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Trost B, Walker S, Haider SA, Sung WWL, Pereira S, Phillips CL, Higginbotham EJ, Strug LJ, Nguyen C, Raajkumar A, Szego MJ, Marshall CR, Scherer SW. Impact of DNA source on genetic variant detection from human whole-genome sequencing data. J Med Genet 2019; 56:809-817. [PMID: 31515274 PMCID: PMC6929712 DOI: 10.1136/jmedgenet-2019-106281] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/04/2019] [Accepted: 07/20/2019] [Indexed: 12/28/2022]
Abstract
BACKGROUND Whole blood is currently the most common DNA source for whole-genome sequencing (WGS), but for studies requiring non-invasive collection, self-collection, greater sample stability or additional tissue references, saliva or buccal samples may be preferred. However, the relative quality of sequencing data and accuracy of genetic variant detection from blood-derived, saliva-derived and buccal-derived DNA need to be thoroughly investigated. METHODS Matched blood, saliva and buccal samples from four unrelated individuals were used to compare sequencing metrics and variant-detection accuracy among these DNA sources. RESULTS We observed significant differences among DNA sources for sequencing quality metrics such as percentage of reads aligned and mean read depth (p<0.05). Differences were negligible in the accuracy of detecting short insertions and deletions; however, the false positive rate for single nucleotide variation detection was slightly higher in some saliva and buccal samples. The sensitivity of copy number variant (CNV) detection was up to 25% higher in blood samples, depending on CNV size and type, and appeared to be worse in saliva and buccal samples with high bacterial concentration. We also show that methylation-based enrichment for eukaryotic DNA in saliva and buccal samples increased alignment rates but also reduced read-depth uniformity, hampering CNV detection. CONCLUSION For WGS, we recommend using DNA extracted from blood rather than saliva or buccal swabs; if saliva or buccal samples are used, we recommend against using methylation-based eukaryotic DNA enrichment. All data used in this study are available for further open-science investigation.
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Affiliation(s)
- Brett Trost
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Susan Walker
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Syed A Haider
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson W L Sung
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sergio Pereira
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Charly L Phillips
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Edward J Higginbotham
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lisa J Strug
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Statistical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Charlotte Nguyen
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Akshaya Raajkumar
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael J Szego
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada.,Department of Family and Community Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christian R Marshall
- Department of Paediatric Laboratory Medicine, Genome Diagnostics, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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Microarray experiments and factors which affect their reliability. Biol Direct 2015; 10:46. [PMID: 26335588 PMCID: PMC4559324 DOI: 10.1186/s13062-015-0077-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/24/2015] [Indexed: 12/12/2022] Open
Abstract
Oligonucleotide microarrays belong to the basic tools of molecular biology and allow for simultaneous assessment of the expression level of thousands of genes. Analysis of microarray data is however very complex, requiring sophisticated methods to control for various factors that are inherent to the procedures used. In this article we describe the individual steps of a microarray experiment, highlighting important elements and factors that may affect the processes involved and that influence the interpretation of the results. Additionally, we describe methods that can be used to estimate the influence of these factors, and to control the way in which they affect the expression estimates. A comprehensive understanding of the experimental protocol used in a microarray experiment aids the interpretation of the obtained results. By describing known factors which affect expression estimates this article provides guidelines for appropriate quality control and pre-processing of the data, additionally applicable to other transcriptome analysis methods that utilize similar sample handling protocols.
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Equal performance of self-collected and health care worker-collected pharyngeal swabs for group a streptococcus testing by PCR. J Clin Microbiol 2014; 53:573-8. [PMID: 25502528 DOI: 10.1128/jcm.02500-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A process employing patient- or parent-collected pharyngeal swabs for group A Streptococcus (GAS) testing would expedite diagnosis and treatment, reduce patient exposure to the health care setting, and decrease health care costs. Our aim was to determine the concordance between patient- or parent-collected (self-collected) and health care worker (HCW)-collected pharyngeal swabs for detection of GAS by PCR. From 9 October 2012 to 21 March 2013, patients presenting with a sore throat meeting criteria for GAS testing and not meeting criteria for severe disease were offered the opportunity to collect their own pharyngeal swab. The HCW also collected a swab. Paired swabs were tested by GAS real-time PCR, allowing semiquantitative comparisons between positive results. Of the 402 participants, 206 had a swab collected by the patient and 196 a swab collected by the parent. The percent positivity results were 33.3% for HCW-collected swabs and 34.3% for self-collected swabs (P = 0.41). The overall concordance between the two collection strategies was 94.0% (95% confidence interval [CI], 91.3 to 96.0). Twenty-four of the paired swabs had discordant results, with 10 and 14 positives detected only with the HCW- and self-collected swabs, respectively (P = 0.41). The person collecting the swab in the self-collected arm, the order of collection, and prior swab collection training did not influence results. Among the 124 specimens that were positive by both collection methods, the amount of GAS DNA was higher in the self-collected versus the HCW-collected swabs (P = 0.008). Self-collected pharyngeal swabs provide a reliable alternative to HCW collection for detection of GAS and offer a strategy for improved health care delivery.
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