scholarly journals VTAM: A robust pipeline for validating metabarcoding data using internal controls

2020 ◽  
Author(s):  
Aitor González ◽  
Vincent Dubut ◽  
Emmanuel Corse ◽  
Reda Mekdad ◽  
Thomas Dechatre ◽  
...  
Keyword(s):  
Internal Control ◽  
False Negative ◽  
Internal Controls ◽  
Data Curation ◽  
Sequence Variant ◽  
List Type ◽  
Data Filtering ◽  
Sample Contamination ◽  
Lack Of Control ◽  
Control Samples

AbstractMetabarcoding studies should be carefully designed to minimize false positives and false negative occurrences. The use of internal controls, replicates, and several overlapping markers is expected to improve the bioinformatics data analysis.VTAM is a tool to perform all steps of data curation from raw fastq data to taxonomically assigned ASV (Amplicon Sequence Variant or simply variant) table. It addresses all known technical error types and includes other features rarely present in existing pipelines for validating metabarcoding data: Filtering parameters are obtained from internal control samples; cross-sample contamination and tag-jump are controlled; technical replicates are used to ensure repeatability; it handles data obtained from several overlapping markers.Two datasets were analysed by VTAM and the results were compared to those obtained with a pipeline based on DADA2. The false positive occurrences in samples were considerably higher when curated by DADA2, which is likely due to the lack of control for tag-jump and cross-sample contamination.VTAM is a robust tool to validate metabarcoding data and improve traceability, reproducibility, and comparability between runs and datasets.

scholarly journals An Internal Control for Routine Diagnostic PCR: Design, Properties, and Effect on Clinical Performance

1998 ◽  
Vol 36 (1) ◽  
pp. 191-197 ◽  
Author(s):  
Maurice Rosenstraus ◽  
Zhuang Wang ◽  
Sheng-Yung Chang ◽  
David DeBonville ◽  
Joanne P. Spadoro
Keyword(s):  
Internal Control ◽  
Clinical Performance ◽  
False Negative ◽  
Test Sample ◽  
Internal Controls ◽  
Target Sequence ◽  
Positive Signal ◽  
Diagnostic Pcr ◽  
Unique Probe ◽  
Target Nucleic Acid

We constructed internal controls (ICs) to provide assurance that clinical specimens are successfully amplified and detected. The IC nucleic acids contain primer binding regions identical to those of the target sequence and contain a unique probe binding region that differentiates the IC from amplified target nucleic acid. Because only 20 copies of the IC are introduced into each test sample, a positive IC signal indicates that amplification was sufficient to generate a positive signal from targets present at the limit of test sensitivity. The COBAS AMPLICOR Chlamydia trachomatis, Neisseria gonorrhoeae, Mycobacterium tuberculosis, and human hepatitis C virus tests exhibited inhibition rates ranging from 5 to 9%. Approximately 64% of these inhibitory specimens were not inhibitory when a second aliquot was tested. Because repeatedly inhibitory specimens were not reported as false negative and because additional infected specimens were detected during retesting, test sensitivities were 1 to 6% greater than they would have been if the IC had not been used.

scholarly journals VTAM: A robust pipeline for validating metabarcoding data using optimized parameters based on internal controls

2021 ◽  
Vol 4 ◽  
Author(s):  
Emese Meglécz ◽  
Vincent Dubut ◽  
Emmanuel Corse ◽  
Aitor González
Keyword(s):  
Internal Control ◽  
False Positive ◽  
Good Practice ◽  
False Negative ◽  
Negative Control ◽  
Arbitrary Parameter ◽  
Sequence Variant ◽  
Design Data ◽  
Taxonomic Assignments ◽  
Negative Controls

Metabarcoding has become a powerful approach to study biodiversity from environmental samples but it is still prone to some pitfalls. Several papers have called for good practice in study design, data production and analyses to ensure repeatability and comparability between studies. Notably, the importance of mock community samples, negative controls, and replicates is frequently highlighted (Alberdi et al. 2018, O'Rourke et al. 2020). However, their use in bioinformatics pipelines is often limited to post hoc verification of expectations by the user. Indeed, one of the biggest challenges in metabarcoding analyses is to take into account the trade-off between false positive (FP) and false negative (FN) occurrences. We thus developed the VTAM (Validation and Taxonomic Assignation of Metabarcoding data) pipeline, which is the first tool to use explicitly the negative control and mock samples to find optimal parameters to minimize false positive and negative occurrences. In addition, VTAM addresses all known technical error types including tag-jumps, repeatability among replicates, and also it is able to integrate more than one overlapping markers to further minimize false negative occurrences. In order to evaluate VTAM, we compared it with two other pipelines: a pipeline based on DADA2 (Callahan et al. 2016) and LULU (Frøslev et al. 2017), and a pipeline based on OBITools3 (Boyer et al. 2016) and metabaR (Zinger et al. 2020). Two datasets from fish and bat diet studies were analysed with the three different pipelines. Based on mock and negative samples, we demonstrate that VTAM showed the best precision for mock samples in both datasets, while specificity in negative controls were comparable among the three pipelines (Fig. 1). VTAM therefore constitutes a complete pipeline to filter and validate metabarcoding data, from raw FASTQ data to Amplicon Sequence Variant tables with taxonomic assignments. Our pipeline aggregates a series of features rarely grouped in a single pipeline and performs a non-arbitrary parameter optimization based on internal control samples to generate conservative but informative metabarcoding datasets. We believe VTAM provides a very valuable tool for the validation of metabarcoding data, which is essential for conducting robust analyses of biodiversity.

scholarly journals Inhibition monitoring in veterinary molecular testing

2019 ◽  
Vol 32 (6) ◽  
pp. 758-766 ◽  
Author(s):  
Lifang Yan ◽  
Kathy L. Toohey-Kurth ◽  
Beate M. Crossley ◽  
Jianfa Bai ◽  
Amy L. Glaser ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Internal Control ◽  
Control Strategies ◽  
False Negative ◽  
Internal Controls ◽  
Molecular Testing ◽  
Acid Extraction ◽  
Negative Results ◽  
False Negative Results ◽  
Laboratory Technology

Many of the sample matrices typically used for veterinary molecular testing contain inhibitory factors that can potentially reduce analytic sensitivity or produce false-negative results by masking the signal produced by the nucleic acid target. Inclusion of internal controls in PCR-based assays is a valuable strategy not only for monitoring for PCR inhibitors, but also for monitoring nucleic acid extraction efficiency, and for identifying technology errors that may interfere with the ability of an assay to detect the intended target. The Laboratory Technology Committee of the American Association of Veterinary Laboratory Diagnosticians reviewed the different types of internal controls related to monitoring inhibition of PCR-based assays, and provides information here to encourage veterinary diagnostic laboratories to incorporate PCR internal control strategies as a routine quality management component of their molecular testing.

The Severity of Internal Controls over Financial Reporting Deficiencies: Differences among Types and Industries

2014 ◽  
pp. 55-77
Author(s):  
Tatiana Mazza ◽  
Stefano Azzali
Keyword(s):  
Information Technology ◽  
Financial Reporting ◽  
Internal Control ◽  
Service Industry ◽  
Listed Companies ◽  
Internal Controls ◽  
Service Companies ◽  
Finance Industry ◽  
Material Weaknesses ◽  
Fixed Assets

This study analyzes the severity of Internal Control over Financial Reporting deficiencies (Deficiencies, Significant Deficiencies and Material Weaknesses) in a sample of Italian listed companies, in the period 2007- 2012. Using proprietary data the severity of the deficiencies is tested for account-specific, entity level and information technology controls and for industries (manufacturing and services vs finance industries). The results on ICD severity is compared with one of the most frequent ICD (Acc_Period End/Accounting Policies): for account-specific, ICD in revenues, purchase, fixed assets and intangible, loans and insurance are more severe while ICD in Inventory are less severe. Differences in ICD severity have been found in the characteristic account: ICD in loan and insurance for finance industry and ICD in revenue, purchase for manufacturing and service industry are more severe. Finally, we found that ICD in entity level and information technology controls are less severe than account specific ICD in all industries. However, the results on entity level and information technology deficiencies could also mean that the importance of these types of control are under-evaluated by the manufacturing and service companies.

PENGARUH PDRB DAN UKURAN TERHADAP INTERNAL CONTROL PEMERINTAH DAERAH DENGAN PAD SEBAGAI INTERVENING

ProBank ◽  
2018 ◽  
Vol 3 (1) ◽  
pp. 64-75
Author(s):  
Prima Utama Wardoyo Putro
Keyword(s):  
Internal Control ◽  
Central Government ◽  
Control Variable ◽  
Secondary Data ◽  
Internal Controls ◽  
Regional Government ◽  
Path Testing ◽  
Size Growth ◽  
Fiscal Balance ◽  
Research Populations

Law No 32 year on 2004 about Regional Government and Law No 33 years on 2004 about Fiscal Balance between the Central Government and Regional Government are a new regulation relating to the implementation of regional autonomy in Indonesia. Giving the authority to manage its own region required an internal control system that can monitor of all by central government. The problem in this study is: Is there are any influence between growth, size, and PAD through Regional Government Internal Controls weakness with PAD as an intervening variable. The research populations are the financial statements and reports on the results of the entire province in Indonesia totaling 33 provinces. Source of data which are used are secondary data, and data collection by using the documentation method. The results of partial testing showed that PAD and Growth have significant affects to the Internal Controls, whereas size has not significant effect. Simultaneous testing showed a significant effect between the independent and dependent variables. The test results path testing showed that growth has no significant effect to internal control through PAD as an intervening variable and size has a significant effect to internal control variable through PAD as an intervening variable. The results of determinant coefficient by simultan test amount 28.7%. Its mean that Internal Control can be explained by Growth, Size and PAD, the remaining 71.3% influenced by factors other than study. Keyword: Internal Control, Size, Growth, and Income

Real Earnings Management before and after Reporting SOX 404 Material Weaknesses

2015 ◽  
Vol 30 (1) ◽  
pp. 119-141 ◽  
Author(s):  
Tuukka Järvinen ◽  
Emma-Riikka Myllymäki
Keyword(s):  
Earnings Management ◽  
Internal Control ◽  
Internal Controls ◽  
Real Earnings Management ◽  
Public Disclosure ◽  
High Quality ◽  
The Public ◽  
Material Weaknesses ◽  
Internal Control System ◽  
Before And After

SYNOPSIS The purpose of this study is to investigate whether SOX Section 404 material weaknesses manifest in real earnings management behavior. The empirical findings indicate that, compared to companies with effective internal controls, companies with existing material weaknesses in their internal controls engage in more manipulation of real activities (particularly inventory overproduction). This implies that the weak commitment by management to provide effective internal control system and high-quality financial information relates to a tendency to use real earnings management methods. Moreover, we find evidence suggesting that companies employ real earnings management (overproduction and reduction of discretionary expenses) after disclosing previous year's material weaknesses. We conjecture that the public disclosure of material weaknesses induces management to strive to mitigate the expected negative reactions of stakeholders to the disclosure by engaging in real earnings management, which is not easily detected or constrained by outsiders. Overall, this study suggests that material weaknesses in internal controls signal an environment where management is more inclined to employ real earnings management.

The Search for Order in Municipal Administration: Herman A. Metz and the New York City Experience, 1898–1909

2020 ◽  
Vol 47 (1) ◽  
pp. 55-74
Author(s):  
Ryan P. McDonough ◽  
Paul J. Miranti ◽  
Michael P. Schoderbek
Keyword(s):  
New York ◽  
New York City ◽  
Internal Control ◽  
York City ◽  
Internal Controls ◽  
Data Availability ◽  
Financial Reports ◽  
The Public ◽  
Operational Activities ◽  
The City

ABSTRACT This paper examines the administrative and accounting reforms coordinated by Herman A. Metz around the turn of the 20th century in New York City. Reform efforts were motivated by deficiencies in administering New York City's finances, including a lack of internal control over monetary resources and operational activities, and opaque financial reports. The activities of Comptroller Metz, who collaborated with institutions such as the New York Bureau of Municipal Research, were paramount in initiating and implementing the administrative and accounting reforms in the city, which contributed to reform efforts across the country. Metz promoted the adoption of functional cost classifications for city departments, developed flowcharts for improved transaction processing, strengthened internal controls, and published the 1909 Manual of Accounting and Business Procedure of the City of New York, which laid the groundwork for transparent financial reports capable of providing vital information about the city's activities and subsidiary units. JEL Classifications: H72, M41, N91. Data Availability: Data are available from the public sources cited in the text.

Accelerated Filing Deadlines, Internal Controls, and Financial Statement Quality: The Case of Originating Misstatements

2015 ◽  
Vol 29 (3) ◽  
pp. 551-575 ◽  
Author(s):  
Colleen M. Boland ◽  
Scott N. Bronson ◽  
Chris E. Hogan
Keyword(s):  
Internal Control ◽  
Internal Controls ◽  
Data Availability ◽  
Financial Statement ◽  
Similar Increase ◽  
Section 404 ◽  
Regulatory Changes ◽  
Rule Change ◽  
Initial Decrease

SYNOPSIS We examine whether regulations requiring accelerated filing deadlines and internal control reporting and testing affect financial statement reliability. Unlike prior research, we examine whether these regulatory changes are associated with an increase in the likelihood that misstatements originate in the period following the respective change. If the implementation of these rules causes a misstatement, then the misstatement would most likely occur in the period immediately following the rule change. We provide evidence that accelerated filers (AFs) experience an increase in the likelihood of an originating misstatement following the acceleration of filing deadlines from 90 to 75 days. Large accelerated filers (LAFs), however, do not experience a similar increase following this acceleration or the subsequent acceleration from 75 to 60 days. After the implementation of the SOX Section 404 internal control requirements, we find that the likelihood of an originating misstatement declined for AFs but not for LAFs. Taken together, the findings suggest that, although AFs experienced an initial decrease in financial statement reliability, this decrease was temporary. Data Availability: Data are publicly available from the sources identified in the text.

Board Independence and Internal Control Weakness: Evidence from SOX 404 Disclosures

2016 ◽  
Vol 36 (2) ◽  
pp. 45-62 ◽  
Author(s):  
Yangyang Chen ◽  
W. Robert Knechel ◽  
Vijaya Bhaskar Marisetty ◽  
Cameron Truong ◽  
Madhu Veeraraghavan
Keyword(s):  
Internal Control ◽  
Internal Controls ◽  
Board Independence ◽  
Negative Relation ◽  
Internal Control Weaknesses ◽  
A Company ◽  
Jel Classifications

SUMMARY In this paper, we investigate whether board independence has an impact on the likelihood that a company reports weaknesses in internal controls. Using a sample of 11,226 firm-year observations spanning the period 2004–2012, we establish several findings. First, we document a negative relation between board independence and the disclosure of internal control weaknesses. We also document that the negative relation is stronger for firms with unitary leadership (combined positions of CEO and chairman) than for firms with dual leadership. Next, we show that board independence is associated with both fewer account-specific and company-level weaknesses. Finally, we show that board independence is associated with timely remediation of internal control weaknesses and that the implementation of Auditing Standard No. 5 in 2007 weakens the effect of board independence on the disclosure of ICW. JEL Classifications: G10; G18.

External Auditors' Involvement in the Internal Audit Function's Work Plan and Subsequent Reliance Before and After a Negative Audit Discovery

2016 ◽  
Vol 35 (4) ◽  
pp. 159-173 ◽  
Author(s):  
Byron J. Pike ◽  
Lawrence Chui ◽  
Kasey A. Martin ◽  
Renee M. Olvera
Keyword(s):  
Internal Control ◽  
Internal Audit ◽  
Internal Controls ◽  
Professional Standards ◽  
Data Availability ◽  
Internal Auditors ◽  
External Auditors ◽  
Internal Audit Function ◽  
Anchoring Bias ◽  
Before And After

SUMMARY To reduce redundancies and increase efficiency in the evaluation of internal controls (PCAOB 2007, 402–403), professional standards encourage coordination between external auditors and their clients' internal audit function (IAF). Recent surveys of internal auditors find that a component of this coordination is external auditors' involvement in developing the IAF's audit plans. Nevertheless, it is not known how such involvement affects external auditors' reliance on the internal control test work of the IAF, either before or after a negative audit discovery. Based on an experiment with 107 experienced auditors, we find that external auditors involved in the development of the IAF's audit plan perceive the IAF as more objective and that both objectivity and involvement contribute to these auditors' placing more reliance on the IAF as compared to external auditors with no involvement. This initial reliance results in the involved auditors' proposing reductions to the audit budget and re-performing less of the IAF's work. Consistent with an anchoring bias, we find that involvement leads to external auditors' continuing to place greater reliance on the IAF's work, even after they become aware of a negative audit discovery that should not have occurred had the client's controls been effective. Data Availability: Data are available from the authors on request.

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