High-Throughput and Cost-Effective Characterization of Induced Pluripotent Stem Cells

Stem Cell Reports. 2017 Apr 11;8(4):1101-1111. doi: 10.1016/j.stemcr.2017.03.011.


Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) offers the possibility of studying the molecular mechanisms underlying human diseases in cell types difficult to extract from living patients, such as neurons and cardiomyocytes. To date, studies have been published that use small panels of iPSC-derived cell lines to study monogenic diseases. However, to study complex diseases, where the genetic variation underlying the disorder is unknown, a sizable number of patient-specific iPSC lines and controls need to be generated. Currently the methods for deriving and characterizing iPSCs are time consuming, expensive, and, in some cases, descriptive but not quantitative. Here we set out to develop a set of simple methods that reduce cost and increase throughput in the characterization of iPSC lines. Specifically, we outline methods for high-throughput quantification of surface markers, gene expression analysis of in vitro differentiation potential, and evaluation of karyotype with markedly reduced cost.

Keywords: SNP arrays; differentiation potential; digital karyotyping; flow cytometry; fluorescent cell barcoding; high-throughput methods; induced pluripotent stem cells; pluripotency characterization; qPCR.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Biomarkers / metabolism
  • Cell Differentiation
  • Cell Line
  • Cellular Reprogramming / genetics
  • Cost-Benefit Analysis
  • Genetic Variation*
  • Genotype
  • High-Throughput Screening Assays / economics
  • High-Throughput Screening Assays / instrumentation
  • High-Throughput Screening Assays / methods*
  • Humans
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism*
  • Karyotyping / economics
  • Karyotyping / methods*
  • Myocytes, Cardiac / cytology
  • Myocytes, Cardiac / metabolism*
  • Neurons / cytology
  • Neurons / metabolism*
  • Phenotype


  • Biomarkers