Loomis Stephanie J, Olson Lana M, Pasquale Louis R, Wiggs Janey, Mirel Daniel, Crenshaw Andrew, Parkin Melissa, Rahhal Brandon, Tetreault Stephanie, Kraft Peter, Tworoger Shelley S, Haines Jonathan L, Kang Jae H
Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114, USA.
Biomark Insights. 2010 May 20;5:49-55. doi: 10.4137/bmi.s5062.
It is unclear if buccal cell samples contain sufficient human DNA with adequately sized fragments for high throughput genetic bioassays. Yet buccal cell sample collection is an attractive alternative to gathering blood samples for genetic epidemiologists engaged in large-scale genetic biomarker studies. We assessed the genotyping efficiency (GE) and genotyping concordance (GC) of buccal cell DNA samples compared to corresponding blood DNA samples, from 32 Nurses' Health Study (NHS) participants using the Illumina Infinium 660W-Quad platform. We also assessed how GE and GC accuracy varied as a function of DNA concentration using serial dilutions of buccal DNA samples. Finally we determined the nature and genomic distribution of discordant genotypes in buccal DNA samples. The mean GE of undiluted buccal cell DNA samples was high (99.32%), as was the GC between the paired buccal and blood samples (99.29%). GC between the dilutions versus the undiluted buccal DNA was also very high (>97%), though both GE and GC notably declined at DNA concentrations less than 5 ng/mul. Most (>95%) genotype determinations in buccal cell samples were of the "missing call" variety (as opposed to the "alternative genotype call" variety) across the spectrum of buccal DNA concentrations studied. Finally, for buccal DNA concentration above 1.7 ng/ul, discordant genotyping calls did not cluster in any particular chromosome. Buccal cell-derived DNA represents a viable alternative to blood DNA for genotyping on a high-density platform.
目前尚不清楚颊细胞样本是否含有足够的人类DNA以及具有足够大小的片段,以用于高通量基因生物测定。然而,对于从事大规模基因生物标志物研究的基因流行病学家来说,收集颊细胞样本是采集血液样本的一个有吸引力的替代方法。我们使用Illumina Infinium 660W-Quad平台,评估了32名护士健康研究(NHS)参与者的颊细胞DNA样本与相应血液DNA样本相比的基因分型效率(GE)和基因分型一致性(GC)。我们还通过对颊细胞DNA样本进行系列稀释,评估了GE和GC准确性如何随DNA浓度变化。最后,我们确定了颊细胞DNA样本中不一致基因型的性质和基因组分布。未稀释的颊细胞DNA样本的平均GE很高(99.32%),配对的颊细胞和血液样本之间的GC也很高(99.29%)。稀释样本与未稀释的颊细胞DNA之间的GC也非常高(>97%),不过在DNA浓度低于5 ng/μl时,GE和GC都显著下降。在所研究的颊细胞DNA浓度范围内,颊细胞样本中大多数(>95%)的基因型测定属于“缺失呼叫”类型(与“替代基因型呼叫”类型相对)。最后,对于颊细胞DNA浓度高于1.7 ng/μl的情况,不一致的基因分型呼叫在任何特定染色体上都没有聚集。颊细胞来源的DNA在高密度平台上进行基因分型时是血液DNA的可行替代物。