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Concordance of Next Generation Sequence-based and Sequence SpecificOligonucleotide Probe-based HLA-DRB1 genotyping

机译：下一代基于序列和序列特定的一致性基于寡核苷酸探针的HLA-DRB1基因分型

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Next generation sequencing (NGS) of clonally amplified DNA, using Roche 454 technology, was used to genotype HLA-DRB1, DRB3, DRB4, and DRB5 loci (exon 2 only) from a set of 993 samples from newborns with maternally-reported African American ancestry. DRB1 exon 2 was genotyped previously on the same sample set using sequence-specific oligonucleotide probe (SSOP) technology. Comparison of the genotype calls from both methods indicated concordance of 92.3%. Some discordance was expected due to the higher resolution of NGS data, compared to SSOP data. This resulted from selection of the incorrect allele from the ambiguity string produced by SSOP genotyping. Of 76 discordant genotypes, only three were due to resolution of ambiguity with the NGS method. The low percent of changes due to the increased resolution of the NGS method instills confidence in the overall value of previous data genotyped with moderate resolution methods, i.e., the vast majority of alleles present in a population are those that are detectable at moderate resolution. The remaining 73 discordant genotypes resulted from preventable errors in sample handling, data interpretation, and data entry. These results underscore the potential for errorthat can result from factors such as low quality genomic DNA, manual data entry,and interpretation of marginal genotyping results. Optimization of genomic DNAquality, automation of genotyping steps wherever possible, and use of thehighest resolution technology available can lead to dramatic improvements in HLAgenotype data quality. NGS-based methodology generated data of superior qualityand accuracy compared to the SSOP system.
机译：使用Roche 454技术对克隆扩增的DNA进行下一代测序（NGS），对来自993例新生儿的母体报告非裔美国人的样本中的HLA-DRB1，DRB3，DRB4和DRB5基因座进行基因分型（仅外显子2）。祖先。使用序列特异性寡核苷酸探针（SSOP）技术，先前在同一样本集上对DRB1外显子2进行了基因分型。两种方法对基因型的比较表明一致性为92.3％。由于NGS数据比SSOP数据具有更高的分辨率，因此预计会有一些不一致。这是由于从SSOP基因分型产生的歧义字符串中选择了错误的等位基因。在76个不一致的基因型中，只有3个是由于使用NGS方法解决了歧义。由于NGS方法分辨率提高而导致的变化百分比较低，这使人们对使用中分辨率方法进行基因分型的先前数据的整体价值充满信心，即，群体中存在的绝大多数等位基因都是在中分辨率下可检测到的等位基因。其余73个不一致的基因型是由于样本处理，数据解释和数据输入中的可预防错误所致。这些结果强调了潜在的错误可能是由于低质量的基因组DNA，手动输入数据，和边际基因分型结果的解释。基因组DNA的优化质量，尽可能自动进行基因分型的步骤以及使用可用的最高分辨率技术可以显着改善HLA基因型数据质量。基于NGS的方法生成了高质量的数据和SSOP系统相比，准确性更高。

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