The utility of DNA extracted from saliva for genome-wide molecular research platforms

Bruinsma, Fiona; Joo, Jihoon E.; Wong, Ee Ming; Giles, Graham G.; Southey, Melissa C.

doi:10.1186/s13104-017-3110-y

Cited by 28 publications

(23 citation statements)

References 13 publications

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“…Blood and saliva are the most used sources of DNA for genetic studies, especially in humans [47], cats [48], and dogs [44]. However, our results indicate that tail-hair follicles seem to be more optimal than these two sources for large-scale genetic studies in camels especially for its ease of collection, transport, and storage prior to DNA extraction and for providing sufficient DNA amounts for genotyping and sequencing.…”

Section: Discussionmentioning

confidence: 82%

Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair

et al. 2019

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Camels are livestock with unique adaptations to hot-arid regions. To effectively study camel traits, a biobank of camel DNA specimens with associated biological information is needed. We examined whole-blood, saliva (buccal swabs), and tail-hair follicle samples to determine which is the best source for establishing a DNA biobank. We inspected five amounts of each of whole-blood, buccal swabs, and tail-hair follicles in nine camels, both qualitatively via gel electrophoresis and quantitatively using a NanoDrop spectrophotometer. We also tested the effects of long term-storage on the quality and quantity of DNA, and measured the rate of degradation, by analyzing three buccal swab samples and 30 tail-hair follicles over a period of nine months. Good quality DNA, in the form of visible large size DNA bands, was extracted from all three sources, for all five amounts. The five volumes of whole-blood samples (20–100μl) provided ~0.4–3.6 μg, the five quantities of buccal swabs (1–5) produced ~0.1–12 μg, while the five amounts of tail-hair follicles (10–50) resulted in ~0.7–25 μg. No differences in the rate of degradation of buccal swab and tail-hair follicle DNA were detected, but there was clearly greater deterioration in the quality of DNA extracted from buccal swabs when compared to tail-hair follicles. We recommend using tail-hair samples for camel DNA biobanking, because it resulted in both an adequate quality and quantity of DNA, along with its ease of collection, transportation, and storage. Compared to its success in studies of other domesticated animals, we anticipate that using ~50 tail-hair follicles will provide sufficient DNA for sequencing or SNP genotyping.

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Section: Discussionmentioning

confidence: 82%

Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair

et al. 2019

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“…Several buccal and saliva sample collection kits are commercially available; however, recent studies show variability among the yield and quality of DNA isolated from buccal cell and saliva kits and should be considered when determining a preferred collection method. [42][43][44] Because patients in our clinic are beginning chemotherapy regimens and require routine pretreatment blood sampling for organ function assessments, we utilized blood specimens to extract DNA for the purposes of the GatorPGx panel. However, the GatorPGx panel is also validated for buccal cell and saliva samples for use in other populations as appropriate.…”

Section: Selection Of Drug-gene Pairsmentioning

confidence: 99%

How to Transition from Single‐Gene Pharmacogenetic Testing to Preemptive Panel‐Based Testing: A Tutorial

Marrero

Cicali

Arwood

et al. 2020

Clin Pharma and Therapeutics

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There have been significant advancements in precision medicine and approaches to medication selection based on pharmacogenetic results. With the availability of direct‐to‐consumer genetic testing and growing awareness of genetic interindividual variability, patient demand for more precise, individually tailored drug regimens is increasing. The University of Florida (UF) Health Precision Medicine Program (PMP) was established in 2011 to improve integration of genomic data into clinical practice. In the ensuing years, the UF Health PMP has successfully implemented several single‐gene tests to optimize the precision of medication prescribing across a variety of clinical settings. Most recently, the UF Health PMP launched a custom‐designed pharmacogenetic panel, including pharmacogenes relevant to supportive care medications commonly prescribed to patients undergoing chemotherapy treatment, referred to as “GatorPGx.” This tutorial provides guidance and information to institutions on how to transition from the implementation of single‐gene pharmacogenetic testing to a preemptive panel‐based testing approach. Here, we demonstrate application of the preemptive panel in the setting of an adult solid tumor oncology clinic. Importantly, the information included herein can be applied to other clinical practice settings.

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“…DNA derived from blood, plasma, dried blood spots, saliva, fresh-frozen and FFPE material have all been successfully assayed using this platform. 42,55,56 Bisulphite sequencing methods include reduced-representation bisulphite sequencing (RRBS), 57 MethylC-seq, 58 targeted bisulphite sequencing and whole-genome bisulphite sequencing (WGBS). 59 These methods quantitatively detect methylation at single base resolution and, depending on the assay, can evaluate methylation at a specific region (e.g.…”

Section: Timing Of Sample Collection For Dna Methylation Measurementmentioning

confidence: 99%

Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer

2020

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Current risk prediction models estimate the probability of developing breast cancer over a defined period based on information such as family history, non-genetic breast cancer risk factors, genetic information from high and moderate risk breast cancer susceptibility genes and, over the past several years, polygenic risk scores (PRS) from more than 300 common variants. The inclusion of additional data such as PRS improves risk stratification, but it is anticipated that the inclusion of epigenetic marks could further improve model performance accuracy. Here, we present the case for including information on DNA methylation marks to improve the accuracy of these risk prediction models, and consider how this approach contrasts genetic information, as identifying DNA methylation marks associated with breast cancer risk differs inherently according to the source of DNA, approaches to the measurement of DNA methylation, and the timing of measurement. We highlight several DNA-methylation-specific challenges that should be considered when incorporating information on DNA methylation marks into risk prediction models, using BRCA1, a highly penetrant breast cancer susceptibility gene, as an example. Only after careful consideration of study design and DNA methylation measurement will prospective performance of the incorporation of information regarding DNA methylation marks into risk prediction models be valid.

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The utility of DNA extracted from saliva for genome-wide molecular research platforms

Cited by 28 publications

References 13 publications

Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair

Quality and quantity of dromedary camel DNA sampled from whole-blood, saliva, and tail-hair

How to Transition from Single‐Gene Pharmacogenetic Testing to Preemptive Panel‐Based Testing: A Tutorial

Integrating DNA methylation measures to improve clinical risk assessment: are we there yet? The case of BRCA1 methylation marks to improve clinical risk assessment of breast cancer

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