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

TitleThe Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses.
Publication TypeJournal Article
Year of Publication2015
AuthorsChen K, Hu Z, Xia Z, Zhao D, Li W, Tyler JK
JournalMol Cell Biol
Volume36
Issue5
Pagination662-7
Date Published2015 Dec 28
ISSN1098-5549
KeywordsAnimals, Chromatin Immunoprecipitation, DNA Copy Number Variations, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA, Sequence Analysis, RNA
Abstract

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.

DOI10.1128/MCB.00970-14
Alternate JournalMol Cell Biol
PubMed ID26711261
PubMed Central IDPMC4760223
Grant ListR01HG007538 / HG / NHGRI NIH HHS / United States
R01 CA095641 / CA / NCI NIH HHS / United States
R01GM64475 / GM / NIGMS NIH HHS / United States
R01 GM064475 / GM / NIGMS NIH HHS / United States
R01CA95641 / CA / NCI NIH HHS / United States
R01 HG007538 / HG / NHGRI NIH HHS / United States
Related Faculty: 
Jessica K. Tyler, Ph.D.

Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464
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