Table 2.

Technical challenges and strategies for iPSC comparisons.

TECHNICAL CHALLENGE	POSSIBLE CAUSE	EXPERIMENTAL STRATEGY
Variability between iPSCs	Genetic background	Increase sample size; use genome editing or RNAi on isogenic cells
	Gender/age differences	Include gender/aged matched controls
	Clone-to-clone variability	Study 2 or more clones per patient
	Lentiviral integration	Use non-integrating episomal vectors or Sendai virus to reprogram
	Experimental conditions	Plate and assay lines side-by-side with controls
Inconsistent differentiation	iPSC culture conditions	Equilibrate all lines to one growth condition for all lines prior to starting the experiment
	Partially reprogrammed lines	Validate morphology, markers, self-renewal, and teratoma formation for each line
	Protocol insufficiently robust	Optimize differentiation protocol
	Disease gene affects differentiation	Increase sample size and perform rescue experiments
	Memory of somatic cell lineage	Establish controls from same somatic cell type
Inconsistent mutant phenotype	Outlier iPSC lines	Present individual patient data alongside pooled data
	Allelic differences	Sequence genes and assess genotype-phenotype relationship
	Secondary defects in source tissue	Reprogram a cell type unaffected by the disease