The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses

• Published in: Molecular and cellular biology Vol. 36; no. 5; pp. 662 - 667
• Main Authors: Chen, Kaifu, Hu, Zheng, Xia, Zheng, Zhao, Dongyu, Li, Wei, Tyler, Jessica K.
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 01.03.2016; American Society for Microbiology
• Subjects: Animals; Chromatin Immunoprecipitation - methods; DNA Copy Number Variations; Genome-Wide Association Study - methods; High-Throughput Nucleotide Sequencing - methods; Humans; Sequence Analysis, DNA - methods; Sequence Analysis, RNA - methods
• ISSN: 1098-5549; 0270-7306; 1098-5549
• DOI: 10.1128/MCB.00970-14

Genome-wide analyses of changes in gene expression, transcription factor occupancy on DNA, histone modification patterns on chromatin, genomic copy number variation, and nucleosome positioning have become popular in many modern laboratories, yielding a wealth of information during health and disease states. However, most of these studies have overlooked an inherent normalization problem that must be corrected with spike-in controls. Here we describe the reason why spike-in controls are so important and explain how to appropriately design and use spike-in controls for normalization. We also suggest ways to retrospectively renormalize data sets that were wrongly interpreted due to omission of spike-in controls.