7 research outputs found

    Rapid SNP diagnostics using asymmetric isothermal amplification and a new mismatch-suppression technology. Nature Methods

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    We developed a rapid single nucleotide polymorphism (SNP) detection system named smart amplification process version 2 (SMAP 2). Because DNA amplification only occurred with a perfect primer match, amplification alone was sufficient to identify the target allele. To achieve the requisite fidelity to support this claim, we used two new and complementary approaches to suppress exponential background DNA amplification that resulted from mispriming events. SMAP 2 is isothermal and achieved SNP detection from whole human blood in 30 min when performed with a new DNA polymerase that was cloned and isolated from Alicyclobacillus acidocaldarius (Aac pol). Furthermore, to assist the scientific community in configuring SMAP 2 assays, we developed software specific for SMAP 2 primer design. With these new tools, a high-precision and rapid DNA amplification technology becomes available to aid in pharmacogenomic research and molecular-diagnostics applications. The availability of the human genome sequence 1,2 and genome diversity databases 3-5 at the beginning of the 21 st century are causing a paradigm shift away from the standard protocol of medical care toward genotyped medicine. This new type of medicine is based on the accumulating knowledge of gene polymorphisms (SNPs) and their relationship to specific phenotypes, such as disease predisposition, drug metabolism and disease development. A key step for the development of individualized medicine is the ability to rapidly test patients for these SNPs and/or other mutations correlated to diseases and disease predisposition. Supporting this point, the US Food and Drug Administration has required the drug industry to publicly provide SNP data examined in the process of procuring a drug license. Today SNP genotyping technologies 6-9 are still a bottleneck in drug discovery research and clinical applications. But high-throughput gene analysis and SNP detection technologies will inevitably become both cheaper and faster in the future. Besides SNP genotyping, these improved sequence-detection technologies would also allow and advance studies in other disciplines such as population genetics, the global surveillance of infectious disease and the study of somatic mutations in human cancer. Almost all previously developed SNP-detection systems consist of two steps: amplification (usually by PCR) and detection of SNP (using DNA fragments amplified in the first step). This approach is reasonably fast, but to shorten the time required and simplify the detection, it is ideal to develop a one-step method, in which the amplification itself can be the SNP detection signal. The difficulty in developing such a technology is in the suppression of the background amplification. For example, primers for allele-specific primer PCR are designed with the nucleotide mismatch at the 3¢ end of the PCR primers, but the misamplified PCR products primed from mismatched primers are still exponentially amplified, producing background signals that must be addressed. Here we report SMAP 2, the first rapid one-step SNP detection technology in which the amplification of the targeted DNA is the signal of the target SNP itself

    Empagliflozin in Patients with Chronic Kidney Disease

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    Background The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients. Methods We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m(2) of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m(2) with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to < 10 ml per minute per 1.73 m(2), a sustained decrease in eGFR of & GE;40% from baseline, or death from renal causes) or death from cardiovascular causes. Results A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P < 0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P=0.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups. Conclusions Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo
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