A community effort to identify and correct mislabeled samples in proteogenomic studies.
Ontology highlight
ABSTRACT:
SUBMITTER: Yoo S
PROVIDER: S-EPMC8134945 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:In high-throughput molecular profiling studies, genotype labels can be wrongly assigned at various experimental steps; the resulting mislabeled samples seriously reduce the power to detect the genetic basis of phenotypic variation. We have developed an approach to detect potential mislabeling, recover the "ideal" genotype and identify "best-matched" labels for mislabeled samples. On average, we identified 4% of samples as mislabeled in eight published datasets, highlighting the necessity of applying a "data cleaning" step before standard data analysis.
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Project description:BackgroundResearchers typically sequence a given individual multiple times, either re-sequencing the same DNA sample (technical replication) or sequencing different DNA samples collected on the same individual (biological replication) or both. Before merging the data from these replicate sequence runs, it is important to verify that no errors, such as DNA contamination or mix-ups, occurred during the data collection pipeline. Methods to detect such errors exist but are often ad hoc, cannot handle missing data and several require phased data. Because they require some combination of genotype calling, imputation, and haplotype phasing, these methods are unsuitable for error detection in low- to moderate-depth sequence data where such tasks are difficult to perform accurately. Additionally, because most existing methods employ a pairwise-comparison approach for error detection rather than joint analysis of the putative replicates, results may be difficult to interpret.ResultsWe introduce a new method for error detection suitable for shallow-, moderate-, and high-depth sequence data. Using Bayes Theorem, we calculate the posterior probability distribution over the set of relations describing the putative replicates and infer which of the samples originated from an identical genotypic source.ConclusionsOur method addresses key limitations of existing approaches and produced highly accurate results in simulation experiments. Our method is implemented as an R package called BIGRED (Bayes Inferred Genotype Replicate Error Detector), which is freely available for download: https://github.com/ac2278/BIGRED .
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Project description:Next generation fungal amplicon sequencing is being used with increasing frequency to study fungal diversity in various ecosystems; however, the influence of sample preparation on the characterization of fungal community is poorly understood. We investigated the effects of four procedural modifications to library preparation for high-throughput sequencing (HTS). The following treatments were considered: 1) the amount of soil used in DNA extraction, 2) the inclusion of additional steps (freeze/thaw cycles, sonication, or hot water bath incubation) in the extraction procedure, 3) the amount of DNA template used in PCR, and 4) the effect of sample pooling, either physically or computationally. Soils from two different ecosystems in Minnesota, USA, one prairie and one forest site, were used to assess the generality of our results. The first three treatments did not significantly influence observed fungal OTU richness or community structure at either site. Physical pooling captured more OTU richness compared to individual samples, but total OTU richness at each site was highest when individual samples were computationally combined. We conclude that standard extraction kit protocols are well optimized for fungal HTS surveys, but because sample pooling can significantly influence OTU richness estimates, it is important to carefully consider the study aims when planning sampling procedures.
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Project description:Identifying genomic alterations of cancer proteins has guided the development of targeted therapies, but proteomic analyses are required to validate and reveal new treatment opportunities. Herein, we develop a new algorithm, OPPTI, to discover overexpressed kinase proteins across 10 cancer types using global mass spectrometry proteomics data of 1,071 cases. OPPTI outperforms existing methods by leveraging multiple co-expressed markers to identify targets overexpressed in a subset of tumors. OPPTI-identified overexpression of ERBB2 and EGFR proteins correlates with genomic amplifications, while CDK4/6, PDK1, and MET protein overexpression frequently occur without corresponding DNA- and RNA-level alterations. Analyzing CRISPR screen data, we confirm expression-driven dependencies of multiple currently-druggable and new target kinases whose expressions are validated by immunochemistry. Identified kinases are further associated with up-regulated phosphorylation levels of corresponding signaling pathways. Collectively, our results reveal protein-level aberrations-sometimes not observed by genomics-represent cancer vulnerabilities that may be targeted in precision oncology.
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Project description:Study objectivesObstructive sleep apnea-hypopnea (OAH) diagnosis in children is based on the quantification of flow and respiratory effort (RE). Pulse transit time (PTT) is one validated tool to recognize RE. Pattern analysis of mandibular movements (MM) might be an alternative method to detect RE. We compared several patterns of MM to concomittant changes in PTT during OAH in children with adenotonsillar hypertrophy.MethodsParticipants33 consecutive children with snoring and symptoms/signs of OAH.MeasurementsMMs were measured during polysomnography with a magnetometer device (Brizzy Nomics, Liege, Belgium) placed on the chin and forehead. Patterns of MM were evaluated representing peak to peak fluctuations > 0.3 mm in mandibular excursion (MML), mandibular opening (MMO), and sharp MM (MMS), which closed the mouth on cortical arousal (CAr).ResultsThe median (95% CI) hourly rate of at least 1 MM (MML, or MMO, or MMS) was 18.1 (13.2-36.3) and strongly correlated with OAHI (p = 0.003) but not with central apnea-hypopnea index (CAHI; p = 0.292). The durations when the MM amplitude was > 0.4 mm and PTT > 15 ms were strongly correlated (p < 0.001). The mean (SD) of MM peak to peak amplitude was larger during OAH than CAH (0.9 ± 0.7 mm and 0.2 ± 0.3 mm; p < 0.001, respectively). MMS at the termination of OAH had larger amplitude compared to MMS with CAH (1.5 ± 0.9 mm and 0.5 ± 0.7 mm, respectively, p < 0.001).ConclusionsMM > 0.4 mm occurred frequently during periods of OAH and were frequently terminated by MMS corresponding to mouth closure on CAr. The MM findings strongly correlated with changes in PTT. MM analysis could be a simple and accurate promising tool for RE characterization and optimization of OAH diagnosis in children.
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Project description:Efforts to precisely identify tumor human leukocyte antigen (HLA) bound peptides capable of mediating T cell-based tumor rejection still face important challenges. Recent studies suggest that non-canonical tumor-specific HLA peptides derived from annotated non-coding regions could elicit anti-tumor immune responses. However, sensitive and accurate mass spectrometry (MS)-based proteogenomics approaches are required to robustly identify these non-canonical peptides. We present an MS-based analytical approach that characterizes the non-canonical tumor HLA peptide repertoire, by incorporating whole exome sequencing, bulk and single-cell transcriptomics, ribosome profiling, and two MS/MS search tools in combination. This approach results in the accurate identification of hundreds of shared and tumor-specific non-canonical HLA peptides, including an immunogenic peptide derived from an open reading frame downstream of the melanoma stem cell marker gene ABCB5. These findings hold great promise for the discovery of previously unknown tumor antigens for cancer immunotherapy.
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Project description:In the past decades, actigraphy has emerged as a promising, cost-effective, and easy-to-use tool for ambulatory sleep recording. Polysomnography (PSG) validation studies showed that actigraphic sleep estimates fare relatively well in healthy sleepers. Additionally, round-the-clock actigraphy recording has been used to study circadian rhythms in various populations. To this date, however, there is little evidence that the diagnosis, monitoring, or treatment of insomnia can significantly benefit from actigraphy recordings. Using a case-control design, we therefore critically examined whether mean or within-subject variability of actigraphy sleep estimates or circadian patterns add to the understanding of sleep complaints in insomnia. We acquired actigraphy recordings and sleep diaries of 37 controls and 167 patients with varying degrees of insomnia severity for up to 9 consecutive days in their home environment. Additionally, the participants spent one night in the laboratory, where actigraphy was recorded alongside PSG to check whether sleep, in principle, is well estimated. Despite moderate to strong agreement between actigraphy and PSG sleep scoring in the laboratory, ambulatory actigraphic estimates of average sleep and circadian rhythm variables failed to successfully differentiate patients with insomnia from controls in the home environment. Only total sleep time differed between the groups. Additionally, within-subject variability of sleep efficiency and wake after sleep onset was higher in patients. Insomnia research may therefore benefit from shifting attention from average sleep variables to day-to-day variability or from the development of non-motor home-assessed indicators of sleep quality.
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Project description:IntroductionWe aimed to examine the contribution of subjective cognitive decline (SCD) to reduce the number of β-amyloid (Aβ) positron emission tomography scans required for recruiting Aβ+ clinically normal individuals in clinical trials.MethodsThree independent cohorts (890 clinically normal: 72 yrs ± 6.7; Female: 43.4%; SCD+: 24%; apolipoprotein E [APOE] ε4+: 28.5%; Aβ+: 32%) were used. SCD was dichotomized from one question. Using logistic regression, we classified Aβ+ using the SCD dichotomy, APOEε4, sex, and age.ResultsSCD increased odds of Aβ+ by 1.58 relative to non-SCD. Female APOEε4 carriers with SCD exhibited higher odds of Aβ+ (OR = 3.34), whereas male carriers with SCD showed a weaker, opposing effect (OR = 0.37). SCD endorsement reduces the number of Aβ positron emission tomography scans to recruit Aβ+ individuals by 13% and by 9% if APOEε4 status is known.ConclusionSCD helps to classify those with high Aβ, even beyond the substantial effect of APOE genotype. Collecting SCD is a feasible method for targeting recruitment for those likely on the AD trajectory.
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