OBJECTIVES: To derive the probability equation given by STR allele frequencies of identity by state （IBS） score shared by unrelated individual pairs. METHODS: By comparing the STR genotypes of two unrelated individuals, three mutually exclusive combinations could be obtained： （1） sharing 2 identical alleles, a₂=1, otherwise a₂=0; （2） sharing 1 identical allele, a₁=1, otherwise a₁=0; （3） sharing 0 identical allele, a₀=1, otherwise a₀=0. And the IBS score of the one STR locus in this unrelated individual pair could be given by the formula： ibs=2a₂+a₁. The probability of a₂=1 （p₂）, a₁=1 （p₁） and a₀=1 （p₀） were derived and expressed in powers of the allele frequencies. Subsequently, for a genotyping system including n independent STR loci, the characteristics of binomial distribution of IBS score shared by a pair of unrelated individuals could be given by p₂_l and p₁_l （l=1, 2, …, n）. RESULTS: All the general equations of p₂, p₁ and p₀ were derived from the basic conceptions of a₂, a₁ and a₀, respectively. Given f_i （i=1, 2, …, m） as the ith allele frequency of a STR locus, the general equations of p₂, p₁ and p₀ could be respectively expressed in powers of f_i： [Formula: see text],[Formula: see text] and [Formula: see text]. The sum of p₂, p₁ and p₀ must be equal to 1. Then, the binomial distribution of IBS score shared by unrelated individual pairs genotyped with n independently STR loci could be written by： IBS~B（2n, π）, and the general probability, π, could be given by the formula： [Formula: see text]. CONCLUSIONS In the biological full sibling identification, the probability of null hypothesis corresponding to any specific IBS score can be directly calculated by the general equations presented in this study, which is the basement of the evidence explanation.
Alleles ; Forensic Genetics ; Gene Frequency ; Genotype ; Humans ; Irritable Bowel Syndrome/genetics* ; Microsatellite Repeats ; Probability ; Siblings

Objective To derive the general equation of the probability distribution of identity by state （IBS） score among biological full sibling pairs by calculating STR allele frequency. Methods Based on the Mendelian genetics law and the hypothesis that parents of biological full siblings （FS） were unrelated individuals, the IBS score and corresponding probability of different genotype combinations in the offspring when unrelated individuals of different genotype combinations give birth to two offsprings were derived. Results Given f_i （i=1, 2, …, m） as the frequency of the ith allele of a STR locus, the probability of sharing 2 alleles （p2FS）, 1 allele （p1FS） or 0 allele （p0FS） with biological full sibling pairs on the locus can be respectively expressed as follows： (see the text). The sum of p2FS, p1FS and p0FS must be 1. As for the multiple genotyping system that contained n STR loci, IBS scores between biological full sibling pairs conform to binomial distribution： IBS~B（2n, π1）. The population rate π1, can be given by the formula： (see the text). Conclusion The alternative hypothesis in biological full sibling testing is that two appraised individuals are biological full siblings. The probability of the corresponding alternative hypothesis of any STR locus combination or IBS score can be directly calculated by the equations presented in this study, and the calculation results are the basis for explanations of the evidence.
Alleles ; Forensic Genetics ; Gene Frequency ; Genotype ; Humans ; Irritable Bowel Syndrome/genetics* ; Probability ; Siblings

OBJECTIVES: To establish a query table of IBS critical value and identification power for the detection systems with different numbers of STR loci under different false judgment standards. METHODS: Samples of 267 pairs of full siblings and 360 pairs of unrelated individuals were collected and 19 autosomal STR loci were genotyped by Goldeneye™ 20A system. The full siblings were determined using IBS scoring method according to the 'Regulation for biological full sibling testing'. The critical values and identification power for the detection systems with different numbers of STR loci under different false judgment standards were calculated by theoretical methods. RESULTS: According to the formal IBS scoring criteria, the identification power of full siblings and unrelated individuals was 0.764 0 and the rate of false judgment was 0. The results of theoretical calculation were consistent with that of sample observation. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci was successfully established. CONCLUSIONS The IBS scoring method defined by the regulation has high detection efficiency and low false judgment rate, which provides a relatively conservative result. The query table of IBS critical value for identification of full sibling detection systems with different numbers of STR loci provides an important reference data for the result judgment of full sibling testing and owns a considerable practical value.
Alleles ; Genotype ; Humans ; Irritable Bowel Syndrome/genetics* ; Reproducibility of Results ; Research Design ; Siblings

OBJECTIVES: To compare the application value of the likelihood ratio (LR) method and identity by state (IBS) method in the identification involving half sibling relationships, and to provide a reference for the setting of relevant standards for identification of half sibling relationship. METHODS: (1) Based on the same genetic marker combinations, the reliability of computer simulation method was verified by comparing the distributions of cumulated identity by state score (CIBS) and combined full sibling index in actual cases with the distributions in simulated cases. (2) In different numbers of three genetic marker combinations, the simulation of full sibling, half sibling and unrelated individual pairs, each 1 million pairs, was obtained; the CIBS, as well as the corresponding types of cumulative LR parameters, were calculated. (3) The application value of LR method was compared with that of IBS method, by comparing the best system efficiency provided by LR method and IBS method when genetic markers in different amounts and of different types and accuracy were applied to distinguish the above three relational individual pairs. (4) According to the existing simulation data, the minimum number of genetic markers required to distinguish half siblings from the other two relationships using different types of genetic markers was estimated by curve fitting. RESULTS: (1) After the rank sum test, under the premise that the real relationship and the genetic marker combination tested were the same, there was no significant difference between the simulation method and the results obtained in the actual case. (2) In most cases, under the same conditions, the system effectiveness obtained by LR method was greater than that by IBS method. (3) According to the existing data, the number of genetic markers required for full-half siblings and half sibling identification could be obtained by curve fitting when the system effectiveness reached 0.95 or 0.99. CONCLUSIONS When distinguishing half sibling from full sibling pairs or unrelated pairs, it is recommended to give preference to the LR method, and estimate the required number of markers according to the identification types and the population data, to ensure the identification effect.
Humans ; Siblings ; Genetic Markers ; Computer Simulation ; Irritable Bowel Syndrome/genetics* ; Reproducibility of Results ; Genotype

Blastocystis is a common unicellular intestinal protozoa in humans and animals, and the most common clinical manifestations of infections include abdominal pain and diarrhea. Based on the sequence of the small-subunit ribosomal RNA (SSU rRNA) gene, 28 subtypes of B. hominis (ST1 to ST17, ST21 and ST23 to ST32) have been characterized. Previous studies have demonstrated that B. hominis infection is strongly associated with inflammatory bowel disease (IBD), irritable bowel syndrome (IBS) and other intestinal diseases, which threatens the health and quality of life among patients with B. hominis infection and is considered as an important public health problem. This review summarizes the progress of researches on B. hominis infection among IBD and IBS patients during the past 20 years, so as to provide insights into management of blastocystosis in China.
Animals ; Humans ; Irritable Bowel Syndrome/parasitology* ; Blastocystis Infections/complications* ; Quality of Life ; Blastocystis hominis/genetics* ; Feces/parasitology* ; Inflammatory Bowel Diseases/parasitology*

BACKGROUND: Irritable bowel syndrome (IBS) is reported associated with the alteration of gut microbial composition termed as dysbiosis. However, the pathogenic mechanism of IBS remains unclear, while the studies of Chinese individuals are scarce. This study aimed to understand the concept of dysbiosis among patients with Chinese diarrhea-predominant IBS (IBS-D), as a degree of variance between the gut microbiomes of IBS-D population and that of a healthy population. METHODS: The patients with IBS-D were recruited (assessed according to the Rome III criteria, by IBS symptom severity score) from the Outpatient Department of Gastroenterology of Peking University Third Hospital, and volunteers as healthy controls (HCs) were enrolled, during 2013. The 16S rRNA sequences were extracted from fecal samples. Ribosomal database project resources, basic local alignment search tool, and SparCC software were used to obtain the phylotype composition of samples and the internal interactions of the microbial community. Herein, the non-parametric test, Wilcoxon rank-sum test was carried out to find the statistical significance between HC and IBS-D groups. All the P values were adjusted to q values to decrease the error rate. RESULTS: The study characterized the gut microbiomes of Chinese patients with IBS-D, and demonstrated that the dysbiosis could be characterized as directed alteration of the microbiome composition leading to greater disparity between relative abundance of two phyla, Bacteroidetes (Z = 4.77, q = 1.59 × 10) and Firmicutes (Z = -3.87, q = 5.83 × 10). Moreover, it indicated that the IBS symptom features were associated with the dysbiosis of whole gut microbiome, instead of one or several certain genera even they were dominating. Two genera, Bacteroides and Lachnospiracea incertae sedis, were identified as the core genera, meanwhile, the non-core genera contribute to a larger pan-microbiome of the gut microbiome. Furthermore, the dysbiosis in patients with IBS-D was associated with a reduction of network complexity of the interacted microbial community (HC vs. IBS-D: 639 vs. 154). The disordered metabolic functions of patients with IBS-D were identified as the potential influence of gut microbiome on the host (significant difference with q < 0.01 between HC and IBS-D). CONCLUSIONS This study supported the view of the potential influence of gut microbiome on the symptom of Chinese patients with IBS-D, and further characterized dysbiosis in Chinese patients with IBS-D, thus provided more pathological evidences for IBS-D with the further understanding of dysbiosis.
Diarrhea ; microbiology ; Dysbiosis ; microbiology ; Feces ; microbiology ; Gastrointestinal Microbiome ; genetics ; Humans ; Irritable Bowel Syndrome ; microbiology ; Models, Theoretical ; RNA, Ribosomal, 16S ; genetics

OBJECTIVE: To compare the curative effect on diarrhea-predominant irritable bowel syndrome (IBS-D) between acupuncture for regulating METHODS: A total of 231 patients with IBS-D were randomized into an acupuncture group (154 cases) and a western medication group (77 cases) at the ratio of 2 to 1. In the acupuncture group, acupuncture was applied to acupoint regimen for regulating RESULTS: After treatment and in follow-up, the total scores of IBS-SSS in the patients of the two groups were all reduced as compared with those before treatment ( CONCLUSION Acupuncture for regulating
Acupuncture Therapy ; Diarrhea/therapy* ; Humans ; Irritable Bowel Syndrome/therapy* ; Quality of Life ; Serotonin Plasma Membrane Transport Proteins/genetics* ; Spleen ; Treatment Outcome

BACKGROUND/AIMS: Serotonin is thought to be an important neurotransmitter in the pathogenesis of irritable bowel syndrome (IBS). It is reported that functional polymorphism in the promotor region of the serotonin transporter gene is related with the subtypes of IBS and shows racial difference. However, a functional relation between polymorphism and IBS is not clear. The aim of this study was to investigate 5-hydroxytryptamine transporter (5-HTT) gene polymorphism in patients with IBS. METHODS: For fifty-six healthy controls and 33 patients with IBS fulfilling Rome II criteria, 5'-flank promotor region of 5-HTT gene was analyzed by polymerase chain reaction. RESULTS: The genotypes of healthy controls were S/S (57.1%), S/L (37.5%), and L/L (5.4%). Those of IBS patients were S/S (54.5%), S/L (36.4%), and L/L (9.1%). IBS patients were divided into three groups: diarrhea predominant (n=15; S/S, 40%; S/L, 53.3%; L/L, 6.7%), constipation predominant (n=12; S/S, 75.0%; S/L, 8.3%; L/L, 16.7%), diarrhea-constipation alternating type (n=6; S/S, 50%; S/L, 50%). There was no statistical difference in the 5-HTT gene polymorphism between patients and controls, and according to the subtypes of IBS patients (p=0.135). CONCLUSIONS: There was no relationship between serotonin transporter gene polymorphism and IBS. However, allele S/S genotype was most prominent genotype in both controls and patients.
Adult ; English Abstract ; Female ; Humans ; Irritable Bowel Syndrome/*genetics ; Male ; Membrane Glycoproteins/*genetics ; Membrane Transport Proteins/*genetics ; Middle Aged ; Nerve Tissue Proteins/*genetics ; *Polymorphism, Genetic ; Serotonin/genetics

OBJECTIVE: To observe the effect of electroacupuncture (EA) at "Tianshu" (ST 25) and "Shangjuxu" (ST 37) on mental state, visceral sensitivity and protein expression of nerve growth factor (NGF), tyrosine kinase receptor A (TrkA) and transient receptor potential vanilloid 1 (TRPV1) of colonic tissue in diarrhea-predominant irritable bowel syndrome (IBS-D) rats, and to explore its possible mechanism on treating IBS-D. METHODS: A total of 36 male SD rats of SPF grade were randomized into a blank group, a model group, an EA group and a western medication group, 9 rats in each group. In the model group, the EA group and the western medication group, IBS-D model was established by enema of dinitrobenzene sulfonic acid (DNBS) combined with chronic restraint stress method. In the EA group, EA was applied at "Tianshu" (ST 25) and "Shangjuxu" (ST 37), with disperse-dense wave, in frequency of 2 Hz/100 Hz, 20 min each time, once a day for 7 days. In the western medication group, pinaverium bromide suspension was given by gavage (15 mg•kg^-1•d^-1) for 7 days. Before and after model establishment, and after intervention, the body mass, 24 h food intake and fecal water content were observed, the visceral sensitivity was detected by abdominal withdrawal reflex (AWR); after intervention, the mental state was evaluated by elevated plus maze (EPM) test, the protein expression of NGF, TrkA and TRPV1 was detected by immunohistochemistry and Western blot in the 4 groups. RESULTS: After model establishment, compared with the blank group, the body mass and 24 h food intake were decreased (P<0.05), first systolic latency of AWR was shortened and number of contraction wave of AWR was increased (P<0.05), and fecal water content was increased (P<0.05) in the model group, the EA group and the western medication group. After intervention, compared with the blank group, open arm residence time ratio (OT%) of EPM was decreased (P<0.05) and protein expression of NGF, TrkA, TRPV1 in colonic tissue was increased in the model group (P<0.05); compared with the model group, the body mass and 24 h food intake were increased (P<0.05), first systolic latency of AWR was lengthened and number of contraction wave of AWR was decreased (P<0.05), the fecal water content was decreased (P<0.05), OT% of EPM was increased (P<0.05), and protein expression of NGF, TrkA, TRPV1 in colonic tissue was decreased (P<0.05) in the EA group and the western medication group. CONCLUSION Electroacupuncture at "Tianshu" (ST 25) and "Shangjuxu" (ST 37) can relieve the anxiety and depression-like behaviors in IBS-D rats, down-regulate the protein expression of NGF, TrkA, TRPV1 in colonic tissue, so as to reduce the visceral sensitivity and relieve symptoms.
Male ; Rats ; Animals ; Receptor Protein-Tyrosine Kinases ; Rats, Sprague-Dawley ; Irritable Bowel Syndrome/therapy* ; Sulfonic Acids ; Nerve Growth Factors ; TRPV Cation Channels/genetics*

OBJECTIVE: To assess whether the same biological conclusion, diagnostic or curative effects regarding microbial composition of irritable bowel syndrome (IBS) patients could be reached through different bioinformatics pipelines, we used two common bioinformatics pipelines (Uparse V2.0 and Mothur V1.39.5)to analyze the same fecal microbial 16S rRNA high-throughput sequencing data. METHODS: The two pipelines were used to analyze the diversity and richness of fecal microbial 16S rRNA high-throughput sequencing data of 27 samples, including 9 healthy controls (HC group), 9 diarrhea IBS patients before (IBS group) and after Rifaximin treatment (IBS-treatment, IBSt group). Analyses such as microbial diversity, principal co-ordinates analysis (PCoA), nonmetric multidimensional scaling (NMDS) and linear discriminant analysis effect size (LEfSe) were used to find out the microbial differences among HC group vs. IBS group and IBS group vs. IBSt group. RESULTS: (1) Microbial composition comparison of the 27 samples in the two pipelines showed significant variations at both family and genera levels while no significant variations at phylum level; (2) There was no significant difference in the comparison of HC vs. IBS or IBS vs. IBSt (Uparse: HC vs. IBS, F=0.98, P=0.445; IBS vs. IBSt, F=0.47,P=0.926; Mothur: HC vs.IBS, F=0.82, P=0.646; IBS vs. IBSt, F=0.37, P=0.961). The Shannon index was significantly decreased in IBSt; (3) Both workshops distinguished the significantly enriched genera between HC and IBS groups. For example, Nitrosomonas and Paraprevotella increased while Pseudoalteromonadaceae and Anaerotruncus decreased in HC group through Uparse pipeline, nevertheless Roseburia 62 increased while Butyricicoccus and Moraxellaceae decreased in HC group through Mothur pipeline.Only Uparse pipeline could pick out significant genera between IBS and IBSt, such as Pseudobutyricibrio, Clostridiaceae 1 and Clostridiumsensustricto 1. CONCLUSION There were taxonomic and phylogenetic diversity differences between the two pipelines, Mothur can get more taxonomic details because the count number of each taxonomic level is higher. Both pipelines could distinguish the significantly enriched genera between HC and IBS groups, but Uparse was more capable to identity the difference between IBS and IBSt groups. To increase the reproducibility and reliability and to retain the consistency among similar studies, it is very important to consider the impact on different pipelines.
Case-Control Studies ; Computational Biology ; DNA, Bacterial/analysis* ; Diarrhea ; Feces ; Gastrointestinal Microbiome/genetics* ; Humans ; Irritable Bowel Syndrome/microbiology* ; Phylogeny ; RNA, Ribosomal, 16S ; Reproducibility of Results ; Rifamycins ; Rifaximin