Department of Oncology and Strangeway's Research Laboratory, University of Cambridge, Cambridge, UK.
BMC Med Genomics. 2012 May 30;5:19. doi: 10.1186/1755-8794-5-19.
The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility of using saliva-extracted DNA in comparison to blood-derived DNA, across two genotyping platforms: Applied Biosystems Taqman™ and Illumina Beadchip™ genome-wide arrays.
Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek®) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by Gen-Probe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed.
Total DNA yields were lower from saliva (mean 24 μg, range 0.2-52 μg) than from blood (mean 210 μg, range 58-577 μg) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA.
We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.
随着临床试验中生物样本采集的趋势不断增加，需要为患者和临床医生提供方便且可接受的样本采集程序。本研究比较了两种基因分型平台（Applied Biosystems Taqman™ 和 Illumina Beadchip™ 全基因组芯片）中唾液提取 DNA 与血液衍生 DNA 的可行性。
从乳腺癌化疗药物的遗传药理学（PGSNPS）研究中招募了患者。从 79 名研究参与者中采集了配对的血液和唾液样本。使用 Oragene DNA 自采集试剂盒（DNAgenotek®）从唾液中采集和提取 DNA。EDTA 血液样本（中位数体积 8 毫升）的 DNA 由英国 Gen-Probe、Livingstone 提取。评估了 DNA 产量、DNA 质量的标准指标、配对重复样本的基因型检出率和基因型一致性。
唾液中的总 DNA 产量（平均值 24 μg，范围 0.2-52 μg）低于血液（平均值 210 μg，范围 58-577 μg），调整采集的生物材料体积后仍存在 2 倍差异。唾液 DNA 中的蛋白质污染和 DNA 片段化程度更高。79 份唾液样本中有 78 份可用于 Illumina Beadchip 芯片，使用 Taqman 检测。从 79 份唾液样本中随机选择 4 份用于在 Illumina Beadchip 芯片上进行重复基因分型。所有样本均使用 Taqman 检测进行基因分型。血液和唾液衍生 DNA 的匹配对之间的基因型检出率和基因型一致性评估了 DNA 质量，均达到了较高水平（>97%）。
我们得出结论，使用 Taqman 检测或全基因组芯片进行基因分型时，来自唾液和血液样本的 DNA 是可比的。唾液采样有可能增加临床试验中的参与者招募，同时减少多中心样本采集所需的资源和组织。
