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ABSTRACT: We developed a software program, NDesign, for the design of a study intended for detecting rare variants from next-generation sequencing (NGS) data. In this study design, the optimal depth of coverage and the average depth of coverage are first evaluated, and then the ability of the designed experiment to obtain a desired power is determined. NDesign has been developed to calculate both these depths, as well as to evaluate the power of the designed experiment. It has a simple implementation in the JavaScript language, and is expected to enable researchers to design optimal NGS studies.
Journal of Human Genetics 07/2012; 57(10):676-8. · 2.57 Impact Factor
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ABSTRACT: Our objective was to describe outpatient medical care costs of patients with rheumatoid arthritis (RA) in the prebiologics period in Japan. The outpatient costs of 6,771 RA patients (17,666 patient years) who were enrolled in an observational cohort study at the Institute of Rheumatology, Rheumatoid Arthritis (IORRA), in Tokyo, Japan, were calculated from the billing records dated from 2000 to 2004. Associations between outpatient costs and variables such as age, RA duration, RA disease activities, and disability levels were assessed. The average outpatient cost gradually increased (+7.7% in 4 years) from 271,498 JPY per year in 2000 to 292,417 JPY per year in 2004. Medications accounted for approximately 50% of total outpatient costs, which increased 29.6% during the 4 years. The outpatient costs increased in association with aging, longer RA duration, higher Disease Activity Score of 28 Joints (DAS28), and higher Japanese version of Health Assessment Questionnaire (J-HAQ) score. Generalized linear regression analysis revealed that both DAS28 and J-HAQ scores were the most significant factors associated with outpatient costs (p < 0.001). Outpatient costs for patients with RA increased year after year over the 4-year period under observation in Japan. Medical costs were higher with increasing RA disease activity and disability levels.
Modern Rheumatology 10/2009; 20(1):46-53. · 1.58 Impact Factor
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ABSTRACT: To analyze the possible beneficial effects of statins on the disease activity of patients with rheumatoid arthritis (RA) using a database from a large observational cohort study.
We studied a total of 7512 patients enrolled in a single-institute based prospective observational cohort of RA patients (IORRA); their information was collected biannually. In this study, cross-sectional data of 4152 patients (female 83.3%, average age 58.4 yrs) in October 2003 were analyzed (Mann-Whitney U-test).
Among 4152 patients with RA, 279 (6.7%) were taking statins; patients taking statins had lower C-reactive protein (0.85 vs 1.24 mg/dl, respectively) and lower swollen joint counts (1.80 vs 2.55), but more frequently used corticosteroids (2.88 vs 2.40 mg/day) compared to patients not taking statins. Serum cholesterol level was closely related to the use of corticosteroids. Thus, an adjustment with the dose of corticosteroid was conducted; even taking account of the effects of steroids, RA disease activity indicated by patient's assessment for pain, physician's assessment, and swollen joint counts was significantly lower in patients with statins compared to those without.
This study indicates that statins have beneficial effects in reducing RA disease activity in the daily practice of rheumatology.
The Journal of Rheumatology 06/2007; 34(5):964-8. · 3.69 Impact Factor
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ABSTRACT: For prevention of joint destruction in rheumatoid arthritis, optimal management of therapy with disease-modifying antirheumatic drugs is essential. Pharmacogenomic evidence, if reliable, may be incorporated in the treatment of rheumatoid arthritis to achieve a more efficient activity control with minimized adverse events.
We conducted retrospective studies to validate our previous three different results about the association between adverse events or efficacy of two different disease-modifying antirheumatic drugs and genomic variations. Association between single nucleotide polymorphisms in N-acetyltransferase 2 gene (NAT2) and adverse events by sulfasalazine and association between C677T or A1298C in 5,10-methylenetetrahydrofolate reductase gene (MTHFR) and responses to methotrexate were examined.
Patients without the wild-type haplotype at NAT2 were more likely to suffer from overall adverse events [n=186, P=0.001, relative risk (RR) 3.31, 95% confidence interval (CI) 1.76-6.22] and severe adverse events (P=0.015, RR 24.6, 95% CI 2.37-254.53) by sulfasalazine. Patients with the T allele at C677T in MTHFR were more susceptible to overall adverse events (n=156, P=0.003; RR 2.4, 95% CI 1.29-4.55) while patients with the C allele at A1298C were less likely to be treated with a higher dose (>6 mg/week) of methotrexate in one year of treatment (n=159, P=0.008, RR 1.84, 95% CI 1.12-3.01). In all three association studies, the results were essentially the same as previously reported.
As three studies on the associations between genomic variations and adverse events or efficacy of two different disease-modifying antirheumatic drugs were replicated, the usefulness of the tests is worth being tested in clinical practice.
Pharmacogenetics and Genomics 06/2007; 17(6):383-90. · 3.48 Impact Factor
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Eiichi Tanaka, Shigeo Kamitsuji,
Eisuke Inoue,
Toru Yamada,
Ayako Nakajima,
Etsuko Takeuchi,
Akiko Yanagisawa,
Ryouichi Misaka,
Mutsuo Shigemoto,
Katsuko Yamashita,
Tetsuo Imamura,
Masako Hara,
Taisuke Tomatsu,
Terunobu Saito,
Gerson Lauren,
George Triadafilopoulos,
Naoyuki Kamatani,
Gurkirpal Singh,
Hisashi Yamanaka
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ABSTRACT: We evaluated the effects of the use of nonsteroidal anti-inflammatory drugs (NSAIDs) on endoscopic and histological findings in patients with rheumatoid arthritis (RA) before and after the eradication of Helicobacter pylori infection. Helicobacter pylori (H. pylori) eradication using lansoprazole 30 mg, amoxicillin 750 mg, and clarithromycin 200 mg twice daily for 1 week was conducted in 44 patients (mean age: 56.5 years) with RA. Using the updated Sydney system, endoscopic and histological findings of the greater curvature of the antrum, the greater curvature of the upper corpus, and the lesser curvature of the lower corpus were compared before and after eradication, for a mean follow-up period of 3.5 months. Overall, H. pylori eradication was successful in 32 patients (72.7%). Of these 32 patients, 23 were NSAID users. In the successful eradication group, (1) there was no significant change on endoscopic findings, including gastric erythema and erosion in all three regions irrespective of NSAIDs use; (2) of 17 active ulcers before eradication in NSAIDs users, all healed except for one duodenal ulcer that persisted, where one patient newly developed a gastric ulcer, one developed erosive duodenitis, and two developed reflux esophagitis, all in NSAID users; (3) neutrophil infiltration and chronic inflammation were significantly improved in all three regions after H. pylori eradication irrespective of use of NSAIDs, while atrophic change and intestinal metaplasia did not change. In the eradication failure group; (1) there was no significant change on endoscopic and histological findings in the three regions; (2) two of three ulcers present before eradication on NSAID users persisted even after eradication, and no new cases of gastric ulcer or erosive duodenitis occurred. In conclusion, over a mean follow-up period of 3.5 months, use of NSAIDs in Japanese patients with RA did not impair the healing process of gastric and duodenal ulcers nor did it affect the endoscopic and histological improvements associated with H. pylori eradication.
Modern Rheumatology 02/2007; 17(3):228-34. · 1.58 Impact Factor
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ABSTRACT: An algorithm for estimating haplotypes associated with several quantitative phenotypes is proposed. The concept of a receiver operating characteristic (ROC) curve was introduced, and a linear combination of the quantitative phenotypic values was considered. This set of values was divided into two parts: values for subjects with and without a particular haplotype. The goodness of its partition was evaluated by the area under the ROC curve (AUC). The AUC value varied from 0 to 1; this value was close to 1 when the partition had high accuracy. Therefore, the strength of association between phenotypes and haplotypes was considered to be proportional to the AUC value. In our algorithm, the parameters representing a degree of association between the haplotypes and phenotypes were estimated so as to maximize the AUC value; further, the haplotype with the maximum AUC value was considered to be the best haplotype associated with the phenotypes. This algorithm was implemented by using R language. The effectiveness of our algorithm was evaluated by applying it to real genotype data of the Calpine-10 gene obtained from diabetics. The results showed that our algorithm was more reasonable and advantageous for use with several quantitative phenotypes than the generalized linear model or the neural network model.
Journal of Human Genetics 02/2006; 51(4):314-25. · 2.57 Impact Factor
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Ayako Nakajima, Shigeo Kamitsuji,
Akira Saito,
Eiichi Tanaka,
Katsuji Nishimura,
Naoshi Horikawa,
Norio Ozaki,
Taisuke Tomatsu,
Masako Hara,
Naoyuki Kamatani,
Hisashi Yamanaka
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ABSTRACT: The aim of this study was to evaluate the factors responsible for depressed mood in rheumatoid arthritis (RA). Clinical and laboratory measures were collected from 4558 RA patients enrolled in a large clinical cohort study for RA conducted at the Institute of Rheumatology, Tokyo Women's Medical University (IORRA study). A two-question depressed screening included in the U.S. Preventive Services Task Force recommendation were utilized to identify "depressed patients." A total of 1875 (41.1%) were identified as "depressed patients" who presented with symptoms suggestive of depression. Patient's Visual Analog Scale (VAS) for general health (43.3 mm vs 24.6 mm, P < 0.0001) and pain (40.9 mm vs 23.8 mm, P < 0.0001) and the disability index scores measured by the Health Association Questionnaire (HAQ) (0.986 vs 0.574, P < 0.0001) were significantly higher in depressed patients than in nondepressed patients. The presence of three or more comorbidities (odds ratio [OR] 2.157, P < 0.0001), infection (OR 1.754, P < 0.0001), and joint surgery (OR 1.878, P < 0.0001) were significantly correlated with depressed mood in RA. The results of the Generalized Linear Model analysis showed that HAQ disability index (P < 0.0001) and patient's VAS for general health (P < 0.0001) were also strongly and significantly associated to the response variable "probability of depressed patients." Patient appraisal of poor general health and greater disability were associated with depressed mood in RA.
Modern Rheumatology 01/2006; 16(3):151-7. · 1.58 Impact Factor
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ABSTRACT: To determine the most sensitive scoring method for assessment of rheumatoid arthritis (RA) disease activity using the American College of Rheumatology Core Data Set.
The subjects were 4,530 patients with RA (mean age 57.9 years, mean disease duration 12.7 years) who participated in a large observational cohort study of RA patients. The 68 joints assessed were classified into 15 joint areas, and each joint variable was categorized based on the presence or absence of swelling or pain in these areas. Multiple linear regression and analysis of variance were used to evaluate the significance of effects of these 15 joint areas on variables for assessment of RA disease activity such as patient's assessment of pain on a visual analog scale (VAS), patient's and physician's global assessment of disease activity on a VAS, HAQ (Health Assessment Questionnaire), and Japanese HAQ.
Although the 3 most frequently affected joints were the wrist, metacarpophalangeal joints, and proximal interphalangeal joints, the 5 joints with the largest contributions to all of the variables assessed for disease activity were the shoulder, elbow, and knee joints, followed by the wrist and ankle joints. The combination of shoulder, elbow, and knee joints accounted for approximately 70% of the contribution to all the variables, while addition of the wrist and ankle joints increased this value to approximately 90%.
Scoring for assessment of RA disease activity would be more sensitive if separate joints such as the shoulder, elbow, knee, wrist, and ankle joints were weighted differently.
Arthritis & Rheumatism 01/2006; 53(6):864-71. · 7.87 Impact Factor
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ABSTRACT: Stochastic neural network is a hierarchical network of stochastic neurons which emit 0 or 1 with the probability determined by the values of inputs. We have developed an efficient training algorithm so as to maximize the likelihood of such a neural network. This algorithm enables us to apply the stochastic neural network to a practical problem like prediction of fall or rise of Tokyo Stock Price Index (TOPIX). We trained it with the data from 1994 to 1996 and predicted the fall or rise of 1 day ahead of TOPIX for the period from 1997 to 2000. The result is quite promising. The accuracy of the prediction of the stochastic network is the 60.28%, although those of non-stochastic neural network, autoregressive model and GARCH model are 50.02, 51.38 and 57.21%, respectively. However, the stochastic neural network is not so advantageous over other networks or models for prediction of the TOPIX used for training. This means that the stochastic neural network is less over fitting to the training data than others, and results in the best prediction. We will demonstrate how the stochastic neural network learns well non-linear structure behind of the data in comparison to other models or networks, including Generalized Linear model (GLM). Copyright Springer Science + Business Media, Inc. 2003
Asia-Pacific Financial Markets 02/2003; 10(2):187-204.
