PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (26)
 

Clipboard (0)
None

Select a Filter Below

Journals
more »
Year of Publication
1.  N-n-butyl haloperidol iodide inhibits H2O2-induced Na+/Ca2+-exchanger activation via the Na+/H+ exchanger in rat ventricular myocytes 
N-n-butyl haloperidol iodide (F2), a novel compound, has shown palliative effects in myocardial ischemia/reperfusion (I/R) injury. In this study, we investigated the effects of F2 on the extracellular signal-regulated kinase kinase (MEK)/extracellular signal-regulated kinase (ERK)/Na+/H+ exchanger (NHE)/Na+/Ca2+ exchanger (NCX) signal-transduction pathway involved in H2O2-induced Ca2+ overload, in order to probe the underlying molecular mechanism by which F2 antagonizes myocardial I/R injury. Acute exposure of rat cardiac myocytes to 100 μM H2O2 increased both NHE and NCX activities, as well as levels of phosphorylated MEK and ERK. The H2O2-induced increase in NCX current (INCX) was nearly completely inhibited by the MEK inhibitor U0126 (1,4-diamino-2,3-dicyano-1,4-bis[o-aminophenylmercapto] butadiene), but only partly by the NHE inhibitor 5-(N,N-dimethyl)-amiloride (DMA), indicating the INCX increase was primarily mediated by the MEK/mitogen-activated protein kinase (MAPK) pathway, and partially through activation of NHE. F2 attenuated the H2O2-induced INCX increase in a concentration-dependent manner. To determine whether pathway inhibition was H2O2-specific, we examined the ability of F2 to inhibit MEK/ERK activation by epidermal growth factor (EGF), and NHE activation by angiotensin II. F2 not only inhibited H2O2-induced and EGF-induced MEK/ERK activation, but also completely blocked both H2O2-induced and angiotensin II-induced increases in NHE activity, suggesting that F2 directly inhibits MEK/ERK and NHE activation. These results show that F2 exerts multiple inhibitions on the signal-transduction pathway involved in H2O2-induced INCX increase, providing an additional mechanism for F2 alleviating intracellular Ca2+ overload to protect against myocardial I/R injury.
doi:10.2147/DDDT.S63163
PMCID: PMC4166912  PMID: 25246767
N-n-butyl haloperidol; hydrogen peroxide; Na+/Ca2+ exchanger; Na+/H+ exchanger
2.  Enhanced Performance by Time-Frequency-Phase Feature for EEG-Based BCI Systems 
The Scientific World Journal  2014;2014:420561.
We introduce a new motor parameter imagery paradigm using clench speed and clench force motor imagery. The time-frequency-phase features are extracted from mu rhythm and beta rhythms, and the features are optimized using three process methods: no-scaled feature using “MIFS” feature selection criterion, scaled feature using “MIFS” feature selection criterion, and scaled feature using “mRMR” feature selection criterion. Support vector machines (SVMs) and extreme learning machines (ELMs) are compared for classification between clench speed and clench force motor imagery using the optimized feature. Our results show that no significant difference in the classification rate between SVMs and ELMs is found. The scaled feature combinations can get higher classification accuracy than the no-scaled feature combinations at significant level of 0.01, and the “mRMR” feature selection criterion can get higher classification rate than the “MIFS” feature selection criterion at significant level of 0.01. The time-frequency-phase feature can improve the classification rate by about 20% more than the time-frequency feature, and the best classification rate between clench speed motor imagery and clench force motor imagery is 92%. In conclusion, the motor parameter imagery paradigm has the potential to increase the direct control commands for BCI control and the time-frequency-phase feature has the ability to improve BCI classification accuracy.
doi:10.1155/2014/420561
PMCID: PMC4087262  PMID: 25045733
3.  Expression of three essential antioxidants of Helicobacter pylori in clinical isolates*  
Objective: Helicobacter pylori maintains long-term persistence in the host and combats oxidative stress via many antioxidant proteins, which are expected to be relevant to bacterial-associated gastric diseases. We aimed to investigate the expression of three essential antioxidants in H. pylori strains isolated from patients with different clinical outcomes. Methods: Forty H. pylori strains were isolated from endoscopic biopsy specimens of gastric mucosa from 13 patients with gastric cancer, 13 with peptic ulcer, and 14 with gastritis. The expression of thioredoxin 1 (Trx1), arginase (RocF), and alkyl hydroperoxide reductase (AhpC) in H. pylori was measured by real-time PCR. Comparisons among multiple sample sets were analyzed using a one-way ANOVA test. Pearson’s correlation test was used to assess relationships among multiple continuous variables. Results: Trx1 expression of H. pylori in gastric cancer and peptic ulcer tissues was higher than that in tissues with gastritis. RocF expression of H. pylori in gastric cancer tissues was higher than that in tissues exhibiting peptic ulcer and gastritis. However, we did not find any differences in AhpC expression in samples from patients with different clinical outcomes. The expression of Trx1 and RocF had a positive, linear correlation. The expression of Trx1 and AhpC had a positive correlation without a linear trend. We found no correlation between the expression of RocF and AhpC. Conclusions: Our observations indicate that the expression of Trx1 and RocF in H. pylori might be related to gastric carcinogenesis. In H. pylori, the expression of members of the antioxidant system may be correlated and relevant to gastric cancer.
doi:10.1631/jzus.B1300171
PMCID: PMC4076607  PMID: 24793768
Antioxidant; Gastric cancer; Helicobacter pylori; Oxidative stress
4.  Cellular immunotherapy using irradiated lung cancer cell vaccine co-expressing GM-CSF and IL-18 can induce significant antitumor effects 
BMC Cancer  2014;14:48.
Background
Although the whole tumor cell vaccine can provide the best source of immunizing antigens, there is still a limitation that most tumors are not naturally immunogenic. Tumor cells genetically modified to secrete immune activating cytokines have been proved to be more immunogenic. IL-18 could augment proliferation of T cells and cytotoxicity of NK cells. GM-CSF could stimulate dendritic cells, macrophages and enhance presentation of tumor antigens. In our study, we used mouse GM-CSF combined with IL-18 to modify Lewis lung cancer LL/2, then investigated whether vaccination could suppress tumor growth and promote survival.
Methods
The Lewis lung cancer LL/2 was transfected with co-expressing mouse GM-CSF and IL-18 plasmid by cationic liposome, then irradiated with a sublethal dose X ray (100 Gy) to prepare vaccines. Mice were subcutaneously immunized with this inactivated vaccine and then inoculated with autologous LL/2 to estimate the antitumor efficacy.
Results
The studies reported here showed that LL/2 tumor cell vaccine modified by a co-expressing mouse GM-CSF and IL-18 plasmid could significantly inhibit tumor growth and increased survival of the mice bearing LL/2 tumor whether prophylactic or adoptive immunotherapy in vivo. A significant reduction of proliferation and increase of apoptosis were also observed in the tumor treated with vaccine of co-expressing GM-CSF and IL-18. The potent antitumor effect correlated with higher secretion levels of pro-inflammatory cytokines such as IL-18, GM-CSF, interferon-γ in serum, the proliferation of CD4+ IFN-γ+, CD8+ IFN-γ+ T lymphocytes in spleen and the infiltration of CD4+, CD8+ T in tumor. Furthermore, the mechanism of tumor-specific immune response was further proved by 51Cr cytotoxicity assay in vitro and depletion of CD4, CD8, NK immune cell subsets in vivo. The results suggested that the antitumor mechanism was mainly depended on CD4+, CD8+ T lymphocytes.
Conclusions
These results provide a new insight into therapeutic mechanisms of IL-18 plus GM-CSF modified tumor cell vaccine and provide a potential clinical cancer immunotherapeutic agent for improved antitumor immunity.
doi:10.1186/1471-2407-14-48
PMCID: PMC3922726  PMID: 24475975
Cancer immunotherapy; IL-18; GM-CSF; Cell vaccine; Apoptosis
5.  Expression of serum amyloid A in uterine cervical cancer 
Diagnostic Pathology  2014;9:16.
Background
As an acute-phase protein, serum amyloid A (SAA) is expressed primarily in the liver. However, its expression in extrahepatic tissues, especially in tumor tissues, was also demonstrated recently. In our study, we investigated the expression of SAA in uterine cervical carcinomas, and our results suggested its potential as a serum biomarker.
Methods
Quantitative real-time polymerase chain reaction (RT-PCR), immunohistochemistry (IHC) and enzyme-linked immunosorbent assay (ELISA) were used to evaluate the SAA gene and protein expression levels in the tissues and sera of patients with non-neoplastic lesions (NNLs), cervical intraepithelial neoplasia (CIN) and cervical carcinoma (CC).
Results
Compared with NNLs, the SAA gene (SAA1 and SAA4) expression levels were significantly higher in uterine CC (mean copy numbers: 138.7 vs. 5.01, P < 0.000; and 1.8 vs. 0.079, P = 0.001, respectively) by real-time PCR. IHC revealed cytoplasmic SAA protein staining in tissues from adenocarcinoma and squamous cell carcinoma of the cervix. The median serum concentrations (μg/ml) of SAA were 6.02 in patients with NNLs and 10.98 in patients with CIN (P = 0.31). In contrast, the median serum SAA concentration was 23.7 μg/ml in uterine CC patients, which was significantly higher than the SAA concentrations of the NNL group (P = 0.002) and the CIN group (P = 0.024).
Conclusions
Our data suggested that SAA might be a uterine CC cell product. High SAA concentrations in the serum of CC patients may have a role in monitoring disease occurrence and could have therapeutic applications.
Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1433263219102962.
doi:10.1186/1746-1596-9-16
PMCID: PMC3907664  PMID: 24447576
Uterine cervical carcinoma; Serum amyloid A; Tumor marker
6.  Unusual combined thymic mucoepidermoid carcinoma and thymoma: a case report and review of literature 
Background
In rare condition, combined thymic epithelial tumors showing either type A or type B thymomas areas combined with thymic carcinoma components may occur in thymus. Mucoepidermoid carcinoma (MEC) of the thymus is rare in thymic carcinoma, and so far there is no report to describe a combined epithelial tumor of thymus with MEC component. We report an unusual case of combined thymic MEC/type B2 thymoma in a middle-aged male occurring in a mass of anterior mediastinum. Case report: A 51-year-old Chinese male patient presented with a 6-month history of right ptosis and progressive muscle weakness. Computed tomography (CT) examination revealed a solitary, well-circumscribed mass was in the anterior mediastinum with mild heterogeneous enhancement. Histologically, the mass contained two separated components and displayed typically histological features of low-grade MEC and type B2 thymoma, respectively. There was no gradual transition of these two components observed in mass, and no enlarged lymph node was found in the surrounding tissues. A diagnosis of combined thymic MEC/type B2 thymoma was made. The patient received thymectomy to resect the mass totally. After surgery, chemotherapy with regiments of cisplatin and mitomycin, and radiotherapy of the main tumor bed were performed on the patient. There was no evidence of tumor recurrence during the period of 12 months follow-up.
Conclusion
To our best knowledge, this is the first report of combined thymic epithelial tumor with MEC component. Although this tumor is rare, the diagnosis of a thymic MEC should be taken into consideration when a combined epithelial tumor is occasionally encountered in thymus.
Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/9721397571157894
doi:10.1186/1746-1596-9-8
PMCID: PMC3938068  PMID: 24444077
Thymic neoplasm; Combined thymic epithelial tumor; Mucoepidermoid carcinoma; Thymoma; Differential diagnosis
7.  Epistatic effects of ACE I/D and AGT gene variants on left ventricular mass in hypertensive patients: The HyperGEN Study 
Journal of human hypertension  2011;26(2):133-140.
Identifying predictors of left ventricular hypertrophy has been an active study topic because of its association with cardiovascular morbidity and mortality. We examined the epistatic effect (gene-gene interaction) of two genes (ACE I/D; AGT -6G-A, M235T, -20A-C) in the renin-angiotension system (RAS) on left ventricular mass (LVM) among hypertensive participants in the HyperGEN study.
Included were 2156 participants aged 20–87 years (60% women, 63% African American). We employed mixed linear regression models to assess main effects of four genetic variants on echocardigraphically determined LVM (indexed for height), and ACE-by-AGT epistatic effects. There was evidence that AGT -6G-A was associated with LVM among white participants: Adjusted mean LVM (g/m2.7) increased with ‘G’ allele copy number (‘AA’:41.2, ‘AG’:42.3, ‘GG’:44.0; p=0.03). There was also evidence of an ACE I/D-by-AGT -20A-C epistatic effect among white participants (interaction p=0.03): Among ACE ‘DD’ participants, AGT -20A-C ‘C’ allele carriers had lower mean LVM than ‘AA’ homozygotes (‘DD/CC’:39.2, ‘DD/AC’:39.9, ‘DD/AA’:43.9), with no similar significant effect among ACE ‘I’ allele carriers (‘ID/CC’:47.2, ‘ID/AC’:43.4, ‘ID/AA’:42.6; ‘II/CC’: NA, ‘II/AC’:41.3, ‘II/AA’:43.1).
These findings indicate that RAS variants in at least two genes may interact to modulate LVM.
doi:10.1038/jhh.2010.131
PMCID: PMC3775641  PMID: 21248783
Left ventricular mass; left ventricular hypertrophy; ACE gene; AGT gene; epistasis; hypertension
8.  Ovarian masses in children and adolescents in China: analysis of 203 cases 
Objective
The true incidence of ovarian tumors in children is unknown. Few studies beyond case reports and case series have been published concerning pediatric ovarian tumors. Herein we review a large number of ovarian tumor cases.
Methods
The charts of 203 patients who presented with adnexal masses were reviewed.
Results
The patient’s ranged in age from 2 to 18 years (mean = 15.6 years), with 30 being premenarchal (14.8%). The incidence of ovarian tumor increases with age, especially in patients older than 14 years. The main complaint was abdominal pain or abdominal distension in 117 patients (57.7%). A high AFP level in a pre-pubic girl with an adnexal mass is indicative of a malignant ovarian tumor. The 214 adnexal masses (11 patients had bilateral cysts) consisted of benign tumorous oophoropathy (107 masses, 50.0%), borderline and malignant tumors (29 masses, 13.6%), and nontumorous oophoropathy (78 masses, 36.5%). Of the 136 neoplasia, germ cell tumors accounted for 71.5%. Surgical intervention was performed in 98.5% of cases. There were statistically decreased blood loss, surgery duration and days of hospitalization with the laparoscopic procedure when compared with open surgery.
Conclusions
Abdominal pain is the most common complaint in young patients with adnexal masses. AFP is the most useful diagnostic biomarker of ovarian tumors in young females. Laparoscopic resection of ovarian cysts is an alternative operation approach.
doi:10.1186/1757-2215-6-47
PMCID: PMC3729529  PMID: 23826706
Ovarian mass; Pediatric; Germ cell; Epithelial tumor; Laparoscope
9.  Mining Gold Dust under the Genome Wide Significance Level: A Two-Stage Approach to Analysis of GWAS 
Genetic epidemiology  2010;35(2):111-118.
We propose a two-stage approach to analyze genome-wide association (GWA) data in order to identify a set of promising single-nucleotide polymorphisms (SNPs). In stage one, we select a list of top signals from single SNP analyses by controlling false discovery rate (FDR). In stage two, we use the least absolute shrinkage and selection operator (LASSO) regression to reduce false positives. The proposed approach was evaluated using simulated quantitative traits based on genome-wide SNP data on 8,861 Caucasian individuals from the Atherosclerosis Risk in Communities (ARIC) Study. Our first stage, targeted at controlling false negatives, yields better power than using Bonferroni corrected significance level. The LASSO regression reduces the number of significant SNPs in stage two: it reduces false positive SNPs and it reduces true positive SNPs also at simulated causal loci due to linkage disequilibrium. Interestingly, the LASSO regression preserves the power from stage one, i.e., the number of causal loci detected from the LASSO regression in stage two is almost the same as in stage one, while reducing false positives further. Real data on systolic blood pressure in the ARIC study was analyzed using our two-stage approach which identified two significant SNPs, one of which was reported to be genome-significant in a meta-analysis containing a much larger sample size. On the other hand, a single SNP association scan did not yield any significant results.
doi:10.1002/gepi.20556
PMCID: PMC3624896  PMID: 21254218
LASSO; FDR; multi-marker; association; power
10.  Optimization of Hydrogen Peroxide Detection for a Methyl Mercaptan Biosensor 
Sensors (Basel, Switzerland)  2013;13(4):5028-5039.
Several kinds of modified carbon screen printed electrodes (CSPEs) for amperometric detection of hydrogen peroxide (H2O2) are presented in order to propose a methyl mercaptan (MM) biosensor. Unmodified, carbon nanotubes (CNTs), cobalt phthalocyanine (CoPC), Prussian blue (PB), and Os-wired HRP modified CSPE sensors were fabricated and tested to detect H2O2, applying a potential of +0.6 V, +0.6 V, +0.4 V, −0.2 V and −0.1 V (versus Ag/AgCl), respectively. The limits of detection of these electrodes for H2O2 were 3.1 μM, 1.3 μM, 71 nM, 1.3 μM, 13.7 nM, respectively. The results demonstrated that the Os-wired HRP modified CSPEs gives the lowest limit of detection (LOD) for H2O2 at a working potential as low as −0.1 V. Os-wired HRP is the optimum choice for establishment of a MM biosensor and gives a detection limit of 0.5 μM.
doi:10.3390/s130405028
PMCID: PMC3673124  PMID: 23591963
methyl mercaptan; hydrogen peroxide; amperometric sensor; screen printed electrode
11.  Optimum Designs for Next Generation Sequencing to Discover Rare Variants for Common Complex Disease 
Genetic epidemiology  2011;35(6):572-579.
Recent advances in next generation sequencing technologies make it affordable to search for rare and functional variants for common complex diseases systematically. We investigated strategies for enriching rare variants in the samples selected for sequencing so as to optimize the power for their discovery. In particular, we investigated the roles of alternative sources of enrichment in families through computer simulations. We showed that linkage information, extreme phenotype, and non-random ascertainment, such as multiply affected families, constitute different sources for enriching rare and functional variants in a sequencing study design. Linkage is well known to have limited power for detecting small genetic effects, and hence not considered to be a powerful tool for discovering variants for common complex diseases. However, those families with some degree of family-specific linkage evidence provide an effective sampling strategy to sub-select the most linkage-informative families for sequencing. Compared with selecting subjects with extreme phenotypes, linkage evidence performs better with larger families, while extreme-phenotype method is more efficient with smaller families. Families with multiple affected siblings were found to provide the largest enrichment of rare variants. Finally, we showed that combined strategies such as selecting linkage informative families from multiply affected families provides an optimum strategy with much higher enrichment of rare functional variants than either strategy alone.
doi:10.1002/gepi.20597
PMCID: PMC3596871  PMID: 21618604
Next generation sequencing; rare variants; enrichment; study design; complex diseases; linkage
12.  Establishment of a new representative model of human ovarian cancer in mice 
Background
Intraperitoneal (i.p.) models that accurately mimic the feature behavior of human ovarian cancer are required to investigate the pathology and therapeutics of the disease. However, established i.p. models which are well-characterized and reliable are few. The purposes of this study are to establish a representative mice i.p. model of the disease and to analyze the consequent pathology.
Methods
Fresh tumor cells fiom the ascites of patient were injected into female NOD/SCID mice intraperitoneally. Histology, Cytogenetic, immunohistochemistry,tumor markers of CA125,AFP, CA-199 and CEA were used to analyze the model.
Results
The mice developed marked abdominal distention within 6 months after inoculated with tumor cells from a patient with epithelial ovarian carcinoma. The mice developed clinically evident intraperitoneal tumors and massive ascites containing numerous tumor cells in clumps. CA125 level in our model was high in both serum and ascites supernatants, while levels of other tumor markers, such as AFP, CA-199 and CEA, were normal. Cytogenetic analysis and immunohistochemical staining confirmed its characteristics resembling human epithelial ovarian tumor.
Conclusions
The model described in this paper accurately mimics the features of ovarian tumor, which may be useful for evaluation of new therapeutics.
doi:10.1186/1757-2215-6-9
PMCID: PMC3573975  PMID: 23384043
Human; Ovary carcinoma; Animal model; CA125; Intraperitoneal
13.  Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure 
Wain, Louise V | Verwoert, Germaine C | O’Reilly, Paul F | Shi, Gang | Johnson, Toby | Johnson, Andrew D | Bochud, Murielle | Rice, Kenneth M | Henneman, Peter | Smith, Albert V | Ehret, Georg B | Amin, Najaf | Larson, Martin G | Mooser, Vincent | Hadley, David | Dörr, Marcus | Bis, Joshua C | Aspelund, Thor | Esko, Tõnu | Janssens, A Cecile JW | Zhao, Jing Hua | Heath, Simon | Laan, Maris | Fu, Jingyuan | Pistis, Giorgio | Luan, Jian’an | Arora, Pankaj | Lucas, Gavin | Pirastu, Nicola | Pichler, Irene | Jackson, Anne U | Webster, Rebecca J | Zhang, Feng | Peden, John F | Schmidt, Helena | Tanaka, Toshiko | Campbell, Harry | Igl, Wilmar | Milaneschi, Yuri | Hotteng, Jouke-Jan | Vitart, Veronique | Chasman, Daniel I | Trompet, Stella | Bragg-Gresham, Jennifer L | Alizadeh, Behrooz Z | Chambers, John C | Guo, Xiuqing | Lehtimäki, Terho | Kühnel, Brigitte | Lopez, Lorna M | Polašek, Ozren | Boban, Mladen | Nelson, Christopher P | Morrison, Alanna C | Pihur, Vasyl | Ganesh, Santhi K | Hofman, Albert | Kundu, Suman | Mattace-Raso, Francesco US | Rivadeneira, Fernando | Sijbrands, Eric JG | Uitterlinden, Andre G | Hwang, Shih-Jen | Vasan, Ramachandran S | Wang, Thomas J | Bergmann, Sven | Vollenweider, Peter | Waeber, Gérard | Laitinen, Jaana | Pouta, Anneli | Zitting, Paavo | McArdle, Wendy L | Kroemer, Heyo K | Völker, Uwe | Völzke, Henry | Glazer, Nicole L | Taylor, Kent D | Harris, Tamara B | Alavere, Helene | Haller, Toomas | Keis, Aime | Tammesoo, Mari-Liis | Aulchenko, Yurii | Barroso, Inês | Khaw, Kay-Tee | Galan, Pilar | Hercberg, Serge | Lathrop, Mark | Eyheramendy, Susana | Org, Elin | Sõber, Siim | Lu, Xiaowen | Nolte, Ilja M | Penninx, Brenda W | Corre, Tanguy | Masciullo, Corrado | Sala, Cinzia | Groop, Leif | Voight, Benjamin F | Melander, Olle | O’Donnell, Christopher J | Salomaa, Veikko | d’Adamo, Adamo Pio | Fabretto, Antonella | Faletra, Flavio | Ulivi, Sheila | Del Greco, M Fabiola | Facheris, Maurizio | Collins, Francis S | Bergman, Richard N | Beilby, John P | Hung, Joseph | Musk, A William | Mangino, Massimo | Shin, So-Youn | Soranzo, Nicole | Watkins, Hugh | Goel, Anuj | Hamsten, Anders | Gider, Pierre | Loitfelder, Marisa | Zeginigg, Marion | Hernandez, Dena | Najjar, Samer S | Navarro, Pau | Wild, Sarah H | Corsi, Anna Maria | Singleton, Andrew | de Geus, Eco JC | Willemsen, Gonneke | Parker, Alex N | Rose, Lynda M | Buckley, Brendan | Stott, David | Orru, Marco | Uda, Manuela | van der Klauw, Melanie M | Zhang, Weihua | Li, Xinzhong | Scott, James | Chen, Yii-Der Ida | Burke, Gregory L | Kähönen, Mika | Viikari, Jorma | Döring, Angela | Meitinger, Thomas | Davies, Gail | Starr, John M | Emilsson, Valur | Plump, Andrew | Lindeman, Jan H | ’t Hoen, Peter AC | König, Inke R | Felix, Janine F | Clarke, Robert | Hopewell, Jemma C | Ongen, Halit | Breteler, Monique | Debette, Stéphanie | DeStefano, Anita L | Fornage, Myriam | Mitchell, Gary F | Smith, Nicholas L | Holm, Hilma | Stefansson, Kari | Thorleifsson, Gudmar | Thorsteinsdottir, Unnur | Samani, Nilesh J | Preuss, Michael | Rudan, Igor | Hayward, Caroline | Deary, Ian J | Wichmann, H-Erich | Raitakari, Olli T | Palmas, Walter | Kooner, Jaspal S | Stolk, Ronald P | Jukema, J Wouter | Wright, Alan F | Boomsma, Dorret I | Bandinelli, Stefania | Gyllensten, Ulf B | Wilson, James F | Ferrucci, Luigi | Schmidt, Reinhold | Farrall, Martin | Spector, Tim D | Palmer, Lyle J | Tuomilehto, Jaakko | Pfeufer, Arne | Gasparini, Paolo | Siscovick, David | Altshuler, David | Loos, Ruth JF | Toniolo, Daniela | Snieder, Harold | Gieger, Christian | Meneton, Pierre | Wareham, Nicholas J | Oostra, Ben A | Metspalu, Andres | Launer, Lenore | Rettig, Rainer | Strachan, David P | Beckmann, Jacques S | Witteman, Jacqueline CM | Erdmann, Jeanette | van Dijk, Ko Willems | Boerwinkle, Eric | Boehnke, Michael | Ridker, Paul M | Jarvelin, Marjo-Riitta | Chakravarti, Aravinda | Abecasis, Goncalo R | Gudnason, Vilmundur | Newton-Cheh, Christopher | Levy, Daniel | Munroe, Patricia B | Psaty, Bruce M | Caulfield, Mark J | Rao, Dabeeru C | Tobin, Martin D | Elliott, Paul | van Duijn, Cornelia M
Nature genetics  2011;43(10):1005-1011.
Numerous genetic loci influence systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans 1-3. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N=74,064) and follow-up studies (N=48,607), we identified at genome-wide significance (P= 2.7×10-8 to P=2.3×10-13) four novel PP loci (at 4q12 near CHIC2/PDGFRAI, 7q22.3 near PIK3CG, 8q24.12 in NOV, 11q24.3 near ADAMTS-8), two novel MAP loci (3p21.31 in MAP4, 10q25.3 near ADRB1) and one locus associated with both traits (2q24.3 near FIGN) which has recently been associated with SBP in east Asians. For three of the novel PP signals, the estimated effect for SBP was opposite to that for DBP, in contrast to the majority of common SBP- and DBP-associated variants which show concordant effects on both traits. These findings indicate novel genetic mechanisms underlying blood pressure variation, including pathways that may differentially influence SBP and DBP.
doi:10.1038/ng.922
PMCID: PMC3445021  PMID: 21909110
14.  catena-Poly[[[diaqua­diformato­cobalt(II)]-μ-1,4-bis­(1H-benzimidazol-1-yl)benzene] dihydrate] 
In the title coordination polymer, {[Co(CHO2)2(C20H14N4)(H2O)2]·2H2O}n, the CoII atom (site symmetry ) is coordinated by two formate O atoms, two water O atoms and two N atoms from two 1,4-bis­(1H-benzimidazol-1-yl)benzene ligands (L), resulting in a distorted trans-CoN2O4 octa­hedral coordin­ation environment. The complete L ligand is generated by crystallographic inversion symmetry and serves to bridge the cobalt ions into a chain propagating in [1 ]. The dihedral angle between the central benzene ring and the imidazole ring system is 38.48 (12)°. O—H⋯O hydrogen bonds involving both the coordinated and uncoordinated water mol­ecules occur and help to link the chains together.
doi:10.1107/S160053681105505X
PMCID: PMC3274843  PMID: 22346892
15.  Enriching rare variants using family-specific linkage information 
BMC Proceedings  2011;5(Suppl 9):S82.
Genome-wide association studies have been successful in identifying common variants for common complex traits in recent years. However, common variants have generally failed to explain substantial proportions of the trait heritabilities. Rare variants, structural variations, and gene-gene and gene-environment interactions, among others, have been suggested as potential sources of the so-called missing heritability. With the advent of exome-wide and whole-genome next-generation sequencing technologies, finding rare variants in functionally important sites (e.g., protein-coding regions) becomes feasible. We investigate the role of linkage information to select families enriched for rare variants using the simulated Genetic Analysis Workshop 17 data. In each replicate of simulated phenotypes Q1 and Q2 on 697 subjects in 8 extended pedigrees, we select one pedigree with the largest family-specific LOD score. Across all 200 replications, we compare the probability that rare causal alleles will be carried in the selected pedigree versus a randomly chosen pedigree. One example of successful enrichment was exhibited for gene VEGFC. The causal variant had minor allele frequency of 0.0717% in the simulated unrelated individuals and explained about 0.1% of the phenotypic variance. However, it explained 7.9% of the phenotypic variance in the eight simulated pedigrees and 23.8% in the family that carried the minor allele. The carrier’s family was selected in all 200 replications. Thus our results show that family-specific linkage information is useful for selecting families for sequencing, thus ensuring that rare functional variants are segregating in the sequencing samples.
doi:10.1186/1753-6561-5-S9-S82
PMCID: PMC3287923  PMID: 22373363
16.  Comparative proteome analysis of Helicobacter pylori clinical strains by two-dimensional gel electrophoresis*  
Objective: To investigate the pathogenic properties of Helicobacter pylori by comparing the proteome map of H. pylori clinical strains. Methods: Two wild-type H. pylori strains, YN8 (isolated from biopsy tissue of a gastric cancer patient) and YN14 (isolated from biopsy tissue of a gastritis and duodenal ulcer patient), were used. Proteomic analysis, using a pH range of 3–10 and 5–8, was performed. The individual proteins were identified by quadrupole time-of-flight (Q-TOF) mass spectrometer and protein database search. Results: Variation in spot patterns directed towards differential protein expression levels was observed between the strains. The gel revealed prominent proteins with several protein “families”. The comparison of protein expressions of the two strains reveals a high variability. Differentially present or absent spots were observed. Nine differentially expressed protein spots identified by Q-TOF included adenosine triphosphate (ATP)-binding protein, disulfide oxidoreductase B (DsbB)-like protein, N utilization substance A (NusA), ATP-dependent protease binding subunit/heat shock protein, hydantoin utilization protein A, seryl-tRNA synthetase, molybdenum ABC transporter ModD, and hypothetical proteins. Conclusions: This study suggests that H. pylori strains express/repress protein variation, not only in terms of the virulence proteins, but also in terms of physiological proteins, when they infect a human host. The difference of protein expression levels between H. pylori strains isolated from gastric cancer and gastritis may be the initiator of inflammation, and result in the different clinical presentation. In this preliminary study, we report seven differential proteins between strains, with molecule weights from approximately 10 kDa to approximately 40 kDa. Further studies are needed to investigate those proteins and their function associated with H. pylori colonization and adaptation to host environment stress.
doi:10.1631/jzus.B1000445
PMCID: PMC3190097  PMID: 21960345
Helicobacter pylori; Proteome; Gastric cancer; Gastritis; Two-dimensional gel electrophoresis
17.  Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study 
Fox, Ervin R. | Young, J. Hunter | Li, Yali | Dreisbach, Albert W. | Keating, Brendan J. | Musani, Solomon K. | Liu, Kiang | Morrison, Alanna C. | Ganesh, Santhi | Kutlar, Abdullah | Ramachandran, Vasan S. | Polak, Josef F. | Fabsitz, Richard R. | Dries, Daniel L. | Farlow, Deborah N. | Redline, Susan | Adeyemo, Adebowale | Hirschorn, Joel N. | Sun, Yan V. | Wyatt, Sharon B. | Penman, Alan D. | Palmas, Walter | Rotter, Jerome I. | Townsend, Raymond R. | Doumatey, Ayo P. | Tayo, Bamidele O. | Mosley, Thomas H. | Lyon, Helen N. | Kang, Sun J. | Rotimi, Charles N. | Cooper, Richard S. | Franceschini, Nora | Curb, J. David | Martin, Lisa W. | Eaton, Charles B. | Kardia, Sharon L.R. | Taylor, Herman A. | Caulfield, Mark J. | Ehret, Georg B. | Johnson, Toby | Chakravarti, Aravinda | Zhu, Xiaofeng | Levy, Daniel | Munroe, Patricia B. | Rice, Kenneth M. | Bochud, Murielle | Johnson, Andrew D. | Chasman, Daniel I. | Smith, Albert V. | Tobin, Martin D. | Verwoert, Germaine C. | Hwang, Shih-Jen | Pihur, Vasyl | Vollenweider, Peter | O'Reilly, Paul F. | Amin, Najaf | Bragg-Gresham, Jennifer L. | Teumer, Alexander | Glazer, Nicole L. | Launer, Lenore | Zhao, Jing Hua | Aulchenko, Yurii | Heath, Simon | Sõber, Siim | Parsa, Afshin | Luan, Jian'an | Arora, Pankaj | Dehghan, Abbas | Zhang, Feng | Lucas, Gavin | Hicks, Andrew A. | Jackson, Anne U. | Peden, John F. | Tanaka, Toshiko | Wild, Sarah H. | Rudan, Igor | Igl, Wilmar | Milaneschi, Yuri | Parker, Alex N. | Fava, Cristiano | Chambers, John C. | Kumari, Meena | JinGo, Min | van der Harst, Pim | Kao, Wen Hong Linda | Sjögren, Marketa | Vinay, D.G. | Alexander, Myriam | Tabara, Yasuharu | Shaw-Hawkins, Sue | Whincup, Peter H. | Liu, Yongmei | Shi, Gang | Kuusisto, Johanna | Seielstad, Mark | Sim, Xueling | Nguyen, Khanh-Dung Hoang | Lehtimäki, Terho | Matullo, Giuseppe | Wu, Ying | Gaunt, Tom R. | Charlotte Onland-Moret, N. | Cooper, Matthew N. | Platou, Carl G.P. | Org, Elin | Hardy, Rebecca | Dahgam, Santosh | Palmen, Jutta | Vitart, Veronique | Braund, Peter S. | Kuznetsova, Tatiana | Uiterwaal, Cuno S.P.M. | Campbell, Harry | Ludwig, Barbara | Tomaszewski, Maciej | Tzoulaki, Ioanna | Palmer, Nicholette D. | Aspelund, Thor | Garcia, Melissa | Chang, Yen-Pei C. | O'Connell, Jeffrey R. | Steinle, Nanette I. | Grobbee, Diederick E. | Arking, Dan E. | Hernandez, Dena | Najjar, Samer | McArdle, Wendy L. | Hadley, David | Brown, Morris J. | Connell, John M. | Hingorani, Aroon D. | Day, Ian N.M. | Lawlor, Debbie A. | Beilby, John P. | Lawrence, Robert W. | Clarke, Robert | Collins, Rory | Hopewell, Jemma C. | Ongen, Halit | Bis, Joshua C. | Kähönen, Mika | Viikari, Jorma | Adair, Linda S. | Lee, Nanette R. | Chen, Ming-Huei | Olden, Matthias | Pattaro, Cristian | Hoffman Bolton, Judith A. | Köttgen, Anna | Bergmann, Sven | Mooser, Vincent | Chaturvedi, Nish | Frayling, Timothy M. | Islam, Muhammad | Jafar, Tazeen H. | Erdmann, Jeanette | Kulkarni, Smita R. | Bornstein, Stefan R. | Grässler, Jürgen | Groop, Leif | Voight, Benjamin F. | Kettunen, Johannes | Howard, Philip | Taylor, Andrew | Guarrera, Simonetta | Ricceri, Fulvio | Emilsson, Valur | Plump, Andrew | Barroso, Inês | Khaw, Kay-Tee | Weder, Alan B. | Hunt, Steven C. | Bergman, Richard N. | Collins, Francis S. | Bonnycastle, Lori L. | Scott, Laura J. | Stringham, Heather M. | Peltonen, Leena | Perola, Markus | Vartiainen, Erkki | Brand, Stefan-Martin | Staessen, Jan A. | Wang, Thomas J. | Burton, Paul R. | SolerArtigas, Maria | Dong, Yanbin | Snieder, Harold | Wang, Xiaoling | Zhu, Haidong | Lohman, Kurt K. | Rudock, Megan E. | Heckbert, Susan R. | Smith, Nicholas L. | Wiggins, Kerri L. | Shriner, Daniel | Veldre, Gudrun | Viigimaa, Margus | Kinra, Sanjay | Prabhakaran, Dorairajan | Tripathy, Vikal | Langefeld, Carl D. | Rosengren, Annika | Thelle, Dag S. | MariaCorsi, Anna | Singleton, Andrew | Forrester, Terrence | Hilton, Gina | McKenzie, Colin A. | Salako, Tunde | Iwai, Naoharu | Kita, Yoshikuni | Ogihara, Toshio | Ohkubo, Takayoshi | Okamura, Tomonori | Ueshima, Hirotsugu | Umemura, Satoshi | Eyheramendy, Susana | Meitinger, Thomas | Wichmann, H.-Erich | Cho, Yoon Shin | Kim, Hyung-Lae | Lee, Jong-Young | Scott, James | Sehmi, Joban S. | Zhang, Weihua | Hedblad, Bo | Nilsson, Peter | Smith, George Davey | Wong, Andrew | Narisu, Narisu | Stančáková, Alena | Raffel, Leslie J. | Yao, Jie | Kathiresan, Sekar | O'Donnell, Chris | Schwartz, Steven M. | Arfan Ikram, M. | Longstreth, Will T. | Seshadri, Sudha | Shrine, Nick R.G. | Wain, Louise V. | Morken, Mario A. | Swift, Amy J. | Laitinen, Jaana | Prokopenko, Inga | Zitting, Paavo | Cooper, Jackie A. | Humphries, Steve E. | Danesh, John | Rasheed, Asif | Goel, Anuj | Hamsten, Anders | Watkins, Hugh | Bakker, Stephan J.L. | van Gilst, Wiek H. | Janipalli, Charles S. | Radha Mani, K. | Yajnik, Chittaranjan S. | Hofman, Albert | Mattace-Raso, Francesco U.S. | Oostra, Ben A. | Demirkan, Ayse | Isaacs, Aaron | Rivadeneira, Fernando | Lakatta, Edward G. | Orru, Marco | Scuteri, Angelo | Ala-Korpela, Mika | Kangas, Antti J. | Lyytikäinen, Leo-Pekka | Soininen, Pasi | Tukiainen, Taru | Würz, Peter | Twee-Hee Ong, Rick | Dörr, Marcus | Kroemer, Heyo K. | Völker, Uwe | Völzke, Henry | Galan, Pilar | Hercberg, Serge | Lathrop, Mark | Zelenika, Diana | Deloukas, Panos | Mangino, Massimo | Spector, Tim D. | Zhai, Guangju | Meschia, James F. | Nalls, Michael A. | Sharma, Pankaj | Terzic, Janos | Kranthi Kumar, M.J. | Denniff, Matthew | Zukowska-Szczechowska, Ewa | Wagenknecht, Lynne E. | Fowkes, Gerald R. | Charchar, Fadi J. | Schwarz, Peter E.H. | Hayward, Caroline | Guo, Xiuqing | Bots, Michiel L. | Brand, Eva | Samani, Nilesh J. | Polasek, Ozren | Talmud, Philippa J. | Nyberg, Fredrik | Kuh, Diana | Laan, Maris | Hveem, Kristian | Palmer, Lyle J. | van der Schouw, Yvonne T. | Casas, Juan P. | Mohlke, Karen L. | Vineis, Paolo | Raitakari, Olli | Wong, Tien Y. | Shyong Tai, E. | Laakso, Markku | Rao, Dabeeru C. | Harris, Tamara B. | Morris, Richard W. | Dominiczak, Anna F. | Kivimaki, Mika | Marmot, Michael G. | Miki, Tetsuro | Saleheen, Danish | Chandak, Giriraj R. | Coresh, Josef | Navis, Gerjan | Salomaa, Veikko | Han, Bok-Ghee | Kooner, Jaspal S. | Melander, Olle | Ridker, Paul M. | Bandinelli, Stefania | Gyllensten, Ulf B. | Wright, Alan F. | Wilson, James F. | Ferrucci, Luigi | Farrall, Martin | Tuomilehto, Jaakko | Pramstaller, Peter P. | Elosua, Roberto | Soranzo, Nicole | Sijbrands, Eric J.G. | Altshuler, David | Loos, Ruth J.F. | Shuldiner, Alan R. | Gieger, Christian | Meneton, Pierre | Uitterlinden, Andre G. | Wareham, Nicholas J. | Gudnason, Vilmundur | Rettig, Rainer | Uda, Manuela | Strachan, David P. | Witteman, Jacqueline C.M. | Hartikainen, Anna-Liisa | Beckmann, Jacques S. | Boerwinkle, Eric | Boehnke, Michael | Larson, Martin G. | Järvelin, Marjo-Riitta | Psaty, Bruce M. | Abecasis, Gonçalo R. | Elliott, Paul | van Duijn , Cornelia M. | Newton-Cheh, Christopher
Human Molecular Genetics  2011;20(11):2273-2284.
The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity.
doi:10.1093/hmg/ddr092
PMCID: PMC3090190  PMID: 21378095
18.  Identification of novel DNA methylation inhibitors via a two-component reporter gene system 
Background
Targeting abnormal DNA methylation represents a therapeutically relevant strategy for cancer treatment as demonstrated by the US Food and Drug Administration approval of the DNA methyltransferase inhibitors azacytidine and 5-aza-2'-deoxycytidine for the treatment of myelodysplastic syndromes. But their use is associated with increased incidences of bone marrow suppression. Alternatively, procainamide has emerged as a potential DNA demethylating agent for clinical translation. While procainamide is much safer than 5-aza-2'-deoxycytidine, it requires high concentrations to be effective in DNA demethylation in suppressing cancer cell growth. Thus, our laboratories have embarked on the pharmacological exploitation of procainamide to develop potent DNA methylation inhibitors through lead optimization.
Methods
We report the use of a DNA methylation two-component enhanced green fluorescent protein reporter system as a screening platform to identify novel DNA methylation inhibitors from a compound library containing procainamide derivatives.
Results
A lead agent IM25, which exhibits substantially higher potency in GSTp1 DNA demethylation with lower cytotoxicity in MCF7 cells relative to procainamide and 5-aza-2'-deoxycytidine, was identified by the screening platform.
Conclusions
Our data provide a proof-of-concept that procainamide could be pharmacologically exploited to develop novel DNA methylation inhibitors, of which the translational potential in cancer therapy/prevention is currently under investigation.
doi:10.1186/1423-0127-18-3
PMCID: PMC3025941  PMID: 21219604
19.  Detecting Gene-Environment Interactions in Genome-Wide Association Data 
Genetic epidemiology  2009;33(Suppl 1):S68-S73.
Despite the importance of gene-environment (G×E) interactions in the etiology of common diseases, little work has been done to develop methods for detecting these types of interactions in genome-wide association study data. This was the focus of Genetic Analysis Workshop 16 Group 10 contributions, which introduced a variety of new methods for the detection of G×E interactions in both case-control and family-based data using both cross-sectional and longitudinal study designs. Many of these contributions detected significant G×E interactions. Although these interactions have not yet been confirmed, the results suggest the importance of testing for interactions. Issues of sample size, quantifying the environmental exposure, longitudinal data analysis, family-based analysis, selection of the most powerful analysis method, population stratification, and computational expense with respect to testing G×E interactions are discussed.
doi:10.1002/gepi.20475
PMCID: PMC2924567  PMID: 19924704
GAW; case-control; family-based; cross-sectional; longitudinal; rheumatoid arthritis; Framingham Heart Study
20.  A microsatellite polymorphism in IGF1 gene promoter and longevity in a Han Chinese population 
BMC Research Notes  2010;3:55.
Background
Previous studies have suggested a probable association between the polymorphism of a microsatellite locus located in the promoter of IGF1 (Insulin-like growth factor 1) gene and the serum level of IGF1, as well as many age-related diseases. Based on these results, we hypothesized that this polymorphism may influence longevity in humans. We performed an association study in a Han Chinese population to test this hypothesis.
Findings
We recruited 493 elderly Han Chinese individuals (females ≥ 94; males ≥ 90) and 425 young individuals (controls) from Dujiangyan (Sichuan province, China). The genotype distributions and allele frequencies of the microsatellite site in the elderly and control groups were compared by chi square test.
Our results suggested that there was no association between the microsatellite polymorphism and longevity in our Han Chinese population. However, there were more male persons with 18/21 genotype in elderly group than that in control group (11.11 vs. 5.45%, p = 0.011). As the difference was not significant when corrected by Bonferroni method, we speculate that the 18/21 genotype can not be functional in longevity; however, it may link with the real functional loci as there is a long haplotype block embracing the microsatellite locus.
Conclusions
There was no association between polymorphism of the microsatellite in promoter of IGF1 gene and longevity in our study. Future association studies containing the long haplotype block are deserved and can test our speculation of the potential linkage of 18/21 genotype and functional loci.
doi:10.1186/1756-0500-3-55
PMCID: PMC2844396  PMID: 20199671
21.  Genetic Effect on Blood Pressure is Modulated by Age: The HyperGEN Study 
Hypertension  2008;53(1):35-41.
Genome-wide linkage analysis was carried out for systolic and diastolic blood pressures in the Hypertension Genetic Epidemiology Network. We investigated the role of gene-age interactions using a recently developed variance components method that incorporates age variation in genetic effects. Substantially improved linkage evidence, in terms of both the number of linkage peaks and their significance levels, was observed. Twenty-six linkage peaks were identified with maximum LOD scores ranging between 3.0 and 4.6, fifteen of which were cross-validated by the literature. The chromosomal region 1p36 that showed the highest lod score in our study was found being supported by evidences from three literature. The new method also led to vastly improved validation across ethnic groups. Ten out of the fifteen supported linkage peaks were cross validated between two different ethnic groups, and two peaks on chromosomal region 1q31 and 16p11 were validated in three ethnic groups. In conclusion, this investigation demonstrates that genetic effects on blood pressure vary by age. The improved genetic linkage results presented here should help in identifying the specific genetic variants that explain the observed results.
doi:10.1161/HYPERTENSIONAHA.108.120071
PMCID: PMC2633773  PMID: 19029486
blood pressure; genetics; hypertension; linkage; gene-age interactions; QTL effect
22.  Application of three-level linear mixed-effects model incorporating gene-age interactions for association analysis of longitudinal family data 
BMC Proceedings  2009;3(Suppl 7):S89.
Longitudinal studies that collect repeated measurements on the same subjects over time have long been considered as being more powerful and providing much better information on individual changes than cross-sectional data. We propose a three-level linear mixed-effects model for testing genetic main effects and gene-age interactions with longitudinal family data. The simulated Genetic Analysis Workshop 16 Problem 3 data sets were used to evaluate the method. Genome-wide association analyses were conducted based on cross-sectional data, i.e., each of the three single-visit data sets separately, and also on the longitudinal data, i.e., using data from all three visits simultaneously. Results from the analysis of coronary artery calcification phenotype showed that the longitudinal association tests were much more powerful than those based on single-visit data only. Gene-age interactions were evaluated under the same framework for detecting genetic effects that are modulated by age.
PMCID: PMC2795992  PMID: 20018085
23.  Genome-wide association analysis of Framingham Heart Study data for the Genetics Analysis Workshop 16: effects due to medication use 
BMC Proceedings  2009;3(Suppl 7):S52.
Problems associated with medication use and the consequent effects on genome-wide association analyses were explored using the Genetic Analysis Workshop 16 Problem 3 data. Lipid phenotypes were simulated in the Framingham Heart Study using several measured variables including causal genes (based on a 500 k SNP panel), smoking, dietary intake, and medication usage. We report a sensitivity analysis of how medication use (which artificially alters lipid values) affects association inferences. Associations were performed for LDL-c under seven different correction schemes: 1) ignore medication use entirely (no correction) and adjust for covariates; 2) delete medicated subjects then adjust for covariates; 3) include medication use (Yes/No) as a covariate during covariate adjustments; 4) correct raw values using clinical trials information then adjust for covariates; 5) correct raw values using the actual simulation protocol ("truth") then adjust for covariates; and 6-7) over-corrections (add arbitrary values) then adjust for covariates. Results indicate that failure to properly correct for medication usage can profoundly affect the heritability, and hence the association results. The empirical results yielded one genome-wide significant locus on chromosome 22 (RS2294207), consistent with the simulation protocol. This signal was detected under all schemes that corrected the raw values (clinical trials, simulation protocol, or over corrections), but was not detected under the first three adjustment schemes (ignore medication use, delete medicated individuals, use medication status as covariate). In summary, we confirm that failure to properly account for medication usage can have a profound impact on genetic associations.
PMCID: PMC2795952  PMID: 20018045
24.  Comparison between single-marker analysis using Merlin and multi-marker analysis using LASSO for Framingham simulated data 
BMC Proceedings  2009;3(Suppl 7):S27.
We compared family-based single-marker association analysis using Merlin and multi-marker analysis using LASSO (least absolute shrinkage and selection operator) for the low-density lipoprotein phenotype at the first visit for all 200 replicates of the Genetic Analysis Workshop 16 Framingham simulated data sets. Using "answers," we selected single-nucleotide polymorphisms (SNPs) on chromosome 22 for comparison of results between single-marker and multi-marker analyses. For the major causal SNP rs2294207 on chromosome 22, both single-marker and multi-marker analyses provided similar results, indicating the importance of this SNP. For the 12 polygenic SNPs on the same chromosome, both single-marker and multi-marker analyses failed to provide statistically significant associations, indicating that their effects were too weak to be detected by either method. The main difference between the two methods was that for the 14 SNPs near the causal SNPs, p-values from Merlin were the next smallest, whereas LASSO often excluded these non-causal neighboring SNPs entirely from the first 10,000 models.
PMCID: PMC2795924  PMID: 20018017
25.  Choledochoscope manometry about different drugs on the Sphincter of Oddi 
AIM: To assess the effects of H2-receptor blocking pharmacon, protease inhibitor, and gastro kinetic agents on the human Sphincter of Oddi (SO) motility by choledochoscope manometry.
METHODS: One hundred and seventy-five patients with T tube installed after cholecystectomy and choledochotomy were assessed by choledochoscope manometry. They were randomly assigned into groups of H2-receptor blocking pharmacon, protease inhibitor, and gastro kinetic agents. The Sphincter of Oddi basal pressure (SOBP), amplitude (SOCA), frequency of contractions (SOF), duodenal pressure (DP), and common bile duct pressure (CBDP) were scored and analyzed.
RESULTS: SOBP and SOCA were significantly decreased after Cimetidine administration, and no statistical difference was seen in the Famotidine group. In the Gabexate mesilate group, SOBP had decreased significantly. In the Ulinastatin group, SOCA decreased when Ulinastatin was given at the rate of 2500 U/min; when Ulinastatin administration was raised to 5000 U/min, SOBP, SOF and SOCA all experienced a fall. SOBP and SOCA for Domperidone and SOCA for Mosapride groups all decreased distinctly after administration.
CONCLUSION: The regular dosage of Cimetidine showed an inhibitory effect on the motility of SO, while Famotidine had no obvious effects otherwise. Gabnexata mesilate, Ulinastatin and gastro kinetic agents also showed inhibitory effects on the SO motility.
doi:10.3748/wjg.14.5907
PMCID: PMC2751903  PMID: 18855992
Sphincter of Oddi; Medicamentum; Choledochoscope manometry

Results 1-25 (26)