Comparison of the TLDA with the Nanodrop and the reference Qubit system

O’Neill, M.; McPartlin, Joseph; Arthure, K; Riedel, S.; McMillan, N D

doi:10.1088/1742-6596/307/1/012047

Cited by 46 publications

(45 citation statements)

References 3 publications

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“…The former measures maximal absorbance of nucleic acids without distinguishing between dsDNA, ssDNA, RNA, and nucleotides. 44 Thus, as expected, our results showed that the UV method gave significantly higher concentrations, both for urine and saliva-derived DNA. The presence of contamination in the sample, i.e., protein (indicated by the A 260 :A 280 ratio, especially in case of urinary DNA) as well as RNA, ssDNA, and other contaminants could influence the UV absorption ultimately leading to an overestimation of the DNA concentration compared to fluorescence spectroscopy.…”

Section: Discussionsupporting

confidence: 85%

Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

et al. 2020

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Genetic epidemiology requires an appropriate approach to measure genetic variation within the population. The aim of this study was to evaluate the characteristics and genotyping results of DNA extracted from 2 human DNA sources, selected for their rapid and noninvasive sampling, and the use of simple and standardized protocols that are essential for large-scale epidemiologic studies. Saliva and urine samples were collected at the same day from 20 subjects aged 9-10 yr. Genomic DNA was extracted using commercial kits. Quantitative and qualitative evaluation was done by assessing the yield, the purity, and integrity of the extracted DNA. As a proof-of-concept, genotyping was performed targeting CC16 A38G and uteroglobin-related protein 1 (UGRP1)-112G/A. Saliva was found to provide the highest yield and concentration of total DNA extracted. Salivary DNA showed higher purity and a significantly less degraded state compared to urinary DNA. Consequently, the salivary DNA gave better genotyping results than urinary DNA. Therefore, if the choice exists, saliva is the preferred noninvasive matrix for genotyping purposes in large-scale genetic epidemiologic studies. Only in particular cases using urine could nevertheless be considered useful, although specific limitations need to be taken into account.

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Section: Discussionsupporting

confidence: 85%

Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

et al. 2020

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“…RNA) are present that absorb at 260 nm (e.g. Qubit: 100 ng/µl; Nanodrop: 150 ng/µl gives an acceptable ratio of 1:1.5; (O’Neill, McPartlin, Arthure, Riedel, & McMillan, 2011).…”

Section: Resultsmentioning

confidence: 99%

“…In our workflow, we first aimed to recover high molecular weight DNA with a Nanodrop/Qubit concentration ratio that was close to one. We then optimized DNA purity based on 260/280 nm ratios, which are indicative of protein contamination, and 260/230 nm ratios, which are indicative of contamination by salts, phenol, and carbohydrates (O’Neill et al, 2011). To achieve this, we first tested a well-established hexadecyltrimethylammonium bromide (CTAB) extraction protocol to extract DNA from E. pauciflora leaves collected in June 2017 from adult trees in the Kosciuszko National park near Thredbo, New South Wales, Australia (Healey et al, 2014; Schwessinger & Rathjen, 2017).…”

Section: Resultsmentioning

confidence: 99%

A comprehensive toolkit to enable MinION sequencing in any laboratory

Schalamun

Kainer²,

Beavan³

et al. 2018

Preprint

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“…Contamination of genomic DNA with fragmented DNA or RNA can lead to overestimation in quantification by spectrophotometer [12, 13]. Therefore, we used the Qubit readings, which should directly reflect the concentration of double-stranded DNA, as our final estimate of DNA concentration in all samples.…”

Section: Discussionmentioning

confidence: 99%

Performance Characterization and Validation of Saliva as an Alternative Specimen Source for Detecting Hereditary Breast Cancer Mutations by Next Generation Sequencing

Meghnani¹,

Mohammed²,

Giauque³

et al. 2016

International Journal of Genomics

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Identification of pathogenic germline mutations by next generation sequencing is a widely accepted tool for predicting the risk of hereditary cancer development. Blood is the most common source of DNA for such tests. However, blood as a sample type has many drawbacks, including the invasive collection method, poor sample stability, and a relatively high cost of collection. Therefore, in the current study we have assessed the suitability of saliva as an alternative source of genomic DNA for the identification of germline mutations in the BRCA1/2 genes by next generation sequencing (NGS). Our results show that all of the samples yielded DNA concentrations sufficient for library preparation. The concentrations of the final libraries, which were generated by PCR using target specific primers, fall into the expected range with no notable difference between libraries generated from DNA derived from saliva or blood. Quality parameters indicate that sequencing performance is comparable across sample source. An average of (98 ± 0.02)% variant calling concordance was obtained between the two specimen sources. Our data recommends saliva as a potential alternative for detecting germline mutation by next generation sequencing.

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Comparison of the TLDA with the Nanodrop and the reference Qubit system

Cited by 46 publications

References 3 publications

Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

Selection of a Noninvasive Source of Human DNA Envisaging Genotyping Assays in Epidemiological Studies: Urine or Saliva?

A comprehensive toolkit to enable MinION sequencing in any laboratory

Performance Characterization and Validation of Saliva as an Alternative Specimen Source for Detecting Hereditary Breast Cancer Mutations by Next Generation Sequencing

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