Comparison of yield and genotyping performance of multiple displacement OmniPlex™ whole genome amplified DNA generated from multiple DNA sources
Comparison of yield and genotyping performance of multiple displacement OmniPlex™ whole genome amplified DNA generated from multiple DNA sources
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DOI：
10.1002/humu.20213
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发表时间：
2005-09-01
期刊：
影响因子：
3.9
通讯作者：
Chanock, SJ
中科院分区：
文献类型：
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作者：
Bergen, AW;Haque, KA;Chanock, SJ
全基因组扩增（WGA）的前景是基因组DNA （gDNA）的数量将不会限制分子遗传分析。基于WGA方案的多重位移扩增（MDA）和OmniPlex (TM) PCR使用来自三个组织来源（漱口水、灰白色被和淋巴细胞）的60个gDNA样本的4和5 ng输入gDNA进行评估。采用AmpFlSTR (R) Identifiler (R) assay和N = 49 TaqMan (R) SNP assay测定gDNA和wgaDNA的基因型，评估WGA DNA （wgaDNA）产量和基因分型性能。短串联重复（STR）和SNP基因分型的完成率和一致性与gDNA相比显著降低。OmniPlex wgaDNA表现出比MDA wgaDNA更大的基因分型性能降低。wgaDNA分型性能的降低分别是由于等位基因（所有方案）和位点（OmniPlex）扩增偏倚导致杂合子和位点缺失，而%GC序列含量（%GC）与TaqMan检测性能显著相关。淋巴母细胞wgaDNA表现出更高的产量（OmniPlex），绒毛wgaDNA表现出更高的STR基因分型完全性（MDA），而漱口水wgaDNA表现出更高的SNP基因分型不一致性（MDA）。wgdna的基因分型分析
The promise of whole genome amplification (WGA) is that genomic DNA (gDNA) quantity will not limit molecular genetic analyses. Multiple displacement amplification (MDA) and the OmniPlex (TM) PCR,based WGA protocols were evaluated using 4 and 5 ng of input gDNA from 60 gDNA samples from three tissue sources (mouthwash, buffy coat, and lymphoblast). WGA DNA (wgaDNA) yield and genotyping performance were evaluated using genotypes determined from gDNA and wgaDNA using the AmpFlSTR (R) Identifiler (R) assay and N = 49 TaqMan (R) SNP assays. Short tandem repeat (STR) and SNP genotyping completion and concordance rates were significantly reduced with wgaDNA from all WGA methods compared with gDNA. OmniPlex wgaDNA exhibited a greater reduction in genotyping performance than MDA wgaDNA. Reduced wgaDNA genotyping performance was due to allelic (all protocols) and locus (OmniPlex) amplification bias leading to heterozygote and locus dropout, respectively, and %GC sequence content (%GC) was significantly correlated with TaqMan assay performance. Lymphoblast wgaDNA exhibited higher yield (OmniPlex), huffy coat wgaDNA exhibited higher STR genotyping completion (MDA), whereas mouthwash wgaDNA exhibited higher SNP genotyping discordance (MDA). Genotyping of wgaDNA generated from