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Shingo Baba

Publications and source records attributed to Shingo Baba.

8 recordsLinked to original sources
PubMed2006

Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics.

Mutation screening is widely used for molecular diagnostics of inherited disorders. Furthermore, it is anticipated that the present and future identification of genetic risk factors for complex disorders will increase the need for high-throughput mutation screening technologies. Capillary array electrophoresis (CAE) SSCP analysis is a low-cost, automated method with a high throughput and high reproducibility. Thus, the method fulfills many of the demands to be met for application in routine molecular diagnostics. However, the need for performing the electrophoresis at three temperatures between 18 degrees C and 35 degrees C for achievement of high sensitivity is a disadvantage of the method. Using a panel of 185 mutant samples, we have analyzed the effect of sample purification, sample medium and separation matrix on the sensitivity of CAE-SSCP analysis to optimize the method for molecular diagnostic use. We observed different effects from sample purification and sample medium at different electrophoresis temperatures, probably reflecting the complex interplay between sequence composition, electrophoresis conditions and sensitivity in SSCP analysis. The effect on assay sensitivity from three different polymers was tested using a single electrophoresis temperature of 27 degrees C. The data suggest that a sensitivity of 98-99% can be obtained using a 10% long chain poly-N,N-dimethylacrylamide polymer.

Acrylamides↗
PubMed2005

dbQSNP: a database of SNPs in human promoter regions with allele frequency information determined by single-strand conformation polymorphism-based methods.

We present a database, dbQSNP (http://qsnp.gen.kyushu-u.ac.jp/), that provides sequence and allele frequency information for single-nucleotide polymorphisms (SNPs) located in the promoter regions of human genes, which were defined by the 5' ends of full-length cDNA clones. We searched for the SNPs in these regions by sequencing or single-strand conformation polymorphism (SSCP) analysis. The allele frequencies of the identified SNPs in two ethnic groups were quantified by SSCP analyses of pooled DNA samples. The accuracy of our estimation is supported by strong correlations between the frequencies in our data and those in other databases for the same ethnic groups. The frequencies vary considerably between the two ethnic groups studied, suggesting the need for population-based collections and allele frequency determination of SNPs, in, e.g., association studies of diseases. We show profiles of SNP densities that are characteristic of transcription start site regions. A fraction of the SNPs revealed a significantly different allele frequency between the groups, suggesting differential selection of the genes involved.

Alleles↗
PubMed2005

Comparison of 18FDG-PET with 99mTc-HMDP scintigraphy for the detection of bone metastases in patients with breast cancer.

OBJECTIVE: Bone is one of the most common sites of metastasis in breast cancer patients. Although bone scintigraphy is widely used to detect metastatic breast cancer, the usefulness of 18FDG-PET for detecting bone metastasis has not been clearly evaluated. The purpose of this study was to compare the diagnostic accuracy of 18FDG-PET with bone scintigraphy in detecting bone metastasis in breast cancer patients. METHODS: Forty-four women aged 35 to 81 years (mean, 56 years) with breast cancer were examined in this study. Both 18FDG-PET and bone scintigraphy were performed for each patient with 0-69 day intervals (mean, 11.5 days). The results of each image interpretation were compared retrospectively. Whole-body bones were classified into 9 anatomical regions. Metastases were confirmed at 45/187 regions in 14 patients by bone biopsy or clinical follow-up including other imaging techniques for a period of at least 6 months afterwards. RESULTS: On a region basis, the sensitivity, specificity, and accuracy of 18FDG-PET were 84%, 99% and 95%, respectively. Although these results were comparable to those of bone scintigraphy, the combination of 18FDG-PET and bone scintigraphy improved the sensitivity (98%) and accuracy (97%) of detection. False negative lesions of bone scintigraphy were mostly bone marrow metastases and those of 18FDG-PET were mostly osteoblastic metastases. 18FDG-PET was superior to bone scintigraphy in the detection of osteolytic lesions (92% vs. 73%), but inferior in the detection of osteoblastic lesions (74% vs. 95%). CONCLUSIONS: This study shows that 18FDG-PET tends to be superior to bone scintigraphy in the detection of osteolytic lesions, but inferior in the detection of osteoblastic lesions. 18FDG-PET should play a complementary role in detecting bone metastasis with bone scintigraphy.

Adult↗
PubMed2005

Extraosseous accumulation of (99m)Tc-HMDP to radiation nephropathy, mimicking recurrent neuroblastoma.

OBJECTIVE: The aim of this study is to clarify the period of extraosseous accumulation of (99m)Tc-hydroxymethylenediphosphonate (HMDP) to radiation nephropathy mimicking recurrent or remnant neuroblastoma in the pararenal region. METHODS: We reviewed five neuroblastoma and one ganglioneuroblastoma patients (2 boys and 4 girls aged 1-9 years) who underwent (99m)Tc-HMDP bone scintigraphies periodically before and after radiation therapy. RESULTS: Increased renal uptake coincident with the radiation port appeared in 5 of 6 patients from 0 to 3 months (mean 1.7 months), and persisted up to 7 months after the completion of radiotherapy. Renal uptake of (99m)Tc-HMDP was gradually decreased, and eventually became accumulation defects in 5 of 6 patients from 6 to 17 months (mean 8.9 months) after radiotherapy. CONCLUSION: When extraosseous accumulation is found after radiation therapy in neuroblastoma patients, radiation nephropathy would be a candidate in the differential diagnosis besides recurrent or remnant tumor.

Bone Neoplasms↗
PubMed2004

Validation of quantitative accuracy of the post-injection transmission-based and transmissionless attenuation correction techniques in neurological FDG-PET.

BACKGROUND: We evaluated the quantitative accuracy of the post-injection transmission-based segmented attenuation correction (SAC) technique and transmissionless calculated attenuation correction (CAC) technique in both 2D and 3D scanning for the brain, and compared the results with those obtained using the pre-injection transmission-based measured attenuation correction (MAC) technique, which is generally accepted as the 'gold standard'. METHODS: We examined [18F]fluorodeoxyglucose (18F-FDG) positron emission tomography (PET) on both a cylindrical phantom and in 10 patients with epilepsy. The statistical analyses were performed using both the region of interest (ROI) method and statistical parametric mapping (SPM). RESULTS: In the ROI analysis, [18F] activity concentration values obtained by the SAC technique were well correlated with those obtained by the MAC technique (2D, R2=0.94; 3D, R2=0.98; P<0.001), although these values were underestimated over the entire brain. The CAC technique was also found to have significant correlation with the MAC technique (2D, R2=0.84; 3D, R2=0.86; P<0.001), but this technique showed apparent overestimation or underestimation in several parts of the brain. In the SPM analysis, there were no significant differences between the SAC and MAC technique, while those values obtained by the CAC technique were significantly lower in the parieto-occipital region and higher in the lower frontal region (P<0.001, uncorrected). CONCLUSION: The SAC technique was superior to the CAC technique in both 2D and 3D scanning, although we found that both the SAC and CAC techniques had some problems in quantitative evaluation. We considered that the SAC technique may yield adequate qualitative measurements of the [18F] activity concentration value after global normalization.

Adult↗
PubMed2002

A single-strand conformation polymorphism method for the large-scale analysis of mutations/polymorphisms using capillary array electrophoresis.

We present a high-throughput single-strand conformation polymorphism (SSCP) method, performed on a commercially available capillary array DNA sequencer. We tested various sieving matrices and electrophoretic conditions, using 51 DNA fragments which included 45 fragments carrying only one single nucleotide polymorphism (SNP), 4 fragments having two SNPs and 2 fragments with insertion or deletion. Resolution of alleles was improved by increasing concentrations of both sieving matrices and buffers, and all examined polymorphisms of DNA fragments were detected, most of them (45 fragments) as clearly split allele peaks in heterozygotes. Allele frequencies of SNPs can be estimated accurately by determining the relative amounts of alleles in pooled DNA. In this method, the turn-around time for the analysis of 96 samples is less than 3 h. These results demonstrate that capillary array-based SSCP is an efficient and accurate technique for the large-scale quantitative analysis of mutations/polymorphisms.

DNA Mutational Analysis↗
PubMed2002

Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA).

PCR single-stranded conformational polymorphism (SSCP) analysis is a simple and rapid electrophoretic technique for the sensitive detection of sequence variants of PCR products. Here we describe a cross-platform program package, quantitative interpretation of SSCP in capillary array (QUISCA), which allows semi-automated quantitative detection of sequence variants separated by multicolor fluorescence-based SSCP electrophoresis using various capillary array apparatus. The program, together with the QUISCAview as a graphical user interface, takes trace data in ASCII format and processes them with three modules: signal denoising/baseline subtraction, color-matrix construction/application, and calibration of peak positions between multiple capillary runs using internal standard peaks. QUISCA is compatible with data from various widely used capillary array sequencers and is suitable not only for finding or typing SNPs in individual DNAs but also for the accurate estimation of the allele frequencies of many SNPs using a pooled DNA strategy. QUISCA can also serve as a versatile core program for various fragment analyses.

Algorithms↗