SNP-RFLPing: restriction enzyme mining for SNPs in genomes

BACKGROUND: The restriction fragment length polymorphism (RFLP) is a common laboratory method for the genotyping of single nucleotide polymorphisms (SNPs). Here, we describe a web-based software, named SNP-RFLPing, which provides the restriction enzyme for RFLP assays on a batch of SNPs and genes from the human, rat, and mouse genomes. RESULTS: Three user-friendly inputs are included: 1) NCBI dbSNP "rs" or "ss" IDs; 2) NCBI Entrez gene ID and HUGO gene name; 3) any formats of SNP-in-sequence, are allowed to perform the SNP-RFLPing assay. These inputs are auto-programmed to SNP-containing sequences and their complementary sequences for the selection of restriction enzymes. All SNPs with available RFLP restriction enzymes of each input genes are provided even if many SNPs exist. The SNP-RFLPing analysis provides the SNP contig position, heterozygosity, function, protein residue, and amino acid position for cSNPs, as well as commercial and non-commercial restriction enzymes. CONCLUSION: This web-based software solves the input format problems in similar softwares and greatly simplifies the procedure for providing the RFLP enzyme. Mixed free forms of input data are friendly to users who perform the SNP-RFLPing assay. SNP-RFLPing offers a time-saving application for association studies in personalized medicine and is freely available at

V-MitoSNP: visualization of human mitochondrial SNPs

BACKGROUND: Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs) is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved. DESCRIPTION: V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1) color-coded visual input by selecting genes of interest on the genome graph, (2) keyword search by locus, disease and mtSNP rs# ID, (3) visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4) sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs) flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP. CONCLUSION: V-MitoSNP is a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies

Can probability of genetic mutation be an indicator of clinical relevance?

AbstractNPM1 gene mutation evaluated on a population basis is a valuable and realistic tool to reflect the pathophysiological relevance of cancer. In a comparison of the NPM1 cDNA of human bladder cancer with its consensus sequence, we have found that a higher NPM1 sequence identity in a population is consistent with poor tumor differentiation, advanced tumor stage, and likelihood of recurrence. These data imply that “probability” of NPM1 mutation is an indicator of status of malignancy

Impact of the static prostatic urethral angle on men with lower urinary tract symptoms

Objective: The purpose of this study was to investigate the relationship between the prostatic urethral angle (PUA) and the peak urinary flow rate (Qmax), as well as the severity of lower urinary tract symptoms (LUTS) in men with benign prostate hyperplasia. Materials and methods: The records of first-visit male patients with LUTS in the outpatient department of our institution were obtained. A transrectal ultrasound was performed on these patients after a detailed physical examination and medical history taking were performed. The International Prostate Symptom Score (IPSS) of the patients, the prostate size, the length of intravesical prostatic protrusion (IPP), and the PUA were evaluated. The patients also underwent uroflowmetry and bladder scan for residual urine. Results: A total of 227 patients were included in this study. The mean PUA was 44.58 ± 12.87°. The mean prostate volume was 39.39 ± 19.79 mL, and the mean IPP was 4.82 ± 6.82 mm. After utilizing multivariate linear regression analysis, PUA was independently associated with IPSS (p < 0.001) and Qmax (p < 0.001). However, prostate volume and IPP were not associated with the above clinical items. None of the prostatic parameters were associated with the amount of postvoiding residual urine. Conclusion: PUA has a remarkable correlation with Qmax and IPSS in men with LUTS. As PUA increased, IPSS also increased, and urinary flow rate decreased, exhibiting an inverse relationship