of AAA patients, and 2.3% (2/88) of the siblings of the spouses had an AAA.
Conclusion
There was a significant difference between the siblings of the AAA patients and those of the spouses both in the frequency of AAA detected by ultrasonography screening and in the overall prevalence of AAA. The overall prevalence of AAA in the siblings of AAA patients was about 8 times that observed among the siblings of their spouses (19.2% vs. 2.3%). These findings confirmed previous reports on high prevalence of AAA among siblings of AAA patients and emphasized the importance of an ultrasonography screening program for siblings of AAA patients.
doi:10.1016/j.jvs.2005.08.002
PMCID: PMC1373672  PMID: 16275443
23.  EXPRESSION OF BONE MORPHOGENETIC PROTEIN 2 IN NORMAL SPONTANEOUS LABOR AT TERM, PRETERM LABOR AND PRETERM PROM 
American journal of obstetrics and gynecology  2005;193(3 Pt 2):1137-1143.
OBJECTIVE
Genome-wide screening studies of the chorioamniotic membranes have unexpectedly identified an increase in the expression of bone morphogenetic protein 2 (BMP2) in spontaneous labor at term. The objective of this study was to determine whether BMP2 mRNA and protein expression are altered in the chorioamniotic membranes of patients with term labor, preterm labor, and preterm premature rupture of membranes (PPROM).
STUDY DESIGN
Chorioamniotic membranes were obtained from patients at term (with and without labor), with preterm labor (with and without histologic chorioamnionitis), and with PPROM (with and without histologic chorioamnionitis). The expression of BMP2 was studied by real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR; n=88) and immunohistochemistry (IHC; n=124). Non-parametric statistics were used for analysis. Primary amnion cells obtained from women at term not in labor were treated with BMP2 to examine whether there was increased prostaglandin E2 expression.
RESULTS
1) The median BMP2 mRNA and protein expression were significantly higher in the membranes of patients with spontaneous labor at term than in those of patients not in labor at term (P < 0.001 for both). 2) BMP2 mRNA and protein expression were increased in patients with preterm labor with histologic chorioamnionitis than in those without histologic chorioamnionitis (P < 0.05 and P < 0.001, respectively). 3) There was no difference in BMP2 mRNA and protein expression in patients with PPROM, regardless of chorioamnionitis (P = 0.13 and P = 0.08). 4) There was a correlation between BMP2 and cyclooxygenase 2 protein expression in chorioamniotic membranes (R = 0.34; P < 0.001).
CONCLUSION
BMP2 mRNA and protein expression are increased in the chorioamniotic membranes of patients with spontaneous labor at term and patients with preterm labor associated with histologic chorioamnionitis. Its expression pattern and biologic effects strongly suggest that BMP2 is involved in human parturition.
doi:10.1016/j.ajog.2005.06.032
PMCID: PMC1351231  PMID: 16157126
parturition; chorioamniotic membrane; immunohistochemistry; real-time quantitative reverse-transcriptase PCR; BMP-2; Preterm labor; Preterm premature rupture of membranes; PPROM
24.  Genetic analysis of polymorphisms in biologically relevant candidate genes in patients with abdominal aortic aneurysms 
Background
Abdominal aortic aneurysms (AAAs) are characterized by histologic signs of chronic inflammation, destructive remodeling of extracellular matrix, and depletion of vascular smooth muscle cells. We investigated the process of extracellular matrix remodeling by performing a genetic association study with polymorphisms in the genes for matrix metalloproteinases (MMPs), tissue inhibitors of metalloproteinases (TIMPs), and structural extracellular matrix molecules in AAA. Our hypothesis was that genetic variations in one or more of these genes contribute to greater or lesser activity of these gene products, and thereby contribute to susceptibility for developing AAAs.
Methods
DNA samples from 812 unrelated white subject (AAA, n = 387; controls, n = 425) were genotyped for 14 polymorphisms in 13 different candidate genes: MMP1(nt−1607), MMP2(nt−955), MMP3(nt−1612), MMP9(nt−1562), MMP10(nt+180), MMP12(nt−82), MMP13(nt−77), TIMP1(nt+434), TIMP1(rs2070584), TIMP2(rs2009196), TIMP3(nt−1296), TGFB1(nt−509), ELN(nt+422), and COL3A1(nt+581). Odds ratios and P values adjusted for gender and country of origin using logistic regression and stratified by family history of AAA were calculated to test for association between genotype and disease status. Haplotype analysis was carried out for the two TIMP1 polymorphisms in male subjects.
Results
Analyses with one polymorphism per test without interactions showed an association with the two TIMP1 gene polymorphisms (nt+434, P = .0047; rs2070584, P = .015) in male subjects without a family history of AAA. The association remained significant when analyzing TIMP1 haplotypes (χ2 P = .014 and empirical P = .009). In addition, we found a significant interaction between the polymorphism and gender for MMP10 (P = .037) in cases without a family history of AAA, as well as between the polymorphism and country of origin for ELN (P = .0169) and TIMP3 (P = .0023) in cases with a family history of AAA.
Conclusions
These findings suggest that genetic variations in TIMP1, TIMP3, MMP10, and ELN genes may contribute to the pathogenesis of AAAs. Further work is needed to confirm the findings in an independent set of samples and to study the functional role of these variants in AAA. It is noteworthy that contrary to a previous study, we did not find an association between the MMP9 (nt−1562) polymorphism and AAA, suggesting genetic heterogeneity of the disease.
Clinical Relevance
Abdominal aortic aneurysms (AAAs) are an important cardiovascular disease, but the genetic and environmental risk factors, which contribute to individual’s risk to develop an aneurysm, are poorly understood. Histologically, AAAs are characterized by signs of chronic inflammation, destructive remodeling of the extracellular matrix, and depletion of vascular smooth muscle cells. We hypothesized that genes involved in these events could harbor changes that make individuals more susceptible to developing aneurysms. This study identified significant genetic associations between DNA sequence changes in tissue inhibitor of metalloproteinase 1 (TIMP1), TIMP3, matrix metalloproteinase 10 (MMP10) and elastin (ELN) genes, and AAA. The results will require confirmation using an independent set of samples. After replication it is possible that these sequence changes in combination with other risk factors could be used in the future to identify individuals who are at increased risk for developing an AAA.
doi:10.1016/j.jvs.2005.02.020
PMCID: PMC1249499  PMID: 15944607
25.  Whole genome expression profiling reveals a significant role for immune function in human abdominal aortic aneurysms 
BMC Genomics  2007;8:237.
Background
Abdominal aortic aneurysms are a common disorder with an incompletely understood etiology. We used Illumina and Affymetrix microarray platforms to generate global gene expression profiles for both aneurysmal (AAA) and non-aneurysmal abdominal aorta, and identified genes that were significantly differentially expressed between cases and controls.
Results
Affymetrix and Illumina arrays included 18,057 genes in common; 11,542 (64%) of these genes were considered to be expressed in either aneurysmal or normal abdominal aorta. There were 3,274 differentially expressed genes with a false discovery rate (FDR) ≤ 0.05. Many of these genes were not previously known to be involved in AAA, including SOST and RUNX3, which were confirmed using Q-RT-PCR (Pearson correlation coefficient for microarray and Q-RT-PCR data = 0.89; p-values for differences in expression between AAA and controls for SOST: 4.87 × 10-4 and for RUNX3: 4.33 × 10-5). Analysis of biological pathways, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), indicated extreme overrepresentation of immune related categories. The enriched categories included the GO category Immune Response (GO:0006955; FDR = 2.1 × 10-14), and the KEGG pathways natural killer cell mediated cytotoxicity (hsa04650; FDR = 5.9 × 10-6) and leukocyte transendothelial migration (hsa04670; FDR = 1.1 × 10-5).
Conclusion
Previous studies have provided evidence for the involvement of the immune system in AAA. The current expression analysis extends these findings by demonstrating broad coordinate gene expression in immunological pathways. A large number of genes involved in immune function were differentially expressed in AAA, and the pathway analysis gave these results a biological context. The data provide valuable insight for future studies to dissect the pathogenesis of human AAA. These pathways might also be used as targets for the development of therapeutic agents for AAA.
doi:10.1186/1471-2164-8-237
PMCID: PMC1934369  PMID: 17634102

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