Immunogenicity of Cemiplimab: Low Incidence of Antidrug Antibodies and Cut-Point Suitability Across Tumor Types

The immunogenicity of cemiplimab, a fully human immunoglobulin G4 monoclonal antibody directed against programmed cell death 1, was assessed in patients across multiple tumor types. The development of antidrug antibodies (ADAs) against cemiplimab was monitored using a validated bridging immunoassay. To identify ADA-positive samples in the assay, statistically determined cut points were established by analyzing baseline clinical study samples from a mixed population of different tumor types, and this validation cut point was used to assess immunogenicity in all subsequent studies. Regulatory guidance requires that ADA assay cut points be verified for appropriateness in different patient populations. Thus, for the cemiplimab ADA assay, we evaluated whether each new oncology population was comparable with the validation population used to set the cut point. Assay responses from 2393 individual serum samples from 8 different tumor types were compared with the validation population, using established statistical methods for cut-point determination and comparison, with no significant differences observed. Across tumor types, the immunogenicity of cemiplimab was low, with an overall treatment-emergent ADA incidence rate of 1.9% and 2.5% at intravenous dose regimens of 3 mg/kg every 2 weeks and 350 mg every 3 weeks, respectively. Moreover, no neutralizing antibodies to cemiplimab were detected in patients with ADA-positive samples, and there was no observed impact of cemiplimab ADAs on pharmacokinetics. Study-specific cut points may be required in some diseases, such as immune and inflammatory diseases; however, based on this analysis, in-study cut points are not required for each new oncology disease indication for cemiplimab.

Replicate Testing of Clinical Endpoints Can Prevent No-Go Decisions for Beneficial Vaccines

In vaccine efficacy trials, inaccurate counting of infection cases leads to systematic under-estimation-or "dilution"-of vaccine efficacy. In particular, if a sufficient fraction of observed cases are false positives, apparent efficacy will be greatly reduced, leading to unwarranted no-go decisions in vaccine development. Here, we propose a range of replicate testing strategies to address this problem, considering the additional challenge of uncertainty in both infection incidence and diagnostic assay specificity/sensitivity. A strategy that counts an infection case only if a majority of replicate assays return a positive result can substantially reduce efficacy dilution for assays with non-systematic (i.e., "random") errors. We also find that a cost-effective variant of this strategy, using confirmatory assays only if an initial assay is positive, yields a comparable benefit. In clinical trials, where frequent longitudinal samples are needed to detect short-lived infections, this "confirmatory majority rule" strategy can prevent the accumulation of false positives from magnifying efficacy dilution. When widespread public health screening is used for viruses, such as SARS-CoV-2, that have non-differentiating features or may be asymptomatic, these strategies can also serve to reduce unneeded isolations caused by false positives.

Big little lies: a compendium and simulation of p-hacking strategies

In many research fields, the widespread use of questionable research practices has jeopardized the credibility of scientific results. One of the most prominent questionable research practices is p-hacking. Typically, p-hacking is defined as a compound of strategies targeted at rendering non-significant hypothesis testing results significant. However, a comprehensive overview of these p-hacking strategies is missing, and current meta-scientific research often ignores the heterogeneity of strategies. Here, we compile a list of 12 p-hacking strategies based on an extensive literature review, identify factors that control their level of severity, and demonstrate their impact on false-positive rates using simulation studies. We also use our simulation results to evaluate several approaches that have been proposed to mitigate the influence of questionable research practices. Our results show that investigating p-hacking at the level of strategies can provide a better understanding of the process of p-hacking, as well as a broader basis for developing effective countermeasures. By making our analyses available through a Shiny app and R package, we facilitate future meta-scientific research aimed at investigating the ramifications of p-hacking across multiple strategies, and we hope to start a broader discussion about different manifestations of p-hacking in practice.

Critical CHD screening programme: a 3-year multicentre experience in Mexico

INTRODUCTION

CHDs are the most common type of birth defect. One in four newborns with a heart defect has a critical CHD. In Mexico, there is a lack of data available to determine its prevalence. Pulse oximetry screening programmes have been implemented worldwide, reporting opportunity areas in algorithm interpretation and data management. Our study aims to share preliminary results of a 3-year experience of a multicentre pulse oximetry screening programme that addresses critical challenges.

MATERIALS AND METHODS

This retrospective study examined the reports of newborns screened from February 2016 to July 2019 from five hospitals. Two algorithms -the New Jersey and the American Academy of Pediatrics- were implemented over consecutive periods. The algorithms' impact was assessed through the calculation of the false-positive rate in an eligible population.

RESULTS

A total of 8960 newborns were eligible for the study; from it, 32.27% were screened under the New Jersey and 67.72% under the American Academy of Pediatrics algorithm - false-positive rate: 1% (CI 95: ± 0.36%) and 0.71% (CI 95: ± 0.21%), respectively. Seventy-nine newborns were referred, six were diagnosed with critical CHD, and six with CHD. The critical CHD estimated prevalence was 6.69:10,000 newborns (CI 95: ± 5.36). Our results showed that the algorithm was not related to the observable false-positive rate reduction.

DISCUSSION

Other factors may play a role in decreasing the false-positive rate. Our experience implementing this programme was that a systematic screening process led to more confident results, newborn's report interpretation, and follow-up.

Studying mutation rate evolution in primates-the effects of computational pipelines and parameter choices

This commentary investigates the important role of computational pipeline and parameter choices in performing mutation rate estimation, using the recent article published in this journal by Bergeron et al. entitled "The germline mutational process in rhesus macaque and its implications for phylogenetic dating" as an illustrative example.

Noninvasive prenatal screening in twin pregnancies with cell-free DNA using the IONA test: a prospective multicenter study

BACKGROUND

In singleton pregnancies, studies investigating cell-free DNA in maternal blood have consistently reported high detection rate and low false-positive rate for the 3 common fetal trisomies (trisomies 21, 18, and 13). The potential advantages of noninvasive prenatal testing in twin pregnancies are even greater than in singletons, in particular lower need for invasive testing and consequent fetal loss rate. However, several organizations do not recommend cell-free DNA in twin pregnancies and call for larger prospective studies.

OBJECTIVE

In response to this, we undertook a large prospective multicenter study to establish the screening performance of cell-free DNA for the 3 common trisomies in twin pregnancies. Moreover, we combined our data with that reported in published studies to obtain the best estimate of screening performance.

STUDY DESIGN

This was a prospective multicenter blinded study evaluating the screening performance of cell-free DNA in maternal plasma for the detection of fetal trisomies in twin pregnancies. The study took place in 6 fetal medicine centers in England, United Kingdom. The primary outcome was the screening performance and test failure rate of cell-free DNA using next generation sequencing (the IONA test). Maternal blood was taken at the time of (or after) a conventional screening test. Data were collected at enrolment, at any relevant invasive testing throughout pregnancy, and after delivery until the time of hospital discharge. Prospective detailed outcome ascertainment was undertaken on all newborns. The study was undertaken and reported according to the Standards for Reporting of Diagnostic Accuracy Studies. A pooled analysis was also undertaken using our data and those in the studies identified by a literature search (MEDLINE, Embase, CENTRAL, Cochrane Library, and ClinicalTrials.gov) on June 6, 2020.

RESULTS

A total of 1003 women with twin pregnancies were recruited, and complete data with follow-up and reference data were available for 961 (95.8%); 276 were monochorionic and 685 were dichorionic. The failure rate was 0.31%. The mean fetal fraction was 12.2% (range, 3%-36%); all 9 samples with a 3% fetal fraction provided a valid result. There were no false-positive or false-negative results for trisomy 21 or trisomy 13, whereas there was 1 false-negative and 1 false-positive result for trisomy 18. The IONA test had a detection rate of 100% for trisomy 21 (n=13; 95% confidence interval, 75-100), 0% for trisomy 18 (n=1; 95% confidence interval, 0-98), and 100% for trisomy 13 (n=1; 95% confidence interval, 3-100). The corresponding false-positive rates were 0% (95% confidence interval, 0-0.39), 0.10% (95% confidence interval, 0-0.58), and 0% (95% confidence interval, 0-0.39), respectively. By combining data from our study with the 11 studies identified by literature search, the detection rate for trisomy 21 was 95% (n=74; 95% confidence interval, 90-99) and the false-positive rate was 0.09% (n=5598; 95% confidence interval, 0.03-0.19). The corresponding values for trisomy 18 were 82% (n=22; 95% confidence interval, 66-93) and 0.08% (n=4869; 95% confidence interval, 0.02-0.18), respectively. There were 5 cases of trisomy 13 and 3881 non-trisomy 13 pregnancies, resulting in a computed average detection rate of 80% and a false-positive rate of 0.13%.

CONCLUSION

This large multicenter study confirms that cell-free DNA testing is the most accurate screening test for trisomy 21 in twin pregnancies, with screening performance similar to that in singletons and very low failure rates (0.31%). The predictive accuracy for trisomies 18 and 13 may be less. However, given the low false-positive rate, offering first-line screening with cell-free DNA to women with twin pregnancy is appropriate in our view and should be considered a primary screening test for trisomy 21 in twins.

A technical and clinical evaluation of the new ThermoFisher BRAHMS unconjugated estriol and inhibin-A assays and their use in second trimester Down syndrome screening

To evaluate second-trimester Down syndrome screening performance of the new ThermoFisher BRAHMS GOLD unconjugated estriol (uE3) and inhibin-A assays. Serum samples were analyzed for levels of uE3 and inhibin-A using the ThermoFisher BRAHMS GOLD immunoanalyzer and compared to other platforms. Levels were transformed to multiples of the median (MoM) in unaffected pregnancies. Log₁₀ MoM distributions in unaffected and Down syndrome pregnancies were assessed for central tendency (mean) and dispersion (SD). Empirical and estimated screening performances were determined. Correlation between BRAHMS and AutoDELFIA^® uE3 and inhibin-A were 0.63 and 0.97, respectively, the respective mean difference was 31.3% [95%CI 50.2% to -112.8%] and -23.3% [95%CI -41.9% to -4.7%]. Passing-Bablok indicated significant systematic (-2.78 [95%CI -3.57 to -2.04]) and proportional bias (1.30 [95%CI 1.15 to -1.47]) between uE3 assays and significant proportional bias (0.71[95%CI 0.65-0.78]) between inhibin-A assays. The uE3 and inhibin-A log₁₀ MoM distribution mean [SD] in unaffected and Down syndrome pregnancies were 0.0024 [SD = 0.2341] and -0.0001 [SD = 0.2078], and -0.2028 [SD = 0.2495] and 0.3645 [SD = 0.2576], respectively. The new BRAHMS uE3 and inhibin-A assays had an 81-83% detection rate for Trisomy21 for a 5% false-positive rate. The new BRAHMS assays achieved the expected screening performance provided the risk estimation model is adjusted to account for the higher BRAHMS uE3 MoM measurement distribution variance.

The incidence and incubation period of false-positive culture results in shoulder surgery

BACKGROUND

Postoperative shoulder infection is a significant complication requiring timely identification and treatment. Indolent infections such as those involving Cutibacterium acnes (formerly Propionibacterium acnes) provide a diagnostic dilemma as they present differently, without the acute symptoms associated with most postoperative bone and joint infections. Furthermore, Cacnes is thought to be a common contaminant isolated from intraoperative cultures. With no consensus algorithm, long-held cultures play a major role in guiding management decisions in potential postoperative shoulder infection. Our study sought to determine the incidence of positive culture results in both open and arthroscopic procedures in noninfected patients, as well as to clarify whether an increase in the incubation time frame leads to an increased rate of culture growth.

METHODS

One hundred patients were prospectively enrolled into either the open or arthroscopic procedure group. Patients with abnormal inflammatory laboratory findings, a history of shoulder surgery, or corticosteroid injection within 6 months of surgery were excluded from the study. Three cultures were obtained for each patient: superficial tissue culture, tissue culture, and "sterile" control swab. Cultures were held for 28 days and checked at regular intervals. All patients were followed up clinically for 6 months to ensure no signs of postoperative infection occurred.

RESULTS

Ultimately, 95 patients were included in the final analysis. The false-positive rate was 17.0% in those who underwent open shoulder surgery and 10.4% in those who underwent arthroscopic shoulder surgery. The incidence of positive Cacnes culture results was 6.4% in the open group, whereas Cacnes was not isolated in the arthroscopic group. All positive bacterial culture results were reported within 7 days of collection. One culture result was positive for mold at 26 days.

CONCLUSION

A relatively high false-positive culture rate occurred in both open and arthroscopic shoulder surgery. Cacnes was the most commonly identified bacterium in cultures in the open surgery group. Knowledge of one's institutional false-positive culture rate could be important in avoiding potentially inappropriate treatment. Additionally, we found that holding cultures longer than 14 days did not lead to an increased rate of false-positive culture results.

Adjusting Coronavirus Prevalence Estimates for Laboratory Test Kit Error

Testing representative populations to determine the prevalence or the percentage of the population with active severe acute respiratory syndrome coronavirus 2 infection and/or antibodies to infection is being recommended as essential for making public policy decisions to ease restrictions or to continue enforcing national, state, and local government rules to shelter in place. However, all laboratory tests are imperfect and have estimates of sensitivity and specificity less than 100%-in some cases, considerably less than 100%. That error will lead to biased prevalence estimates. If the true prevalence is low, possibly in the range of 1%-5%, then testing error will lead to a constant background of bias that most likely will be larger, and possibly much larger, than the true prevalence itself. As a result, what is needed is a method for adjusting prevalence estimates for testing error. Methods are outlined in this article for adjusting prevalence estimates for testing error both prospectively in studies being planned and retrospectively in studies that have been conducted. If used, these methods also would help harmonize study results within countries and worldwide. Adjustment can lead to more accurate prevalence estimates and to better policy decisions. However, adjustment will not improve the accuracy of an individual test.

Nick Martin as a Mentor - A Perspective

Nick Martin has had an outsized influence on the field of behavioral genetics. Much of this influence stems from his mentorship of young scientists. I describe Nick's mentorship, and what makes it special, from a personal perspective.

Prospective evaluation of screening performance of first-trimester prediction models for preterm preeclampsia in an Asian population

BACKGROUND

The administration of aspirin <16 weeks gestation to women who are at high risk for preeclampsia has been shown to reduce the rate of preterm preeclampsia by 65%. The traditional approach to identify such women who are at risk is based on risk factors from maternal characteristics, obstetrics, and medical history as recommended by the American College of Obstetricians and Gynecologists and the National Institute for Health and Care Excellence. An alternative approach to screening for preeclampsia has been developed by the Fetal Medicine Foundation. This approach allows the estimation of patient-specific risks of preeclampsia that requires delivery before a specified gestational age with the use of Bayes theorem-based model.

OBJECTIVE

The purpose of this study was to examine the diagnostic accuracy of the Fetal Medicine Foundation Bayes theorem-based model, the American College of Obstetricians and Gynecologists, and the National Institute for Health and Care Excellence recommendations for the prediction of preterm preeclampsia at 11-13⁺⁶ weeks gestation in a large Asian population STUDY DESIGN: This was a prospective, nonintervention, multicenter study in 10,935 singleton pregnancies at 11-13⁺⁶ weeks gestation in 11 recruiting centers across 7 regions in Asia between December 2016 and June 2018. Maternal characteristics and medical, obstetric, and drug history were recorded. Mean arterial pressure and uterine artery pulsatility indices were measured according to standardized protocols. Maternal serum placental growth factor concentrations were measured by automated analyzers. The measured values of mean arterial pressure, uterine artery pulsatility index, and placental growth factor were converted into multiples of the median. The Fetal Medicine Foundation Bayes theorem-based model was used for the calculation of patient-specific risk of preeclampsia at <37 weeks gestation (preterm preeclampsia) and at any gestation (all preeclampsia) in each participant. The performance of screening for preterm preeclampsia and all preeclampsia by a combination of maternal factors, mean arterial pressure, uterine artery pulsatility index, and placental growth factor (triple test) was evaluated with the adjustment of aspirin use. We examined the predictive performance of the model by the use of receiver operating characteristic curve and calibration by measurements of calibration slope and calibration in the large. The detection rate of screening by the Fetal Medicine Foundation Bayes theorem-based model was compared with the model that was derived from the application of American College of Obstetricians and Gynecologists and National Institute for Health and Care Excellence recommendations.

RESULTS

There were 224 women (2.05%) who experienced preeclampsia, which included 73 cases (0.67%) of preterm preeclampsia. In pregnancies with preterm preeclampsia, the mean multiples of the median values of mean arterial pressure and uterine artery pulsatility index were significantly higher (mean arterial pressure, 1.099 vs 1.008 [P<.001]; uterine artery pulsatility index, 1.188 vs 1.063[P=.006]), and the mean placental growth factor multiples of the median was significantly lower (0.760 vs 1.100 [P<.001]) than in women without preeclampsia. The Fetal Medicine Foundation triple test achieved detection rates of 48.2%, 64.0%, 71.8%, and 75.8% at 5%, 10%, 15%, and 20% fixed false-positive rates, respectively, for the prediction of preterm preeclampsia. These were comparable with those of previously published data from the Fetal Medicine Foundation study. Screening that used the American College of Obstetricians and Gynecologists recommendations achieved detection rate of 54.6% at 20.4% false-positive rate. The detection rate with the use of National Institute for Health and Care Excellence guideline was 26.3% at 5.5% false-positive rate.

CONCLUSION

Based on a large number of women, this study has demonstrated that the Fetal Medicine Foundation Bayes theorem-based model is effective in the prediction of preterm preeclampsia in an Asian population and that this method of screening is superior to the approach recommended by American College of Obstetricians and Gynecologists and the National Institute for Health and Care Excellence. We have also shown that the Fetal Medicine Foundation prediction model can be implemented as part of routine prenatal care through the use of the existing infrastructure of routine prenatal care.

pValid: Validation Beyond the Target-Decoy Approach for Peptide Identification in Shotgun Proteomics

As the de facto validation method in mass spectrometry-based proteomics, the target-decoy approach determines a threshold to estimate the false discovery rate and then filters those identifications beyond the threshold. However, the incorrect identifications within the threshold are still unknown and further validation methods are needed. In this study, we characterized a framework of validation and investigated a number of common and novel validation methods. We first defined the accuracy of a validation method by its false-positive rate (FPR) and false-negative rate (FNR) and, further, proved that a validation method with lower FPR and FNR led to identifications with higher sensitivity and precision. Then we proposed a validation method named pValid that incorporated an open database search and a theoretical spectrum prediction strategy via a machine-learning technology. pValid was compared with four common validation methods as well as a synthetic peptide validation method. Tests on three benchmark data sets indicated that pValid had an FPR of 0.03% and an FNR of 1.79% on average, both superior to the other four common validation methods. Tests on a synthetic peptide data set also indicated that the FPR and FNR of pValid were better than those of the synthetic peptide validation method. Tests on a large-scale human proteome data set indicated that pValid successfully flagged the highest number of incorrect identifications among all five methods. Further considering its cost-effectiveness, pValid has the potential to be a feasible validation tool for peptide identification.

Combined detection of α-fetoprotein and free β-human chorionic gonadotropin in screening for trisomy 21 and management of cases in the moderate risk value range

Down syndrome is the most common cause of prenatal chromosomal abnormalities, and prenatal serum screening is an effective method for decreasing the birth prevalence of children with Down syndrome. The aim of the present study was to observe the effect of duplex screening and investigate the treatment of cases under specific conditions. The medians of free β-human chorionic gonadotropin (HCG) and α-fetoprotein (AFP) were calculated and compared with those embedded in the 2T software. The detection and false-positive rates were analyzed under different conditions, and the distribution of Down syndrome cases was investigated in different risk ranges. Finally, suitable recommendations for further diagnostic investigation were provided according to the status of each individual. The medians of free β-HCG and AFP were found to differ from the corresponding medians embedded in the 2T software (P<0.01), and on the basis of a 5% false-positive rate, the detection rate would increase from 63.6 to 67.8% when compared with medians embedded in the 2T software, indicating we should establish our own medians of free β-HCG and AFP. In addition, residual cases (risk value <1/300) with relevant Down syndrome indications mainly concentrated at risk values between 1/1,000 and 1/300, and partial residual screening cases were verified through diverse methods. These findings indicated that different laboratories should establish their own medians; furthermore, what is classed as moderate risk is extremely important in screening for Down syndrome and reasonable recommendations may be offered under different conditions.

Aneuploidy screening by non-invasive prenatal testing in twin pregnancy

OBJECTIVES

To describe our experience with non-invasive prenatal testing (NIPT) in twin pregnancy.

METHODS

Two sets of maternal blood samples from twin pregnancies were analyzed at our laboratory using NIPT: 115 stored samples from pregnancies with known outcome (Clinical Study A) and 487 prospectively collected samples for which outcomes were requested from providers (Clinical Study B). NIPT was used to screen for the presence of fetal aneuploidy on chromosomes 13, 18, 21, X and Y in all cases, and results were compared with outcomes when known.

RESULTS

In Clinical Study A, all 115 samples were classified correctly by NIPT: three cases of trisomy 21 (one fetus affected), one of monochorionic trisomy 18 (both fetuses affected) and 111 euploid. In Clinical Study B, a NIPT result was reported for 479 (98.4%) of the 487 samples. Aneuploidy was detected or suspected in nine (1.9%) cases: seven cases of trisomy 21 detected, one case of trisomy 21 suspected and one case with trisomy 21 detected and trisomy 18 suspected. Information on aneuploidy outcome was available for 171 (35.7%) cases in Clinical Study B. Of the nine cases with aneuploidy detected or suspected, six were confirmed to be a true positive in at least one twin based on karyotype or birth outcome and two were suspected to be concordant based on ultrasound findings; the one known discordant result was for the aneuploidy suspected case. No false negatives were reported.

CONCLUSION

NIPT performed well in the detection of trisomy 21 in twin pregnancy, with a combined false-positive frequency for trisomies 13, 18 and 21 of 0% for Clinical Study A and 0.2% for Clinical Study B. © 2016 Illumina. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Do mammographic technologists affect radiologists' diagnostic mammography interpretative performance?

OBJECTIVE

The purpose of this study was to determine whether the technologist has an effect on the radiologists' interpretative performance of diagnostic mammography.

MATERIALS AND METHODS

Using data from a community-based mammography registry from 1994 to 2009, we identified 162,755 diagnostic mammograms interpreted by 286 radiologists and performed by 303 mammographic technologists. We calculated sensitivity, false-positive rate, and positive predictive value (PPV) of the recommendation for biopsy from mammography for examinations performed (i.e., images acquired) by each mammographic technologist, separately for conventional (film-screen) and digital modalities. We assessed the variability of these performance measures among mammographic technologists, using mixed effects logistic regression and taking into account the clustering of examinations within women, radiologists, and radiology practices.

RESULTS

Among the 291 technologists performing conventional examinations, mean sensitivity of the examinations performed was 83.0% (95% CI, 80.8-85.2%), mean false-positive rate was 8.5% (95% CI, 8.0-9.0%), and mean PPV of the recommendation for biopsy from mammography was 27.1% (95% CI, 24.8-29.4%). For the 45 technologists performing digital examinations, mean sensitivity of the examinations they performed was 79.6% (95% CI, 73.1-86.2%), mean false-positive rate was 8.8% (95% CI, 7.5-10.0%), and mean PPV of the recommendation for biopsy from mammography was 23.6% (95% CI, 18.8-28.4%). We found significant variation by technologist in the sensitivity, false-positive rate, and PPV of the recommendation for biopsy from mammography for conventional but not digital mammography (p < 0.0001 for all three interpretive performance measures).

CONCLUSION

Our results suggest that the technologist has an influence on radiologists' interpretive performance for diagnostic conventional but not digital mammography. Future studies should examine why this difference between modalities exists and determine if similar patterns are observed for screening mammography.

Erasing errors due to alignment ambiguity when estimating positive selection

Current estimates of diversifying positive selection rely on first having an accurate multiple sequence alignment. Simulation studies have shown that under biologically plausible conditions, relying on a single estimate of the alignment from commonly used alignment software can lead to unacceptably high false-positive rates in detecting diversifying positive selection. We present a novel statistical method that eliminates excess false positives resulting from alignment error by jointly estimating the degree of positive selection and the alignment under an evolutionary model. Our model treats both substitutions and insertions/deletions as sequence changes on a tree and allows site heterogeneity in the substitution process. We conduct inference starting from unaligned sequence data by integrating over all alignments. This approach naturally accounts for ambiguous alignments without requiring ambiguously aligned sites to be identified and removed prior to analysis. We take a Bayesian approach and conduct inference using Markov chain Monte Carlo to integrate over all alignments on a fixed evolutionary tree topology. We introduce a Bayesian version of the branch-site test and assess the evidence for positive selection using Bayes factors. We compare two models of differing dimensionality using a simple alternative to reversible-jump methods. We also describe a more accurate method of estimating the Bayes factor using Rao-Blackwellization. We then show using simulated data that jointly estimating the alignment and the presence of positive selection solves the problem with excessive false positives from erroneous alignments and has nearly the same power to detect positive selection as when the true alignment is known. We also show that samples taken from the posterior alignment distribution using the software BAli-Phy have substantially lower alignment error compared with MUSCLE, MAFFT, PRANK, and FSA alignments.

Temporal epilepsy seizures monitoring and prediction using cross-correlation and chaos theory

Temporal seizures due to hippocampal origins are very common among epileptic patients. Presented is a novel seizure prediction approach employing correlation and chaos theories. The early identification of seizure signature allows for various preventive measures to be undertaken. Electro-encephalography signals are spectrally broken down into the following sub-bands: delta; theta; alpha; beta; and gamma. The proposed approach consists of observing a high correlation level between any pair of electrodes for the lower frequencies and a decrease in the Lyapunov index (chaos or entropy) for the higher frequencies. Power spectral density and statistical analysis tools were used to determine threshold levels for the lower frequencies. After studying all five sub-bands, the analysis has revealed that the seizure signature can be extracted from the delta band and the high frequencies. High frequencies are defined as both the gamma band and the ripples occurring within the 60-120 Hz sub-band. To validate the proposed approach, six patients from both sexes and various age groups with temporal epilepsies originating from the hippocampal area were studied using the Freiburg database. An average seizure prediction of 30 min, an anticipation accuracy of 72%, and a false-positive rate of 0% were accomplished throughout 200 h of recording time.

Comparative effectiveness review: prostate cancer antigen 3 testing for the diagnosis and management of prostate cancer

PURPOSE

We compared the effectiveness of PCA3 (prostate cancer antigen 3) and select comparators for improving initial or repeat biopsy decision making in men at risk for prostate cancer, or treatment choices in men with prostate cancer.

MATERIALS AND METHODS

MEDLINE®, EMBASE®, Cochrane Database and gray literature were searched from January 1990 through May 2012. Included studies were matched, and measured PCA3 and comparator(s) within a cohort. No matched analyses were possible. Differences in independent performance estimates between PCA3 and comparators were computed within studies. Studies were assessed for quality using QUADAS (Quality Assessment of Diagnostic Accuracy Studies) and for strength of evidence using GRADE (Grading of Recommendations Assessment, Development and Evaluation) criteria.

RESULTS

Among 1,556 publications identified, 34 observational studies were analyzed (24 addressed diagnostic accuracy and 13 addressed treatment decisions). Most studies were conducted in opportunistic cohorts of men referred for procedures and were not designed to answer key questions. Two study biases (partial verification and sampling) were addressed by analyses, allowing some conclusions to be drawn. PCA3 was more discriminatory than total prostate specific antigen increases (eg at an observed 50% specificity, summary sensitivities were 77% and 57%, respectively). Analyses indicated that this finding holds for initial and repeat biopsies, and that the markers were independent predictors. For all other biopsy decision making comparisons and associated health outcomes, strength of evidence was insufficient. For treatment decision making, strength of evidence was insufficient for all outcomes and comparators.

CONCLUSIONS

PCA3 had a higher diagnostic accuracy than total prostate specific antigen increases, but strength of evidence was low (limited confidence in effect estimates). Strength of evidence was insufficient to conclude that PCA3 testing leads to improved health outcomes. For all other outcomes and comparators, strength of evidence was insufficient.