通过基因芯片靶向基因分型25K、Affymetrix 500K和Illumina 550K平台对相同单核苷酸多态性进行基因分型的比较。

Comparison of identical single nucleotide polymorphisms genotyped by the GeneChip Targeted Genotyping 25K, Affymetrix 500K and Illumina 550K platforms.

作者信息

Kim Ka-Kyung, Won Hong-Hee, Cho Sang Sun, Park Jun Hee, Kim Min-Ji, Kim Seonwoo, Kim Jong-Won

机构信息

Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, South Korea.

出版信息

Genomics. 2009 Aug;94(2):89-93. doi: 10.1016/j.ygeno.2009.04.005. Epub 2009 Apr 24.

DOI:10.1016/j.ygeno.2009.04.005

PMID:19394417

Abstract

Comparisons of targeted genotyping chips to ready-made chips are important because targeted chips are suitable for fine-scale association mapping with a reasonable cost. Genotypes produced by the Affymetrix Targeted Genotyping (TG) 25K, Affymetrix 500K, and Illumina 550K arrays for regions on chromosomes 2 and 7 of 90 individuals were assessed to investigate genotype accordance between the platforms. The common SNPs in TG the Affymetrix and Illumina arrays showed similar genotype accordance. The consistency rate of the Illumina array to consensus genotypes, i.e., identically called by more than two platforms, was the highest, and that of the Affymetrix array was the lowest. The TG array data showed high accordance and reasonable consistency between platforms.

摘要

将靶向基因分型芯片与现成芯片进行比较很重要，因为靶向芯片适合以合理成本进行精细尺度的关联图谱分析。对90个个体的2号和7号染色体区域，由Affymetrix靶向基因分型（TG）25K芯片、Affymetrix 500K芯片和Illumina 550K芯片产生的基因型进行评估，以研究不同平台间的基因型一致性。Affymetrix TG芯片和Illumina芯片中的常见单核苷酸多态性（SNP）显示出相似的基因型一致性。Illumina芯片与一致性基因型（即由两个以上平台一致检出）的一致率最高，Affymetrix芯片的一致率最低。TG芯片数据显示不同平台间具有高度一致性和合理的一致性。