Diagnostic accuracy of high resolution melting analysis for detection of KRAS mutations: a systematic review and meta-analysis.
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ABSTRACT:
SUBMITTER: Liu YP
PROVIDER: S-EPMC4268648 | biostudies-other | 2014 Dec
REPOSITORIES: biostudies-other
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Project description:The high-resolution melting curve analysis (HRMA) might be a good alternative method for rapid detection of BRAF mutations. However, the accuracy of HRMA in detection of BRAF mutations has not been systematically evaluated. We performed a systematic review and meta-analysis involving 1324 samples from 14 separate studies. The overall sensitivity of HRMA was 0.99 (95% confidence interval (CI) = 0.75-0.82), and the overall specificity was very high at 0.99 (95% CI = 0.94-0.98). The values for the pooled positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 68.01 (95% CI = 25.33-182.64), 0.06 (95% CI = 0.03-0.11), and 1263.76 (95% CI = 393.91-4064.39), respectively. The summary receiver operating characteristic curve for the same data shows an area of 1.00 and a Q* value of 0.97. The high sensitivity and specificity, simplicity, low cost, less labor or time and rapid turnaround make HRMA a good alternative method for rapid detection of BRAF mutations in the clinical practice.
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Project description:BackgroundKRAS mutational analysis is the standard of care prior to initiation of treatments targeting the epidermal growth factor receptor (EGFR) in patients with metastatic colorectal cancer. Sensitive methods are required to reliably detect KRAS mutations in tumor samples due to admixture with non-mutated cells. Many laboratories have implemented sensitive tests for KRAS mutations, but the methods often require expensive instrumentation and reagents, parallel reactions, multiple steps, or opening PCR tubes.MethodsWe developed a highly sensitive, single-reaction, closed-tube strategy to detect all clinically significant mutations in KRAS codons 12 and 13 using the Roche LightCycler® instrument. The assay detects mutations via PCR-melting curve analysis with a Cy5.5-labeled sensor probe that straddles codons 12 and 13. Incorporating a fast COLD-PCR cycling program with a critical denaturation temperature (Tc) of 81°C increased the sensitivity of the assay >10-fold for the majority of KRAS mutations.ResultsWe compared the COLD-PCR enhanced melting curve method to melting curve analysis without COLD-PCR and to traditional Sanger sequencing. In a cohort of 61 formalin-fixed paraffin-embedded colorectal cancer specimens, 29/61 were classified as mutant and 28/61 as wild type across all methods. Importantly, 4/61 (6%) were re-classified from wild type to mutant by the more sensitive COLD-PCR melting curve method. These 4 samples were confirmed to harbor clinically-significant KRAS mutations by COLD-PCR DNA sequencing. Five independent mixing studies using mutation-discordant pairs of cell lines and patient specimens demonstrated that the COLD-PCR enhanced melting curve assay could consistently detect down to 1% mutant DNA in a wild type background.ConclusionsWe have developed and validated an inexpensive, rapid, and highly sensitive clinical assay for KRAS mutations that is the first report of COLD-PCR combined with probe-based melting curve analysis. This assay significantly improved diagnostic accuracy compared to traditional PCR and direct sequencing.
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Project description:BackgroundHigh Resolution Melting Analysis (HRMA) is becoming the preferred method for mutation detection. However, its accuracy in the individual clinical diagnostic setting is variable. To assess the diagnostic accuracy of HRMA for human mutations in comparison to DNA sequencing in different routine clinical settings, we have conducted a meta-analysis of published reports.Methodology/principal findingsOut of 195 publications obtained from the initial search criteria, thirty-four studies assessing the accuracy of HRMA were included in the meta-analysis. We found that HRMA was a highly sensitive test for detecting disease-associated mutations in humans. Overall, the summary sensitivity was 97.5% (95% confidence interval (CI): 96.8-98.5; I(2)?=?27.0%). Subgroup analysis showed even higher sensitivity for non-HR-1 instruments (sensitivity 98.7% (95%CI: 97.7-99.3; I(2)?=?0.0%)) and an eligible sample size subgroup (sensitivity 99.3% (95%CI: 98.1-99.8; I(2)?=?0.0%)). HRMA specificity showed considerable heterogeneity between studies. Sensitivity of the techniques was influenced by sample size and instrument type but by not sample source or dye type.Conclusions/significanceThese findings show that HRMA is a highly sensitive, simple and low-cost test to detect human disease-associated mutations, especially for samples with mutations of low incidence. The burden on DNA sequencing could be significantly reduced by the implementation of HRMA, but it should be recognized that its sensitivity varies according to the number of samples with/without mutations, and positive results require DNA sequencing for confirmation.
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Project description:Assays for detecting somatic mutations are requested with higher sensitivity and more convenience. Here, we describe snapback primer mediated allele clamping enrichment polymerase chain reaction (SPACE-PCR), a novel form of PCR that amplifies minority alleles selectively from mixtures. We replaced regular PCR with SPACE-PCR before sequencing or genotyping assays to improve mutation detection sensitivity by up to 100-fold in detecting EGFR and KRAS somatic mutations. Combined SPACE-PCR with analysis of snapback primer by high resolution melting (SPACE-HRM), the high sensitive system that enables a closed-tube detection of mutations after isolating mutants has been established, as low as 1/10(5)-1/1000 mutant samples can be diagnosed. And finally, in a double-blind experiment of 150 cases of non-small-cell lung cancer (NSCLC) patients, compared with direct DNA sequencing and ADX-EGFR/KRAS mutation detection kit, up to 25% of the PCR-direct sequencing negative cases turned out to be positive in SPACE-HRM mutation tests; the specificity is 100%. Results demonstrated that the SPACE-HRM system we set up is a high sensitive assay that can be used for EGFR and KRAS allele enrichment and reliable detection. We anticipate that the method will be employed in multiple applications in the clinic, including diagnosis, scanner recurrence monitoring, and treatment management.
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Project description:Melanoma has the highest mortality rate among skin cancers, and early-diagnosis is essential to maximize survival rate. The current procedure for melanoma diagnosis is based on dermoscopy, i.e., a qualitative visual inspection of lesions with intrinsic limited diagnostic reliability and reproducibility. Other non-invasive diagnostic techniques may represent valuable solutions to retrieve additional objective information of a lesion. This review aims to compare the diagnostic performance of non-invasive techniques, alternative to dermoscopy, for melanoma detection in clinical settings. A systematic review of the available literature was performed using PubMed, Scopus and Google scholar databases (2010-September 2020). All human, in-vivo, non-invasive studies using techniques, alternative to dermoscopy, for melanoma diagnosis were included with no restriction on the recruited population. The reference standard was histology but dermoscopy was accepted only in case of benign lesions. Attributes of the analyzed studies were compared, and the quality was evaluated using CASP Checklist. For studies in which the investigated technique was implemented as a diagnostic tool (DTA studies), the QUADAS-2 tool was applied. For DTA studies that implemented a melanoma vs. other skin lesions classification task, a meta-analysis was performed reporting the SROC curves. Sixty-two references were included in the review, of which thirty-eight were analyzed using QUADAS-2. Study designs were: clinical trials (13), retrospective studies (10), prospective studies (8), pilot studies (10), multitiered study (1); the remain studies were proof of concept or had undefined study type. Studies were divided in categories based on the physical principle employed by each diagnostic technique. Twenty-nine out of thirty-eight DTA studies were included in the meta-analysis. Heterogeneity of studies' types, testing strategy, and diagnostic task limited the systematic comparison of the techniques. Based on the SROC curves, spectroscopy achieved the best performance in terms of sensitivity (93%, 95% CI 92.8-93.2%) and specificity (85.2%, 95%CI 84.9-85.5%), even though there was high concern regarding robustness of metrics. Reflectance-confocal-microscopy, instead, demonstrated higher robustness and a good diagnostic performance (sensitivity 88.2%, 80.3-93.1%; specificity 65.2%, 55-74.2%). Best practice recommendations were proposed to reduce bias in future DTA studies. Particular attention should be dedicated to widen the use of alternative techniques to conventional dermoscopy.
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Project description:Fast and reliable tests to detect mutations in human cancers are required to better define clinical samples and orient targeted therapies. KRAS mutations occur in 30-50% of colorectal cancers (CRCs) and represent a marker of clinical resistance to cetuximab therapy. In addition, the BRAF V600E is mutated in about 10% of CRCs, and the development of a specific inhibitor of mutant BRAF kinase has prompted a growing interest in BRAF (V600E) detection. Traditional methods, such as PCR and direct sequencing, do not detect low-level mutations in cancer, resulting in false negative diagnoses. In this study, we designed a protocol to detect mutations of KRAS and BRAF(V600E) in 117 sporadic CRCs based on coamplification at lower denaturation temperature PCR (COLD-PCR) and high-resolution melting (HRM). Using traditional PCR and direct sequencing, we found KRAS mutations in 47 (40%) patients and BRAF(V600E) in 10 (8.5%). The use of COLD-PCR in apparently wild-type samples allowed us to identify 15 newly mutated CRCs (10 for KRAS and 5 for BRAF (V600E)), raising the percentage of mutated CRCs to 48.7% for KRAS and to 12.8% for BRAF (V600E). Therefore, COLD-PCR combined with HRM permits the correct identification of less represented mutations in CRC and better selection of patients eligible for targeted therapies, without requiring expensive and time-consuming procedures.
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Project description:Crigler-Najjar syndrome (CNS) type I and type II are usually inherited as autosomal recessive conditions that result from mutations in the UGT1A1 gene. The main objective of the present review is to summarize results of all available evidence on the accuracy of SNP-based pathogenicity detection tools compared to published clinical result for the prediction of in nsSNPs that leads to disease using prediction performance method. A comprehensive search was performed to find all mutations related to CNS. Database searches included dbSNP, SNPdbe, HGMD, Swissvar, ensemble, and OMIM. All the mutation related to CNS was extracted. The pathogenicity prediction was done using SNP-based pathogenicity detection tools include SIFT, PHD-SNP, PolyPhen2, fathmm, Provean, and Mutpred. Overall, 59 different SNPs related to missense mutations in the UGT1A1 gene, were reviewed. Comparing the diagnostic OR, PolyPhen2 and Mutpred have the highest detection 4.983 (95% CI: 1.24 - 20.02) in both, following by SIFT (diagnostic OR: 3.25, 95% CI: 1.07 - 9.83). The highest MCC of SNP-based pathogenicity detection tools, was belong to SIFT (34.19%) followed by Provean, PolyPhen2, and Mutpred (29.99%, 29.89%, and 29.89%, respectively). Hence the highest SNP-based pathogenicity detection tools ACC, was fit to SIFT (62.71%) followed by PolyPhen2, and Mutpred (61.02%, in both). Our results suggest that some of the well-established SNP-based pathogenicity detection tools can appropriately reflect the role of a disease-associated SNP in both local and global structures.
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Project description:BackgroundCirculating tumor cells (CTCs) detection has previously been used for diagnosing gastric cancer. However, the previous studies failed to make an agreement whether the detection of CTCs contributes to the diagnosis of gastric cancer.MethodsA systematic review and meta-analysis was performed to evaluate the overall accuracy of CTCs detection for diagnosing gastric cancer. PubMed, Embase and the Wanfang database were searched in all languages published up to Oct 2012. The pooled sensitivity (SEN), specificity (SPE), positive and negative likelihood ratios (PLR and NLR, respectively), diagnostic odds ratio (DOR) and summary receiver operating characteristic (sROC) curve were calculated to evaluate the overall test performance.ResultsTwenty studies were included in this systematic review and meta-analysis. The diagnostic value of CTCs detection for the gastric cancer was calculated to evaluate the overall test performance. The summary estimates of The pooled sensitivity, specificity, positive and negative likelihood ratios, diagnostic odds ratio were 0.42 (95% confidence interval (CI), 0.21-0.67), 0.99 (95% CI, 0.96-1.00), 58.2 (95% CI, 9.8-345.9), 0.58 (95% CI, 0.38-0.89), and 100 (95% CI, 15-663), respectively. The summary receiver operating characteristic curve was 0.97 (95% CI, 0.95-0.98). Deek's funnel plot asymmetry test found no evidence of study publication bias in the current study (P = 0.49).ConclusionThis systematic review suggests that CTCs detection alone cannot be recommended as a screening test for gastric cancer. However, it might be used as a noninvasive method for the confirmation of the gastric cancer diagnosis.
| S-EPMC3699416 | biostudies-literature
Project description:BackgroundSignificant morbidity, mortality, and financial burden are associated with cardiac rhythm abnormalities. Conventional investigative tools are often unsuccessful in detecting cardiac arrhythmias because of their episodic nature. Smartwatches have gained popularity in recent years as a health tool for the detection of cardiac rhythms.ObjectiveThis study aims to systematically review and meta-analyze the diagnostic accuracy of smartwatches in the detection of cardiac arrhythmias.MethodsA systematic literature search of the Embase, MEDLINE, and Cochrane Library databases was performed in accordance with the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to identify studies reporting the use of a smartwatch for the detection of cardiac arrhythmia. Summary estimates of sensitivity, specificity, and area under the curve were attempted using a bivariate model for the diagnostic meta-analysis. Studies were examined for quality using the Quality Assessment of Diagnostic Accuracy Studies 2 tool.ResultsA total of 18 studies examining atrial fibrillation detection, bradyarrhythmias and tachyarrhythmias, and premature contractions were analyzed, measuring diagnostic accuracy in 424,371 subjects in total. The signals analyzed by smartwatches were based on photoplethysmography. The overall sensitivity, specificity, and accuracy of smartwatches for detecting cardiac arrhythmias were 100% (95% CI 0.99-1.00), 95% (95% CI 0.93-0.97), and 97% (95% CI 0.96-0.99), respectively. The pooled positive predictive value and negative predictive value for detecting cardiac arrhythmias were 85% (95% CI 0.79-0.90) and 100% (95% CI 1.0-1.0), respectively.ConclusionsThis review demonstrates the evolving field of digital disease detection. The current diagnostic accuracy of smartwatch technology for the detection of cardiac arrhythmias is high. Although the innovative drive of digital devices in health care will continue to gain momentum toward screening, the process of accurate evidence accrual and regulatory standards ready to accept their introduction is strongly needed.Trial registrationPROSPERO International Prospective Register of Systematic Reviews CRD42020213237; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=213237.
| S-EPMC8433941 | biostudies-literature
Project description:KRAS mutations have been reported as a reliable biomarker for epidermal growth factor receptor (EGFR) targeted therapy and are also associated with poor prognosis in colorectal cancer (CRC) patients. However, limitations of detecting KRAS mutations in tissues are obvious. KRAS mutations in the peripheral blood can be detected as an alternative to tissue analysis. The objective of this meta-analysis was to evaluate the diagnostic value of cfDNA (circulating free DNA) compared with tissues and to investigate the prognostic potential of cfDNA KRAS mutations in CRC patients. Searches were performed in PubMed, Embase, and Cochrane Library for published studies. We extracted true-positive (TP), false-positive (FP), false-negative (FN), true-negative (TN) values, survival rate of CRC patients with mutant and wild-type KRAS and calculated pooled sensitivity and specificity, positive/negative likelihood ratios [PLRs/NLRs], diagnostic odds ratios [DORs], and corresponding 95% confidence intervals [95% CIs]. We also generated a summary receiver operating characteristic (SROC) curve to evaluate the overall diagnostic potential. Totally, 31 relevant studies were recruited and used for the meta-analysis on the efficacy of cfDNA testing in detecting KRAS mutations. The pooled sensitivity, specificity, PLR, NLR, and DOR were 0.637 (95% CI: 0.607-0.666), 0.943 (95% CI: 0.930-0.954), 10.024 (95% CI: 6.912-14.535), 0.347 (95% CI: 0.269-0.447), and 37.882 (95% CI: 22.473-63.857), respectively. The area under the SROC curve was 0.9392. Together, the results suggest that detecting KRAS mutations in cfDNA has adequate diagnostic efficacy in terms of specificity. There is a promising role for cfDNA in the detection of KRAS mutations in CRC patients. However, prospective studies with larger patient cohorts are still required before definitive conclusions of the prognostic potential of cfDNA KRAS mutations in CRC patients were drawn.
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