Dataset Information

Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer.

ABSTRACT: BACKGROUND:Genome-wide or application-targeted microarrays containing a subset of genes of interest have become widely used as a research tool with the prospect of diagnostic application. Intrinsic variability of microarray measurements poses a major problem in defining signal thresholds for absent/present or differentially expressed genes. Most strategies have used fold-change threshold values, but variability at low signal intensities may invalidate this approach and it does not provide information about false-positives and false negatives. RESULTS:We introduce a method to filter false-positives and false-negatives from DNA microarray experiments. This is achieved by evaluating a set of positive and negative controls by receiver operating characteristic (ROC) analysis. As an advantage of this approach, users may define thresholds on the basis of sensitivity and specificity considerations. The area under the ROC curve allows quality control of microarray hybridizations. This method has been applied to custom made microarrays developed for the analysis of invasive melanoma derived tumor cells. It demonstrated that ROC analysis yields a threshold with reduced missclassified genes in microarray experiments. CONCLUSIONS:Provided that a set of appropriate positive and negative controls is included on the microarray, ROC analysis obviates the inherent problem of arbitrarily selecting threshold levels in microarray experiments. The proposed method is applicable to both custom made and commercially available DNA microarrays and will help to improve the reliability of predictions from DNA microarray experiments.

SUBMITTER: Bilban M

PROVIDER: S-EPMC117791 | biostudies-literature | 2002 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer.

Bilban M M Buehler L K LK Head S S Desoye G G Quaranta V V

BMC genomics 20020717 1

<h4>Background</h4>Genome-wide or application-targeted microarrays containing a subset of genes of interest have become widely used as a research tool with the prospect of diagnostic application. Intrinsic variability of microarray measurements poses a major problem in defining signal thresholds for absent/present or differentially expressed genes. Most strategies have used fold-change threshold values, but variability at low signal intensities may invalidate this approach and it does not provid ...[more]

PMID: 12123529

Similar Datasets

Project description:BackgroundEfforts are underway to eliminate trachoma as a public health problem by 2020. Programmatic guidelines are based on clinical signs that correlate poorly with Chlamydia trachomatis (Ct) infection in post-treatment and low-endemicity settings. Age-specific seroprevalence of anti Ct Pgp3 antibodies has been proposed as an alternative indicator of the need for intervention. To standardise the use of these tools, it is necessary to develop an analytical approach that performs reproducibly both within and between studies.MethodologyDried blood spots were collected in 2014 from children aged 1-9 years in Laos (n = 952) and Uganda (n = 2700) and from people aged 1-90 years in The Gambia (n = 1868). Anti-Pgp3 antibodies were detected by ELISA. A number of visual and statistical analytical approaches for defining serological status were compared.Principal findingsSeroprevalence was estimated at 11.3% (Laos), 13.4% (Uganda) and 29.3% (The Gambia) by visual inspection of the inflection point. The expectation-maximisation algorithm estimated seroprevalence at 10.4% (Laos), 24.3% (Uganda) and 29.3% (The Gambia). Finite mixture model estimates were 15.6% (Laos), 17.1% (Uganda) and 26.2% (The Gambia). Receiver operating characteristic (ROC) curve analysis using a threshold calibrated against external reference specimens estimated the seroprevalence at 6.7% (Laos), 6.8% (Uganda) and 20.9% (The Gambia) when the threshold was set to optimise Youden's J index. The ROC curve analysis was found to estimate seroprevalence at lower levels than estimates based on thresholds established using internal reference data. Thresholds defined using internal reference threshold methods did not vary substantially between population samples.ConclusionsInternally calibrated approaches to threshold specification are reproducible and consistent and thus have advantages over methods that require external calibrators. We propose that future serological analyses in trachoma use a finite mixture model or expectation-maximisation algorithm as a means of setting the threshold for ELISA data. This will facilitate standardisation and harmonisation between studies and eliminate the need to establish and maintain a global calibration standard.

Project description:Performance thresholds are an important tool for determining successful conservation outcomes. They provide an objective means of defining good ecological condition and have been endorsed as an essential part of best practice in protected area (PA) management within the International Union for the Conservation of Nature Green List of Protected and Conserved Areas Standard. With a growing number of PAs attaining Green List status globally, thresholds developed by PAs on the Green List present an excellent resource with which to identify the attributes of well-defined performance thresholds. We examined 349 thresholds associated with PAs on the Green List to determine whether they were specific and measurable (i.e., factors recognized as essential for setting well-defined targets). We assessed whether thresholds were defined quantitatively and whether definitions included ambiguous terms (e.g., stable numbers). We identified six different ways thresholds were expressed and found that many thresholds were expressed as management objectives, rather than ecological condition thresholds, although this trend improved over time. Approximately one-half of the performance thresholds lacked the necessary specificity to delineate successful outcomes. Our results enabled us to develop a checklist of information required to set robust performance thresholds. Recommendations include that thresholds should be quantitatively defined, including quantitative estimates of the limits of acceptable change (LAC) around the target condition. To ensure transparency, a rationale and associated evidence should be provided to support the threshold and the LAC. When accompanied by a rationale and quantitative estimate of the current condition of the value, unambiguously defined thresholds with a quantitative LAC provide an objective means of demonstrating that successful conservation outcomes have been achieved. These recommendations will help conservation managers apply the Green List Standard and improve the measurement of conservation outcomes more broadly.

Project description:BackgroundLiquid biopsy has been proposed to be a promising noninvasive tool to obtain information on tumor progression. Through a clinical observation of a case series of 6 consecutive patients, we aim to determine the value of circulating tumor DNA (ctDNA) for monitoring the tumor burden during the treatment of colorectal cancer (CRC).Materials and methodsWe used capture sequencing of 545 genes to identify somatic alternations in primary tumor tissues of the six CRC patients who underwent radical surgery and in 23 plasma samples collected at serial time points. We compared the mutation patterns and variant allele frequencies (VAFs) between the matched tissue and the plasma samples and evaluated the potential advantage of using ctDNA as a better tumor load indicator to detect disease relapse over carcinoembryonic antigen (CEA), cancer antigen (CA) 19-9 and imaging studies.ResultsWe identified low-frequency mutations with a mean VAF of 0.88% (corresponding to a mean tumor burden of 0.20ng/mL) in the preoperative plasmas of four patients with locally advanced CRC and a subset of mutations shared by their primary tumors. The tumor loads appeared a sudden decrease upon surgery or other adjuvant treatments and then generally maintained at low levels (0.092ng/mL) until disease recurred. ctDNA increased by 13-fold when disease relapsed in one patient while the CEA and CA 19-9 levels remained normal. In this patient, all six somatic mutations identified in the preoperative plasma were detected in the recrudescent plasma again, with five mutations showing allele fraction increase.ConclusionsWe described a multi-time-point profile of ctDNA of CRC patients during the course of comprehensive treatment and observed a correlation of ctDNA level with the clinically evaluated tumor progression. This demonstrated a new strategy by analyzing the heterogeneous ctDNA to evaluate and monitor the tumor burden in the treatment and follow-up of CRC patients, with potentially better potency than conventional biomarkers.

Dataset Information

Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer.

Publications

Defining signal thresholds in DNA microarrays: exemplary application for invasive cancer.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets