BACKGROUND: Human aneuploidy is the leading cause of early pregnancy loss, 
mental retardation, and multiple congenital anomalies. Due to the high mortality 
associated with aneuploidy, the pathophysiological mechanisms of aneuploidy 
syndrome remain largely unknown. Previous studies focused mostly on whether 
dosage compensation occurs, and the next generation transcriptomics sequencing 
technology RNA-seq is expected to eventually uncover the mechanisms of gene 
expression regulation and the related pathological phenotypes in human 
aneuploidy.
RESULTS: Using next generation transcriptomics sequencing technology RNA-seq, we 
profiled the transcriptomes of four human aneuploid induced pluripotent stem 
cell (iPSC) lines generated from monosomy × (Turner syndrome), trisomy 8 
(Warkany syndrome 2), trisomy 13 (Patau syndrome), and partial trisomy 11:22 
(Emanuel syndrome) as well as two umbilical cord matrix iPSC lines as euploid 
controls to examine how phenotypic abnormalities develop with aberrant 
karyotype. A total of 466 M (50-bp) reads were obtained from the six iPSC lines, 
and over 13,000 mRNAs were identified by gene annotation. Global analysis of 
gene expression profiles and functional analysis of differentially expressed 
(DE) genes were implemented. Over 5000 DE genes are determined between 
aneuploidy and euploid iPSCs respectively while 9 KEGG pathways are overlapped 
enriched in four aneuploidy samples.
CONCLUSIONS: Our results demonstrate that the extra or missing chromosome has 
extensive effects on the whole transcriptome. Functional analysis of 
differentially expressed genes reveals that the genes most affected in aneuploid 
individuals are related to central nervous system development and tumorigenesis.