Background/Aims: This study aims to investigate the effect of a fermented rice drink with Lactiplantibacillus plantarum JSA22 on symptoms, blood tests, microbiomes, and fecal metabolites in patients with irritable bowel syndrome (IBS) who were overweight. Methods: Sixty overweight (body mass index ≥ 23 kg/m2 ) patients aged between 20 and 65 with IBS were enrolled. Patients were divided into 2 groups and administered either a fermented rice drink or an nonfermented rice drink for a month. The symptom questionnaire, blood samples, and stool samples for microbiome and metabolite were collected before and after the month of rice drink administration.The primary efficacy variable was the subject’s global assessment of IBS symptoms. Results: In both groups, global IBS symptoms, including abdominal pain, bowel habit, urgency, and abdominal distension, improved significantly (P < 0.01). The abdominal bloating was more significantly improved in the fermented rice drink group than in the nonfermented rice drink group (P < 0.05). Significant changes were not observed in metabolic syndrome-related blood tests or fecal metabolites in either group. However, microbiome analysis showed significant differences in genus levels before and after consuming fermented rice drink, such as in Blautia in stool (P = 0.020) and Prevotella (P = 0.017) and Oribacterium (P = 0.018) in saliva. Conclusions The fermented rice drink with L. plantarum JSA22 showed a beneficial effect in reducing abdominal distension in IBS patients. Bacteria that reduce visceral fat accumulation increased in the stool and saliva of patients who consumed fermented rice drinks.

BACKGROUND: Research on next-generation sequencing (NGS)-based HLA typing is active. To resolve the phase ambiguity and long turn-around-time of conventional high resolution HLA typing, this study developed a NGS-based high resolution HLA typing method that can handle large-scale samples within an efficient testing time. METHODS: For HLA NGS, the condition of nucleic acid extraction, library construction, PCR mechanism, and HLA typing with bioinformatics were developed. To confirm the accuracy of the NGS-based HLA typing method, the results of 192 samples HLA typed by SSOP and 28 samples typed by SBT compared to NGS-based HLA-A, -B and -DR typing. RESULTS: DNA library construction through two-step PCR, NGS sequencing with MiSeq (Illumina Inc., San Diego, USA), and the data analysis platform were established. NGS-based HLA typing results were compatible with known HLA types from 220 blood samples. CONCLUSION: The NSG-based HLA typing method could handle large volume samples with high-throughput. Therefore, it would be useful for HLA typing of bone marrow donation volunteers.
Bone Marrow ; Computational Biology ; Gene Library ; Histocompatibility Testing ; HLA-A Antigens* ; Methods* ; Polymerase Chain Reaction ; Statistics as Topic ; Volunteers

PURPOSE: To evaluate the performance of the Momguard noninvasive prenatal test by tracing the 'screen positive' results based on preliminary samples from Korean cohorts. MATERIALS AND METHODS: This preliminary study is based on data collected by the LabGenomics Clinical Laboratory (Seongnam, Korea) with informed consent. Only pregnant women who underwent both the Momguard test and karyotyping were included in this study. Momguard test results were compared with those of the karyotyping analysis. RESULTS: Among the 38 cases with 'screen positive' results by Momguard, 30 cases also had karyotyping results available. In three trisomy (T) 18 and three T13 cases, the Momguard results were concordant with the karyotyping results. For the T21 cases, except for one case belonging to the mid-risk zone, Momguard results from 23 out of 24 cases matched the karyotyping results. CONCLUSION: Momguard is a highly reliable screening tool for detecting T13, T18, and T21 cases in independent Korean cohort samples.
Aneuploidy ; Cohort Studies ; Down Syndrome ; Female ; Humans ; Informed Consent ; Karyotyping ; Mass Screening ; Pregnant Women ; Prenatal Diagnosis ; Trisomy

Lung cancer in never-smokers ranks as the seventh most common cause of cancer death worldwide, and the incidence of lung cancer in non-smoking Korean women appears to be steadily increasing. To identify the effect of genetic polymorphisms on lung cancer risk in non-smoking Korean women, we conducted a genome-wide association study of Korean female non-smokers with lung cancer. We analyzed 440,794 genotype data of 285 cases and 1,455 controls, and nineteen SNPs were associated with lung cancer development (P < 0.001). For external validation, nineteen SNPs were replicated in another sample set composed of 293 cases and 495 controls, and only rs10187911 on 2p16.3 was significantly associated with lung cancer development (dominant model, OR of TG or GG, 1.58, P = 0.025). We confirmed this SNP again in another replication set composed of 546 cases and 744 controls (recessive model, OR of GG, 1.32, P = 0.027). OR and P value in combined set were 1.37 and < 0.001 in additive model, 1.51 and < 0.001 in dominant model, and 1.54 and < 0.001 in recessive model. The effect of this SNP was found to be consistent only in adenocarcinoma patients (1.36 and < 0.001 in additive model, 1.49 and < 0.001 in dominant model, and 1.54 and < 0.001 in recessive model). Furthermore, after imputation with HapMap data, we found regional significance near rs10187911, and five SNPs showed P value less than that of rs10187911 (rs12478012, rs4377361, rs13005521, rs12475464, and rs7564130). Therefore, we concluded that a region on chromosome 2 is significantly associated with lung cancer risk in Korean non-smoking women.
Adenocarcinoma/*genetics/pathology ; Adult ; Aged ; Asian Continental Ancestry Group/*genetics ; Cell Adhesion Molecules, Neuronal/*genetics ; Chromosomes, Human, Pair 2 ; Female ; *Genome-Wide Association Study ; Genotype ; Humans ; Logistic Models ; Lung Neoplasms/*genetics/pathology ; Models, Genetic ; Nerve Tissue Proteins/*genetics ; Odds Ratio ; Polymorphism, Single Nucleotide ; Republic of Korea

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.
Asian Continental Ancestry Group ; Cataloging ; Coat Protein Complex I ; Genome ; Humans

Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.
Bayes Theorem ; Coat Protein Complex I ; DNA Copy Number Variations ; Ethnic Groups ; Gene Frequency ; Genome ; Humans ; Markov Chains ; Selection, Genetic

Large-scale copy number variants (CNVs) in the human provide the raw material for delineating population differences, as natural selection may have affected at least some of the CNVs thus far discovered. Although the examination of relatively large numbers of specific ethnic groups has recently started in regard to inter-ethnic group differences in CNVs, identifying and understanding particular instances of natural selection have not been performed. The traditional FST measure, obtained from differences in allele frequencies between populations, has been used to identify CNVs loci subject to geographically varying selection. Here, we review advances and the application of multinomial-Dirichlet likelihood methods of inference for identifying genome regions that have been subject to natural selection with the FST estimates. The contents of presentation are not new; however, this review clarifies how the application of the methods to CNV data, which remains largely unexplored, is possible. A hierarchical Bayesian method, which is implemented via Markov Chain Monte Carlo, estimates locus-specific FST and can identify outlying CNVs loci with large values of FST. By applying this Bayesian method to the publicly available CNV data, we identified the CNV loci that show signals of natural selection, which may elucidate the genetic basis of human disease and diversity.
Bayes Theorem ; Coat Protein Complex I ; DNA Copy Number Variations ; Ethnic Groups ; Gene Frequency ; Genome ; Humans ; Markov Chains ; Selection, Genetic

Although the genetic component in the etiology of rheumatoid arthritis (RA) has been consistently suggested, many novel genetic loci remain to uncover. To identify RA risk loci, we performed a genome-wide association study (GWAS) with 100 RA cases and 600 controls using Affymetrix SNP array 5.0. The candidate risk locus (APOM gene) was re-sequenced to discover novel promoter and coding variants in a group of the subjects. Replication was performed with the independent case-control set comprising of 578 RAs and 711 controls. Through GWAS, we identified a novel SNP associated with RA at the APOM gene in the MHC class III region on 6p21.33 (rs805297, odds ratio (OR) = 2.28, P = 5.20 x 10(-7)). Three more polymorphisms were identified at the promoter region of the APOM by the re-sequencing. For the replication, we genotyped the four SNP loci in the independent case-control set. The association of rs805297 identified by GWAS was successfully replicated (OR = 1.40, P = 6.65 x 10(-5)). The association became more significant in the combined analysis of discovery and replication sets (OR = 1.56, P = 2.73 +/- 10(-10)). The individuals with the rs805297 risk allele (A) at the promoter region showed a significantly lower level of APOM expression compared with those with the protective allele (C) homozygote. In the logistic regressions by the phenotype status, the homozygote risk genotype (A/A) consistently showed higher ORs than the heterozygote one (A/C) for the phenotype-positive RAs. These results indicate that APOM promoter polymorphisms are significantly associated with the susceptibility to RA.
Apolipoproteins/*genetics ; Arthritis, Rheumatoid/*genetics ; Case-Control Studies ; DNA/genetics ; Female ; *Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; Heterozygote ; Homozygote ; Humans ; Lipocalins/*genetics ; Luciferases/metabolism ; Male ; Middle Aged ; Polymorphism, Single Nucleotide/*genetics ; Promoter Regions, Genetic/*genetics ; Real-Time Polymerase Chain Reaction ; Risk Factors

BACKGROUND/AIMS: Helicobacter pylori causes extragastric manifestations, including dyslipidemia and metabolic syndrome. However the effects of eradication of H. pylori infection on dyslipidemia and metabolic syndrome have shown conflicting results. We aimed to investigate the effect of eradication therapy on parameters of dyslipidemia and metabolic syndrome and prevalence of metabolic syndrome. MATERIALS AND METHODS: Subjects who received eradication therapy between August 2004 and June 2010 and who underwent health checkup one year after eradication were enrolled in this study. Parameters of dyslipidemia and metabolic syndrome before and after eradication were collected and tested for significant changes. Prevalence of metabolic syndrome before eradication was also compared with that after treatment. RESULTS: Of the 452 subjects enrolled, 324 subjects were males. In male, HDL cholesterol was significantly elevated after eradication treatment in both young (< or =50) and old (>50) age group. Other metabolic parameters such as waist circumference, body mass index, total cholesterol, triglyceride, LDL cholesterol, fasting glucose, systolic and diastolic blood pressure, and c-reactive protein were not significantly different after eradication in both age group. In female, triglyceride increased significantly and HDL cholesterol decreased after eradication in the old age group. But in the young age female group all the metabolic parameters showed no changes. There were no significant changes in prevalence of metabolic syndrome after eradication treatment in both genders. CONCLUSIONS: Helicobacter eradication caused elevation of HDL cholesterol in males. Eradication therapy showed no effect on prevalence of metabolic syndrome.
Blood Pressure ; Body Mass Index ; C-Reactive Protein ; Cholesterol ; Cholesterol, HDL ; Cholesterol, LDL ; Dyslipidemias ; Fasting ; Female ; Glucose ; Helicobacter ; Helicobacter pylori ; Humans ; Lipoproteins ; Male ; Metabolic Syndrome X ; Prevalence ; Waist Circumference

OBJECTIVE: We wanted to evaluate the image quality, diagnostic accuracy and radiation exposure of 64-slice dual-source CT (DSCT) coronary angiography according to the heart rate in symptomatic patients during daily clinical practice. MATERIALS AND METHODS: We performed a retrospective search for the DSCT coronary angiography reports of 729 consecutive symptomatic patients. For the 131 patients who underwent invasive coronary angiography, the image quality, the diagnostic performance (sensitivity, specificity, positive predictive value [PPV] and negative predictive value [NPV] for detecting significant stenosis > or = 50% diameter) and the radiation exposure were evaluated. These values were compared between the groups with differing heart rates (HR): mean HR < 65 or > or = 65 and HR variability (HRV) < 15 or > or = 15. RESULTS: Among the 729 patients, the CT reports showed no stenosis or insignificant coronary artery stenosis in 72%, significant stenosis in 26% and non-diagnostic in 2%. For the 131 patients who underwent invasive coronary angiography, 95% of the patients and 97% of the segments were evaluable, and the overall per-patient/per-segment sensitivity, the perpatient/per-segment specificity, the per-patient/per-segment PPV and the per-patient/per-segment NPV were 100%/90%, 71%/98%, 95%/88% and 100%/97%, respectively. The image quality was better in the HR < 65 group than in the HR > or = 65 group (p = 0.001), but there was no difference in diagnostic performance between the two groups. The mean effective radiation doses were lower in the HR < 65 or HRV < 15 group (p < 0.0001): 5.5 versus 6.7 mSv for the mean HR groups and 5.3 versus 9.3 mSv for the HRV groups. CONCLUSION: Dual-source CT coronary angiography is a highly accurate modality in the clinical setting. Better image quality and a significant radiation reduction are being rendered in the lower HR group.
Adult ; Aged ; Aged, 80 and over ; Artifacts ; Contrast Media/diagnostic use ; Coronary Angiography/*methods ; Coronary Stenosis/*radiography ; Female ; Humans ; Imaging, Three-Dimensional ; Male ; Middle Aged ; Predictive Value of Tests ; Quality Assurance, Health Care ; Radiation Dosage ; Radiographic Image Interpretation, Computer-Assisted/methods ; Retrospective Studies ; Sensitivity and Specificity ; Tomography, X-Ray Computed/*methods