Minimal Loss Of Sensitivity Research Articles

Evaluation of different standard and modified two-tier testing strategies for the laboratory diagnosis of lyme borreliosis in a European setting.

Diagnosis of Lyme borreliosis (LB) relies on clinical symptoms and detection of Borrelia-specific antibodies. Guidelines recommend a two-tier testing (TTT) strategy for disseminated LB: serological screening with a sensitive enzyme immunoassay (EIA) and confirmation with a specific immunoblot. Searching for the most sensitive and specific approach, this retrospective study evaluated standard (STTT) and modified (MTTT) strategies using a well-defined study population. Cases included patients with active Lyme neuroborreliosis (LNB; n = 29) or Lyme arthritis (LA; n = 17). Controls comprised patients treated for LNB (n = 36) or LA (n = 8), healthy individuals who were either untreated (n = 75) or treated for LB (n = 15) in the past, and patients with potentially cross-reactive diseases (n = 16). Sera were subjected to three EIAs and two immunoblots. Reactive screening results were confirmed by immunoblot (STTT) or EIA (MTTT). Solitary IgM results in the screening assay and effects of antibiotic treatment on isotype-specific seropositivity rates were also assessed. Sensitivities of STTT strategies ranged from 90%-97% for LNB and were 100% for LA. MTTT strategies were 100% sensitive. Specificities ranged from 89%-95% for STTT and from 88%-93% for MTTT strategies. Differences between STTT and MTTT strategies were not statistically significant. Solitary IgM reactivity was common among controls. Antibiotic treatment significantly reduced IgM/IgG positivity for LNB patients; for LA patients, a decline was only observed for IgM. In conclusion, MTTT strategies showed a slightly higher sensitivity and similar specificity compared to STTT strategies. Since EIAs are more time- and cost-efficient, MTTT strategies seem more favorable for clinical use. IgG testing enhances specificity with minimal sensitivity loss.

Comparative Analysis of Pooling Methods for SARS-CoV-2 Real-time Polymerase Chain Reaction Testing

Abstract Background: Wide spread coronavirus 2019 (COVID-19) infections in 2020 and 2021 and fewer real-time polymerase chain reaction (PCR) laboratories placed extraordinary demand on molecular diagnostics. To accommodate demand for increased testing volumes, the Indian Council of Medical Research had initially allowed pooling of five samples. This study aimed to conduct a comparative analysis of three sample pooling methods for SARS-CoV-2 testing to assess their effectiveness, sensitivity, and specificity. Methods: In this cross-sectional study, samples intended for SARS-CoV-2 testing were initially tested individually and then combined in a 1:4 positive-to-negative ratio. A total of 90 pools, comprising 450 samples, were analyzed using three distinct pooling methods: swab pooling, viral transport medium (VTM) pooling, and RNA pooling, all targeting the detection of the RdRp gene. PCR testing was conducted for all 90 pools comprising 450 samples in a uniform manner. Results: Swab pooling and RNA pooling methods correctly identified RdRp gene in all samples. VTM pooling method failed to identify RdRp gene in 4 samples. Analysis of cycle threshold (CT) value showed, loss of mean CT value of 2.80 ± 0.86 in swab pooling method with Z score of 6.03, VTM pooling method showed loss of mean CT value of 1.96 ± 0.76 with Z score of 3.22 and RNA pooling method showed loss of mean CT value of 1.73 ± 0.58 with Z score of 4.29 in. P value was statistically significant (<0.001) in all three methods. Conclusion: This study concludes that the RNA pooling method is superior, with minimal sensitivity loss in CT values. Swab pooling is cost-effective for negative pools but impractical for positive ones, while the VTM pooling method offers greater cost-effectiveness compared to RNA pooling.

Pooling of samples to optimise SARS-CoV-2 detection in nasopharyngeal swabs and gargle lavage self-samples for covid-19 diagnostics and surveillance

Background Testing of pooled samples is an effective strategy for increasing testing capacity while saving resources and time. This study aimed to validate pooled testing and gather real-life data on its use for Covid-19 surveillance with a gargle lavage (GL) self-sampling strategy. Methods Two-stage pooled testing with pools of 6 and 12 samples was used for preventive testing of an asymptomatic population and Covid-19 surveillance in Czech schools. Both GL and nasopharyngeal swabs were used for sampling. Results In total, 61,111 samples were tested. The use of pooled testing for large-scale Covid-19 surveillance reduced consumable costs by almost 75% and increased testing capacity up to 3.8-fold compared to standard methods. RT-PCR experiments revealed a minimal loss of sensitivity (0–2.2%) when using pooled samples, enabling the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genes with Ct values >35. The minor loss of sensitivity was counterbalanced by a significantly increased throughput and the ability to substantially increase testing frequencies. Conclusions Pooled testing is considerably more cost-effective and less time-consuming than standard testing for large-scale Covid-19 surveillance even when the prevalence of SARS-CoV-2 is fluctuating. Gargle lavage self-sampling is a non-invasive technique suitable for sample collection without a healthcare worker’s assistance.

Empirical Bayes single nucleotide variant-calling for next-generation sequencing data

One of the fundamental computational problems in cancer genomics is the identification of single nucleotide variants (SNVs) from DNA sequencing data. Many statistical models and software implementations for SNV calling have been developed in the literature, yet, they still disagree widely on real datasets. Based on an empirical Bayesian approach, we introduce a local false discovery rate (LFDR) estimator for germline SNV calling. Our approach learns model parameters without prior information, and simultaneously accounts for information across all sites in the genomic regions of interest. We also propose another LFDR-based algorithm that reliably prioritizes a given list of mutations called by any other variant-calling algorithm. We use a suite of gold-standard cell line data to compare our LFDR approach against a collection of widely used, state of the art programs. We find that our LFDR approach approximately matches or exceeds the performance of all of these programs, despite some very large differences among them. Furthermore, when prioritizing other algorithms’ calls by our LFDR score, we find that by manipulating the type I-type II tradeoff we can select subsets of variant calls with minimal loss of sensitivity but dramatic increases in precision.

Ultrasensitive detection of aromatic water pollutants through protein immobilization driven organic electrochemical transistors.

Xenobiotic aromatic water pollutants pose an extreme threat to environmental sustainability. Due to the lack of detectable functional groups in these compounds and scarcity of selective bio-recognition scaffolds, easy-to-use sensing strategies capable of on-site detection remain unavailable. Herein, to address this lacune, we entail a strategy that combines biosensor scaffolds with organic electronics to create a compact device for environmental aromatic pollution monitoring. As proof of principle, a sensor module capable of rapid, economic, reliable, and ultrasensitive detection of phenol down to 2 ppb (0.02 μM) was designed wherein biosensing protein MopR was coupled with an organic electrochemical transistor (OECT). For effective interfacing of the sensing scaffold MopR, graphene oxide (GO) nanosheets were optimized as a host immobilization matrix. The MopR-GO immobilized sensor module was subsequently substituted as the gate electrode with PEDOT:PSS serving as an organic semiconductor material. The resulting OECT sensor provided a favourable microenvironment for protein activity, maintaining high specificity. Exclusive phenol detection with minimal loss of sensitivity (<5% error) could be achieved in both complex pollutant mixtures and real environmental samples. This fabrication strategy that amalgamates biological biosensors with organic electronics harnesses the potential to achieve detection of a host of emerging pollutants.

Improved detection of aberrant splicing with FRASER 2.0 and the intron Jaccard index

Detection of aberrantly spliced genes is an important step in RNA-seq-based rare-disease diagnostics. We recently developed FRASER, a denoising autoencoder-based method that outperformed alternative methods of detecting aberrant splicing. However, because FRASER's three splice metrics are partially redundant and tend to be sensitive to sequencing depth, we introduce here a more robust intron-excision metric, the intron Jaccard index, that combines the alternative donor, alternative acceptor, and intron-retention signal into a single value. Moreover, we optimized model parameters and filter cutoffs by using candidate rare-splice-disrupting variants as independent evidence. On 16,213 GTEx samples, our improved algorithm, FRASER 2.0, called typically 10 times fewer splicing outliers while increasing the proportion of candidate rare-splice-disrupting variants by 10-fold and substantially decreasing the effect of sequencing depth on the number of reported outliers. To lower the multiple-testing correction burden, we introduce an option to select the genes to be tested for each sample instead of a transcriptome-wide approach. This option can be particularly useful when prior information, such as candidate variants or genes, is available. Application on 303 rare-disease samples confirmed the relative reduction in the number of outlier calls for a slight loss of sensitivity; FRASER 2.0 recovered 22 out of 26 previously identified pathogenic splicing cases with default cutoffs and 24 when multiple-testing correction was limited to OMIM genes containing rare variants. Altogether, these methodological improvements contribute to more effective RNA-seq-based rare diagnostics by drastically reducing the amount of splicing outlier calls per sample at minimal loss of sensitivity.

Preventive Oncology International: A brief history of HPV self-collected vaginal specimens for cervical cancer screening

Since 1998, Preventive Oncology International, Inc. (POI) has been at the forefront of studying human papillomavirus (HPV) self-collection for cervical cancer screening, with a significant focus in China. Through multiple clinical trials over the past 25 years, POI has explored various aspects related to self-collection methodologies. In 2004–2006, POI established that self-collection could be equivalent to direct endocervical samples. Subsequently, a large randomized trial involving 10,000 patients in 2010 further confirmed that self-collected vaginal specimens, tested for high-risk HPV (hrHPV) using a PCR-based assay with high analytic sensitivity, could effectively replace endocervical specimens with minimal loss of sensitivity and a slight decrease in specificity. Throughout the years, POI's research has encompassed several crucial topics, including patient acceptance, the development of new cost-effective, simpler, and faster assays, exploring different collection devices, devising efficient methods of specimen transport, and implementing population-based screening systems. The findings strongly support the integration of self-collection methodologies into cervical cancer control programs worldwide, particularly in medically underserved regions. As HPV self-collection continues to evolve, ongoing research and innovations are expected to play a pivotal role in achieving the global mission of combating cervical cancer.

Right in two: capabilities of ion mobility spectrometry for untargeted metabolomics.

This mini review focuses on the opportunities provided by current and emerging separation techniques for mass spectrometry metabolomics. The purpose of separation technologies in metabolomics is primarily to reduce complexity of the heterogeneous systems studied, and to provide concentration enrichment by increasing sensitivity towards the quantification of low abundance metabolites. For this reason, a wide variety of separation systems, from column chemistries to solvent compositions and multidimensional separations, have been applied in the field. Multidimensional separations are a common method in both proteomics applications and gas chromatography mass spectrometry, allowing orthogonal separations to further reduce analytical complexity and expand peak capacity. These applications contribute to exponential increases in run times concomitant with first dimension fractionation followed by second dimension separations. Multidimensional liquid chromatography to increase peak capacity in metabolomics, when compared to the potential of running additional samples or replicates and increasing statistical confidence, mean that uptake of these methods has been minimal. In contrast, in the last 15years there have been significant advances in the resolution and sensitivity of ion mobility spectrometry, to the point where high-resolution separation of analytes based on their collision cross section approaches chromatographic separation, with minimal loss in sensitivity. Additionally, ion mobility separations can be performed on a chromatographic timescale with little reduction in instrument duty cycle. In this review, we compare ion mobility separation to liquid chromatographic separation, highlight the history of the use of ion mobility separations in metabolomics, outline the current state-of-the-art in the field, and discuss the future outlook of the technology. "Where there is one, you're bound to divide it. Right in two", James Maynard Keenan.

Twist exome capture allows for lower average sequence coverage in clinical exome sequencing

BackgroundExome and genome sequencing are the predominant techniques in the diagnosis and research of genetic disorders. Sufficient, uniform and reproducible/consistent sequence coverage is a main determinant for the sensitivity to detect single-nucleotide (SNVs) and copy number variants (CNVs). Here we compared the ability to obtain comprehensive exome coverage for recent exome capture kits and genome sequencing techniques.ResultsWe compared three different widely used enrichment kits (Agilent SureSelect Human All Exon V5, Agilent SureSelect Human All Exon V7 and Twist Bioscience) as well as short-read and long-read WGS. We show that the Twist exome capture significantly improves complete coverage and coverage uniformity across coding regions compared to other exome capture kits. Twist performance is comparable to that of both short- and long-read whole genome sequencing. Additionally, we show that even at a reduced average coverage of 70× there is only minimal loss in sensitivity for SNV and CNV detection.ConclusionWe conclude that exome sequencing with Twist represents a significant improvement and could be performed at lower sequence coverage compared to other exome capture techniques.

Influence of HKUST-1 and emeraldine based on the long-term stability of emeraldine salt-coated SP-POF for room temperature optical NH3 gas sensing

A long-term sensitivity performance of conducting polymers and metal-organic frameworks coated on side-polished plastic optical fibre (SP-POF) was presented. SP-POF is an excellent option for potential long-distance and remote gas sensing and monitoring application. The presence of functional groups, porosity and surface area of the active materials were validated by Raman, Fourier transform infrared (FT-IR), X-Ray diffraction (XRD) and BET analyses. The sole copper-based metal-organic framework (HKUST-1)-coated SP-POF exhibited a good sensitivity (0.83/vol%) with a response time of 1.54 min. Further, the influence of acid dopants and oxidants on the optical response of doped-polyaniline (the emeraldine salt, ES) to 1% ammonia (NH3) gas was also optimised. Significant influence of HKUST-1 and emeraldine base (EB) on long-term optical NH3 sensitivity of emeraldine salt (ES)-coated SP-POF were related to NH3 desorption rate and affinity of the materials towards atmospheric vapour. ES-EB composite has exhibited higher NH3 sensitivity to the sole ES and ES-(HKUST-1) with minimal loss of sensitivity to a set of high NH3 gas concentrations over 70 days. ES-EB coated SP-POF has exhibited minimal sensitivity loss to NH3 gas throughout the test duration with a 7.8% decrease followed by ES (28.1%) and ES-(HKUST-1) (50.86%). Development of SP-POF coated with ES-EB composite is a viable approach to retain good optical NH3 sensitivity and stability at room temperature with a relative humidity of ~50%.

Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling

ObjectivesLimited testing capacity has characterized the ongoing coronavirus disease 2019 (COVID-19) pandemic in Spain, hampering timely control of outbreaks and opportunities to reduce the escalation of community transmission. This study investigated the potential to use sample pooling, followed by one-step retrotranscription and real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) to increase testing capacity for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). MethodsVarious pool sizes (five, 10 and 15 samples) were evaluated prior to RNA extraction followed by standard RT-qPCR for the diagnosis of COVID-19. The pool size achieving reproducible results with individual sample testing was subsequently used to assess nasopharyngeal samples in a tertiary hospital in August 2020. ResultsA pool size of five samples had higher sensitivity compared with pool sizes of 10 and 15 samples, showing a mean cycle threshold (Ct) shift of 3.5 [standard deviation (SD) 2.2] between the pooled test and positive samples in the pool. Next, a pool size of five was used to test a total of 895 pools (4475 prospective samples) using two different RT-qPCR kits. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct shift [2.2 (SD 2.4)] between the pool and individual samples. This strategy enables detection of individual positive samples in positive pools with Ct of 16.7–39.4. ConclusionsGrouping samples into pools of five for RT-qPCR resulted in an increase in SARS-CoV-2 testing capacity with minimal loss of sensitivity compared with testing each sample individually.

Quantum Limited SIS Receiver Technology for the Detection of Water Isotopologue Emission From Comets

NASA's Planetary Science Decadal Survey has concluded that isotopic measurements of cometary water vapor are a means to unraveling the mysteries involving the origin of Earth's water and the evolution of our solar system. To support this, a recent Jet Propulsion Laboratory internal research program has developed quantum limited superconductor–insulator–superconductor (SIS) receivers in the important 500 $-$ 600 GHz submillimeter frequency band. These instruments can be used to detect the deuterated water (HDO) ground state (1 $_{10}$ –1 $_{01}$ ), H $_2^{16}$ O ortho ground state (1 $_{10}$ –1 $_{01}$ ), and the oxygen isotopologues H $_2^{17}$ O and H $_2^{18}$ O with exquisite sensitivity. To achieve the presented results, we have investigated aluminum oxide (AlO $_x$ ) and aluminum nitride (AlN $_x$ ) barrier SIS tunnel junction mixers on the 6- $\mu$ m silicon-on-insulator substrate. The AlO $_x$ and AlN $_x$ junction mixer blocks utilize diagonal and smooth-profile conical horns, respectively. In both cases, a commercial 4–8-GHz intermediate frequency low-noise amplifier (LNA) has been integrated into the mixer block. The AlO $_x$ (low-current-density) barrier SIS junctions were fabricated with 2- $\mu$ m gold beam-lead technology, whereas in the case of the AlN $_x$ SIS tunnel junction, we use capacitive RF decoupling tabs. The latter approach simplifies fabrication, increases yield, eases the mounting process, and facilitates scaling to higher frequencies. For an actual flight mission, with operation $\leq$ 4.2 K, the allowed heat dissipation of the mixer-integrated LNA needs to be minimized. In this article, we also investigate the receiver sensitivity as a function of the LNA dc power consumption. We find that the dc power consumption of the LNA can be reduced to $\sim$ 1.6 mW with minimal loss in sensitivity. It is anticipated that the continued InP HEMT development for quantum computer applications are likely to reduce the required LNA power dissipation even further.

Urinary cell-free microRNA biomarker could discriminate bladder cancer from benign hematuria.

The most common symptom of bladder cancer (BC) is hematuria. However, not all patients with hematuria are diagnosed with BC. Here, we explored a novel method to discriminate BC from hematuria under nonmalignant conditions by measuring differences in urinary cell-free microRNA (miRNA) expression between patients with BC and those with hematuria. A multicenter study was performed using 543 urine samples obtained from the National Biobank of Korea, including 326 BC, 174 hematuria and 43 pyuria without cancer. The urinary miR-6124 to miR-4511 ratio was considerably higher in BC than in hematuria or pyuria, and enabled the discrimination of BC from patients with hematuria at a sensitivity of >90% (p < 0.001). Conclusively, the proposed noninvasive diagnostic tool based on the expression ratio of urinary cell-free miR-6124 to miR-4511 can reduce unnecessary cystoscopies in patients with hematuria undergoing evaluation for BC, with a minimal loss in sensitivity for detecting cancer.

Validation of a simple, fast liquid chromatography-tandem mass spectrometry method for the simultaneous quantification of 40 antidepressant drugs or their metabolites in plasma

IntroductionAntidepressant (AD) use has increased significantly over the last decades. Therapeutic drug monitoring is recommended for compliance, toxicity and treatment efficiency. ADs also show a high prevalence in forensic cases. Few methods have been developed that combine a fast, easy sample clean-up with a quantification based on liquid chromatography-triple quadrupole mass spectrometry (LC-QQQ). MethodologyA liquid-liquid extraction (LLE) was performed using 200 μL of plasma. The evaporated and reconstituted upper fraction was injected on a LC-QQQ system monitoring 3 transitions per compound. The method was fully validated according to international guidelines. Results & discussionThe chromatographic run time was under 12 min. The LLE was successful in removing interferences with minimal sensitivity loss. Calibration curves ranged from sub-therapeutic to toxic concentrations. Quality control samples showed high accuracy (81%–119%) and precision (≤14%) within and between batches. Stability was tested at ambient temperature and −20 °C. The method was successfully applied to external quality control and case samples. ConclusionThe presented method successfully quantifies 40 compounds of interest. Because of a simple sample clean-up, a relatively short chromatographic run and a wide calibration range this method can be implemented in therapeutic drug monitoring, forensic research and related fields.

AIRVF: a filtering toolbox for precise variant calling in Ion Torrent sequencing.

Ion Torrent sequencing is one of the most frequently used platforms in healthcare research and industry. Despite many advantages, platform-specific artifacts complicate efficient separation of true variants from errors, especially in variants with lower allele frequencies (<15%). Here, we developed a multi-step filtering toolbox AIRVF that works on flowgram, raw and mapped reads and called variants to reduce artifact-driven false variant calls. Tests on sequencing data of standard reference material showed up to ∼98% reduction of false variants when combined to conventional public pipelines and ∼48% to the in-house commercial solution, with a minimal loss of sensitivity. The program with a detailed manual is available at https://sourceforge.net/projects/airvf/. swkim@yuhs.ac. Supplementary data are available at Bioinformatics online.

Utilizing the ultrasensitive Schistosoma up-converting phosphor lateral flow circulating anodic antigen (UCP-LF CAA) assay for sample pooling-strategies

BackgroundMethodological applications of the high sensitivity genus-specific Schistosoma CAA strip test, allowing detection of single worm active infections (ultimate sensitivity), are discussed for efficient utilization in sample pooling strategies. Besides relevant cost reduction, pooling of samples rather than individual testing can provide valuable data for large scale mapping, surveillance, and monitoring.MethodThe laboratory-based CAA strip test utilizes luminescent quantitative up-converting phosphor (UCP) reporter particles and a rapid user-friendly lateral flow (LF) assay format. The test includes a sample preparation step that permits virtually unlimited sample concentration with urine, reaching ultimate sensitivity (single worm detection) at 100% specificity. This facilitates testing large urine pools from many individuals with minimal loss of sensitivity and specificity. The test determines the average CAA level of the individuals in the pool thus indicating overall worm burden and prevalence. When requiring test results at the individual level, smaller pools need to be analysed with the pool-size based on expected prevalence or when unknown, on the average CAA level of a larger group; CAA negative pools do not require individual test results and thus reduce the number of tests.ResultsStraightforward pooling strategies indicate that at sub-population level the CAA strip test is an efficient assay for general mapping, identification of hotspots, determination of stratified infection levels, and accurate monitoring of mass drug administrations (MDA). At the individual level, the number of tests can be reduced i.e. in low endemic settings as the pool size can be increased as opposed to prevalence decrease.ConclusionsAt the sub-population level, average CAA concentrations determined in urine pools can be an appropriate measure indicating worm burden. Pooling strategies allowing this type of large scale testing are feasible with the various CAA strip test formats and do not affect sensitivity and specificity. It allows cost efficient stratified testing and monitoring of worm burden at the sub-population level, ideally for large-scale surveillance generating hard data for performance of MDA programs and strategic planning when moving towards transmission-stop and elimination.

Performance of Spectrogram-Based Seizure Identification of Adult EEGs by Critical Care Nurses and Neurophysiologists.

Continuous EEG screening using spectrograms or compressed spectral arrays (CSAs) by neurophysiologists has shorter review times with minimal loss of sensitivity for seizure detection when compared with visual analysis of raw EEG. Limited data are available on the performance characteristics of CSA-based seizure detection by neurocritical care nurses. This is a prospective cross-sectional study that was conducted in two academic neurocritical care units and involved 33 neurointensive care unit nurses and four neurophysiologists. All nurses underwent a brief training session before testing. Forty two-hour CSA segments of continuous EEG were reviewed and rated for the presence of seizures. Two experienced clinical neurophysiologists masked to the CSA data performed conventional visual analysis of the raw EEG and served as the gold standard. The overall accuracy was 55.7% among nurses and 67.5% among neurophysiologists. Nurse seizure detection sensitivity was 73.8%, and the false-positive rate was 1-per-3.2 hours. Sensitivity and false-alarm rate for the neurophysiologists was 66.3% and 1-per-6.4 hours, respectively. Interrater agreement for seizure screening was fair for nurses (Gwet AC1 statistic: 43.4%) and neurophysiologists (AC1: 46.3%). Training nurses to perform seizure screening utilizing continuous EEG CSA displays is feasible and associated with moderate sensitivity. Nurses and neurophysiologists had comparable sensitivities, but nurses had a higher false-positive rate. Further work is needed to improve sensitivity and reduce false-alarm rates.

A single error is one too many: Examining alternative cutoffs on Trial 2 of the TOMM

ABSTRACTObjective: This study investigated the potential of alternative, more liberal cutoffs on Trial 2 of the Test of Memory Malingering (TOMM) to improve classification accuracy relative to the standard cutoffs (≤44). Method: The sample consisted of 152 patients (49.3% male) with psychiatric conditions (PSY) and traumatic brain injury (TBI) referred for neuropsychological assessment in a medico-legal setting (MAge = 44.4, MEducation = 11.9 years). Classification accuracy for various TOMM Trial 2 cutoffs was computed against three criterion measures.Results: Patients with TBI failed TOMM Trial 2 cutoffs at higher rates than patients with PSY. Trial 2 ≤49 achieved acceptable combinations of sensitivity (0.38–0.67) and specificity (0.89–0.96) in all but one comparison group. Trial 2 ≤48 improved specificity (0.94–0.98) with minimal loss in sensitivity. The standard cutoff (≤44) disproportionally traded sensitivity (0.15–0.50) for specificity (0.96–1.00).Conclusions: One error on TOMM Trial 2 constitutes sufficient evidence to question the credibility of a response set. However, the confidence in classifying a score as invalid continues to increase with each additional error. Even at the most liberal conceivable cutoff (≤49), the TOMM detected only about half of the patients who failed other criterion measures. Therefore, it should never be used in isolation to determine performance validity.

A Cell Type-Specific Expression Signature Predicts Haploinsufficient Autism-Susceptibility Genes.

Recent studies have identified many genes with rare de novo mutations in autism, but a limited number of these have been conclusively established as disease-susceptibility genes due to the lack of recurrence and confounding background mutations. Such extreme genetic heterogeneity severely limits recurrence-based statistical power even in studies with a large sample size. Here, we use cell-type specific expression profiles to differentiate mutations in autism patients from those in unaffected siblings. We report a gene expression signature in different neuronal cell types shared by genes with likely gene-disrupting (LGD) mutations in autism cases. This signature reflects haploinsufficiency of risk genes enriched in transcriptional and post-transcriptional regulators, with the strongest positive associations with specific types of neurons in different brain regions, including cortical neurons, cerebellar granule cells, and striatal medium spiny neurons. When used to prioritize genes with a single LGD mutation in cases, a D-score derived from the signature achieved a precision of 40% as compared with the 15% baseline with a minimal loss in sensitivity. An ensemble model combining D-score with mutation intolerance metrics from Exome Aggregation Consortium further improved the precision to 60%, resulting in 117 high-priority candidates. These prioritized lists can facilitate identification of additional autism-susceptibility genes.

Multi-mode acquisition (MMA): An MS/MS acquisition strategy for maximizing selectivity, specificity and sensitivity of DIA product ion spectra.

In proteomics studies, it is generally accepted that depth of coverage and dynamic range is limited in data-directed acquisitions. The serial nature of the method limits both sensitivity and the number of precursor ions that can be sampled. To that end, a number of data-independent acquisition (DIA) strategies have been introduced with these methods, for the most part, immune to the sampling issue; nevertheless, some do have other limitations with respect to sensitivity. The major limitation with DIA approaches is interference, i.e., MS/MS spectra are highly chimeric and often incapable of being identified using conventional database search engines. Utilizing each available dimension of separation prior to ion detection, we present a new multi-mode acquisition (MMA) strategy multiplexing both narrowband and wideband DIA acquisitions in a single analytical workflow. The iterative nature of the MMA workflow limits the adverse effects of interference with minimal loss in sensitivity. Qualitative identification can be performed by selected ion chromatograms or conventional database search strategies.