Practical determination of LODP (limit of detection for microarray platform) for the evaluation of microarray platforms

Satoru Adachi; Hidetoshi Aoki; Yumi Ueda; Tetsuo Sudo; Ai Nozawa; Shigetaka Koga; Hisashi Suzuki; Sachie Shibayama; Naohiro Noda; Shin-Ichiro Fujii; Sayaka Itoh; Sayaka Kawashima; Yoshihiko Suda; Hiroki Nakae

doi:10.1016/j.ab.2019.113360

Practical determination of LODP (limit of detection for microarray platform) for the evaluation of microarray platforms

Anal Biochem. 2019 Oct 15:583:113360. doi: 10.1016/j.ab.2019.113360. Epub 2019 Jul 6.

Authors

Satoru Adachi¹, Hidetoshi Aoki², Yumi Ueda³, Tetsuo Sudo⁴, Ai Nozawa⁵, Shigetaka Koga⁶, Hisashi Suzuki⁷, Sachie Shibayama⁸, Naohiro Noda⁹, Shin-Ichiro Fujii⁸, Sayaka Itoh¹⁰, Sayaka Kawashima¹¹, Yoshihiko Suda¹², Hiroki Nakae¹¹

Affiliations

¹ Special Project Z1, Zeon Corporation, 1-2-1 Yako, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-9507, Japan.
² Innovation Center, Yokogawa Electric Corporation, 2-9-32 Nakacho, Musashino-shi, Tokyo, 180-8750, Japan.
³ DNA Chip Research, Inc, 1-15-1 Kaigan, Minato-ku, Tokyo, 105-0022, Japan.
⁴ New Frontiers Research Laboratories, Toray Industries, Inc, 10-1 Tebiro 6-chome, Kamakura-shi, Kanagawa, 248-8555, Japan.
⁵ Tsurumi R&D Center, Mitsubishi Chemical Corporation, 10-1 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan.
⁶ ALPS-Engineering Headquarters, Alps Alpine Co. Ltd, 1-7 Yukigaya-otsukamachi, Ota-ku, Tokyo, 145-8501, Japan.
⁷ Research & Development Div, Yokowo Co. Ltd, 5-11 Takinogawa 7-Chome, Kita-ku, Tokyo, 114-8515, Japan.
⁸ National Metrology Institute of Japan (NMIJ), National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8563, Japan.
⁹ Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
¹⁰ Bio-innovation Policy Unit, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan; Japan Bio Measurement & Analysis Consortium, 2-4-10 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
¹¹ Japan Bio Measurement & Analysis Consortium, 2-4-10 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan.
¹² Japan Bio Measurement & Analysis Consortium, 2-4-10 Kojimachi, Chiyoda-ku, Tokyo, 102-0083, Japan. Electronic address: y.suda@jmac.or.jp.

PMID: 31288000
DOI: 10.1016/j.ab.2019.113360

Abstract

The performance indicator called limit of detection for microarray platform (LODP) was defined in ISO 16578:2013. The methods to determine practical LODP were explored. In general, + 3 SD of the background is used as the signal strength of limit of detection and criteria for dividing positive and negative results. Since the negative signal had been defined differently for each microarray platform, signals obtained from Non-Probe Spots (NPS) installed on the microarrays were defined as the "background" of microarrays. LODP was determined as the lowest concentration of which the average signal exceeded Avg. + 3 SD of the background (NPS) and the signal was significantly different from those of the lower and higher adjacent concentration points measured with a diluted series of reference materials. For reliable qualitative analysis, the positive results can be defined as signals higher than those corresponding to LODP and negative results as lower signals, without determining limit of detection for all target probes. The use of LODP also enables comparisons of platform performances without checking sequence dependencies, and assists to select reliable and fitting platforms for experimental purposes.

Keywords: Limit of detection; Microarray; Performance evaluation; Qualitative analysis; Reference material; Reliability.

Publication types

Evaluation Study

MeSH terms

Gene Expression Profiling / methods*
Limit of Detection*
Oligonucleotide Array Sequence Analysis / methods*
RNA / analysis*
Reproducibility of Results

Substances

RNA