Methodology article

Optimization and evaluation of T7 based RNA linear amplification protocols for cDNA microarray analysis

Hongjuan Zhao¹ , Trevor Hastie² , Michael L Whitfield³ , Anne-Lise Børresen-Dale⁴ and Stefanie S Jeffrey¹

¹Department of Surgery, Medical School Lab-Surge Bldg P214, Stanford University, Stanford, CA 94305-5494, USA

²Department of Statistics, Sequoia Hall, Stanford University, Stanford, CA 94305-4065, USA

³Department of Genetics, CCSR 2260, Stanford University, Stanford, CA 94305-5163, USA

⁴Department of Genetics, Norwegian Radium Hospital, University of Oslo, Oslo, Norway

author email corresponding author email

BMC Genomics 2002, 3:31doi:10.1186/1471-2164-3-31

Published:	30 October 2002

Abstract

Background

T7 based linear amplification of RNA is used to obtain sufficient antisense RNA for microarray expression profiling. We optimized and systematically evaluated the fidelity and reproducibility of different amplification protocols using total RNA obtained from primary human breast carcinomas and high-density cDNA microarrays.

Results

Using an optimized protocol, the average correlation coefficient of gene expression of 11,123 cDNA clones between amplified and unamplified samples is 0.82 (0.85 when a virtual array was created using repeatedly amplified samples to minimize experimental variation). Less than 4% of genes show changes in expression level by 2-fold or greater after amplification compared to unamplified samples. Most changes due to amplification are not systematic both within one tumor sample and between different tumors. Amplification appears to dampen the variation of gene expression for some genes when compared to unamplified poly(A)⁺ RNA. The reproducibility between repeatedly amplified samples is 0.97 when performed on the same day, but drops to 0.90 when performed weeks apart. The fidelity and reproducibility of amplification is not affected by decreasing the amount of input total RNA in the 0.3–3 micrograms range. Adding template-switching primer, DNA ligase, or column purification of double-stranded cDNA does not improve the fidelity of amplification. The correlation coefficient between amplified and unamplified samples is higher when total RNA is used as template for both experimental and reference RNA amplification.

Conclusion

T7 based linear amplification reproducibly generates amplified RNA that closely approximates original sample for gene expression profiling using cDNA microarrays.