Increased measurement accuracy for sequence-verified microarray probes
Increased measurement accuracy for sequence-verified microarray probes
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DOI：
10.1152/physiolgenomics.00066.2004
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发表时间：
2004-08-11
影响因子：
4.6
通讯作者：
Mariani, TJ
中科院分区：
文献类型：
--
作者：
Mecham, BH;Wetmore, DZ;Mariani, TJ
微阵列已广泛用于研究全基因组表达模式。尽管这项技术已经取得了巨大的成功，但它的个人测量精度不理想。最近在这方面取得了重大进展。为了进一步探索潜在的可变性，我们试图在全球范围内评估用于查询基因表达的单个探针序列的准确性。对于哺乳动物Affymetrix微阵列，我们发现了出乎意料的大量探针（每个平台上超过19%的探针）不对应于相应的mRNA参考序列（RefSeq）。与不准确探针获得的数据相比，我们发现序列验证探针获得的数据显示1)技术重复的精度提高，2)将数据从一代微阵列翻译到另一代微阵列的准确性提高，3)将数据从olignucleotide翻译到cDNA微阵列的准确性提高，以及4)改善了人类临床标本中生物信息的捕获。这项工作的逻辑结论是，包含最可靠的序列信息的探针提供最准确的结果。我们的数据表明，识别和去除不准确的探针可以显着改善这项技术。
Microarrays have been extensively used to investigate genome-wide expression patterns. Although this technology has been tremendously successful, it has suffered from suboptimal individual measurement precision. Significant improvements in this respect have been recently made. In an effort to further explore the underlying variability, we have attempted to globally assess the accuracy of individual probe sequences used to query gene expression. For mammalian Affymetrix microarrays, we identify an unexpectedly large number of probes (greater than 19% of the probes on each platform) that do not correspond to their appropriate mRNA reference sequence (RefSeq). Compared with data derived from inaccurate probes, we find that data derived from sequence-verified probes show 1) increased precision in technical replicates, 2) increased accuracy translating data from one generation microarray to another, 3) increased accuracy translating data from oligonucleotide to cDNA microarrays, and 4) improved capture of biological information in human clinical specimens. The logical conclusion of this work is that probes containing the most reliable sequence information provide the most accurate results. Our data reveal that the identification and removal of inaccurate probes can significantly improve this technology.