基于Illumina DNA检测面板对从毛发样本中提取的全基因组扩增DNA进行基因分型：性能及与口腔细胞基因组DNA基因分型结果的一致性。

Illumina DNA test panel-based genotyping of whole genome amplified-DNA extracted from hair samples: performance and agreement with genotyping results from genomic DNA from buccal cells.

作者信息

Agalliu Ilir, Schweitzer Peter A, Leanza Suzanne M, Burk Robert D, Rohan Thomas E

机构信息

Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

出版信息

Clin Chem Lab Med. 2009;47(5):516-22. doi: 10.1515/CCLM.2009.106.

DOI:10.1515/CCLM.2009.106

PMID:19397482

Abstract

BACKGROUND

Hair is a DNA source that can be collected easily and inexpensively from participants in epidemiological studies. However, there is concern about DNA quality and quantity. Therefore, we assessed genotyping performance of whole genome amplified (WGA)-DNA extracted from hair using the GenomePlex method and evaluated its agreement with genotyping results of buccal cell DNA from the same individuals, using the Illumina GoldenGate platform.

METHODS

The Illumina DNA test panel includes 360 highly validated single nucleotide polymorphisms (SNPs) selected from the Linkage IV Panel that are distributed across the entire genome. DNA was extracted from both archived hair and buccal cell samples obtained from 44 randomly selected subjects participating in a large cohort study in Canada.

RESULTS

The genotyping success rate was 97.7% for 44 paired samples. However, WGA-DNA from hair failed more during genotyping in comparison to buccal cell DNA. Hair samples with a pre-WGA-DNA>or=1 ng/microL quantified using the PicoGreen assay (n=33) showed an average genotyping completion rate of 98.8% and SNP concordance of 91.2% with genotyping performance of buccal cell DNA. In contrast, samples with a pre-WGA-DNA<1 ng/microL had lower genotyping completion rate (94%) and poor SNP concordance (49%).

CONCLUSIONS

Results suggest that WGA-DNA obtained from hair can produce excellent genotyping call rates and show relatively good SNP concordance with results from buccal cell DNA using high-throughput technology. DNA quantity obtained from hair samples is a crucial determinant of genotyping performance. Larger studies are needed to examine the utility of hair DNA with different genotyping platforms.

摘要

背景

头发是一种DNA来源，可在流行病学研究中轻松且低成本地从参与者身上采集。然而，人们对DNA的质量和数量存在担忧。因此，我们使用基因组全扩增（WGA）方法评估了从头发中提取的DNA的基因分型性能，并使用Illumina GoldenGate平台评估了其与同一受试者口腔细胞DNA基因分型结果的一致性。

方法

Illumina DNA检测面板包括从连锁IV面板中选择的360个经过高度验证的单核苷酸多态性（SNP），这些SNP分布于整个基因组。从44名随机选择的参与加拿大一项大型队列研究的受试者的存档头发和口腔细胞样本中提取DNA。

结果

44对样本的基因分型成功率为97.7%。然而，与口腔细胞DNA相比，头发来源的WGA-DNA在基因分型过程中失败的情况更多。使用PicoGreen分析法定量的预WGA-DNA≥1 ng/μL的头发样本（n = 33）显示，平均基因分型完成率为98.8%，SNP一致性与口腔细胞DNA的基因分型性能为91.2%。相比之下，预WGA-DNA＜1 ng/μL的样本基因分型完成率较低（94%），SNP一致性较差（49%）。