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

Prostatectomy using different lasers for the treatment of benign prostate hyperplasia in aging males

PURPOSE: Endoscopic lasers have become a treatment option for benign prostate hyperplasia (BPH). The study reported here sought to elucidate the benefits and drawbacks of different laser systems in the treatment of patients with BPH. METHODS: The study enrolled 741 patients diagnosed with lower urinary tract symptoms secondary to BPH during the period January 2005 to December 2011. The techniques used in the study were photoselective vaporization of the prostate, thulium laser prostatectomy, and diode laser prostatectomy. Patients were assigned to one of three groups according to the type of laser treatment they received. Outcomes were evaluated using the International Prostate Symptom Score (IPSS), quality of life, maximal urinary flow rate, post-voiding residual urine volume, and prostate-specific antigen (PSA) level. RESULTS: The baseline characteristics of patients who received diode laser prostatectomy show a significant elevated risk and high American Society of Anesthesiology score (P=0.001). Operative time and catheter removal time differed significantly between the three groups (P=0.001). No cases were converted to transurethral resection of the prostate intraoperatively due to bleeding (P=0.142). Among the three groups, there were no significant differences in maximal flow rate, lower post-void residual urine, and postoperative PSA level during the entire follow-up period (P<0.05). Further, no significant differences in postoperative IPSS, quality of life, or bladder neck contracture (P=0.23) were observed. However, a significant difference was observed with regard to prolonged use of Foley catheters and prolonged hospital stay among patients in the diode laser group (P=0.001). CONCLUSION: Laser prostatectomies are effective in dealing with lower urinary tract symptoms. Early subjective functional results (maximal flow rate, IPSS, and post-void residual urine) appeared the same as those obtained following laser prostatectomy. Thus, it appears that lasers are safe and effective as long as the patients are carefully selected for treatment

Neoadjuvant hormone therapy following treatment with robotic-assisted radical prostatectomy achieved favorable in high-risk prostate cancer

PURPOSE: Patients with a high risk of prostate carcinoma typically have higher rates of positive surgical margins and biochemical failure following radical prostatectomy and adjuvant hormone therapy. In this study, we assessed the effects of neoadjuvant hormone therapy (NHT) on prostate carcinoma in high-risk patients following robotic-assisted radical prostatectomy (RARP). METHODS: This retrospective study investigated the medical records of 28 patients who underwent RARP between January 2009 and October 2013. Twenty-two patients underwent NHT prior to RARP. Furthermore, six patients did not undergo NHT prior to RARP. Parameters including age, operating time, blood loss, blood transfusion status, and cancer stage were checked against anatomical correlations. Potential predictors of prolonged operating time and prolonged surgical procedures were assessed using multiple logistic regressions. RESULTS: NHT was shown to be an independent predictor of prolonged total operating time. Tumor stage alterations did not appear to be associated with NHT followed by RARP. The patients who underwent NHT were not more likely to have positive surgical margins, and an increase in patients requiring blood transfusion was not seen. CONCLUSION: NHT appears to increase operative time during RARP. However, the perioperative morbidity of NHT patients undergoing RARP appears to be equivalent with that of non-NHT patients

The outcome of a photoselective vaporization prostatectomy using a high-performance system to treat benign prostatic hyperplasia with acute urinary retention

AbstractObjectivePhotoselective vaporization of the prostate (PVP) is an easy-to-learn procedure which shows promise as an alternative to transurethral resection of the prostate (TURP) in treating acute urinary retention with benign prostatic hyperplasia (BPH). In this retrospective study, we evaluated the safety and efficacy of PVP in patients with urinary retention due to BPH.Materials and MethodsIn total, 48 male patients aged 60–87 (mean, 72) years were included in the study. Preoperative data, postoperative outcomes, and complications were recorded in patients with a history of urinary retention before surgery.ResultsThe average prostate volume was 59.2 (range, 41.71–120.1) mL. The respective preoperative prostate-specific antigen (PSA) level was 10.4 ng/mL, and the operative time was 45 (range, 30–90) min. The total applied laser energy ranged 60–120 (mean, 90 ± 25) kJ. The maximal urinary flow rate after surgery 14 mL/s, and the postvoided residual urine volume was 132 mL. Recorded surgical complications were hematuria in 10.4% and transient urinary retention in 8.3%.ConclusionPVP can improve the uroflow and peak flow rate in patients with urinary retention due to BPH with minimal postoperative discomfort and a low rate of complications

Robotic assisted laparoscopic radical cystectomy for bladder carcinoma: early experience and oncologic outcomes

SummaryAimsRobot-assisted radical cystectomy (RARC) has been a popular mode of therapy in the treatment of bladder carcinoma for several years, and its usage in bladder carcinoma patients is on the rise. We evaluated the usefulness of this mode of therapy by studying the clinical outcomes following RARC for the treatment of bladder carcinoma.MethodsFrom 2006 to 2011, a total of eight patients in our hospital who underwent RARC for bladder carcinomas were enrolled in this study. Clinical outcomes were measured by means of preoperative status, operative strategy and initial outcomes.ResultsFollow-up ranged from 4 to 22 months (mean 10.9 months). The mean operative time was 430.3 minutes, and the operative time decreased with the increasing experience of the surgeon and assistants. The mean estimated blood loss was 762.5 mL. The surgical approach was RARC and orthotopic ileal neobladder in five patients (62.5%), bilateral nephrectomy with RARC in two patients (25%), and RARC with ileal conduit alone in one patient (12.5%). Histological examination showed five instances of stage pT1 tumor, one pT2 tumor, and two instances of original tumor with extravesical disease (pT3b). One patient had lymph node involvement. Postoperative complications included urethral stricture in one case and vesicovaginal fistula in another. The mean hospital stay was 10.8 days (range 7–26 days). None of the patients had a positive surgical margin. There was no surgical mortality in this series.ConclusionRARC is a challenging but safe and minimally-invasive method of treating bladder carcinoma