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Although a number of knockout experiments are available for functional annotation of the genes, a comprehensive understanding of the functional roles of the noncoding DNA variations in the context of human stem cells is lacking. To identify the functional roles of various types of single-nucleotide polymorphisms (SNPs) in human stem cells, we developed a computational tool named PolymorphicSNPScout, which quantifies the disruption to stem cell function that potentially is caused by many SNPs. PolymorphicSNPScout predicts the deleteriousness of SNPs by incorporating the structural and evolutionary features of human noncoding sequences, including the regulatory elements, repetitive sequences, and conserved noncoding sequences. We examined the accuracy of PolymorphicSNPScout in evaluating the impact of the SNPs and the relationships between the deleteriousness and the types of SNPs, and estimated the potential loss of stem cell function arising from genetic variants. The results demonstrated that PolymorphicSNPScout is a powerful bioinformatics tool for the functional annotation of human polymorphisms in the context of stem cells.
Authors’ contributions {#FPar3}
======================
YK, YS, AS, and MY designed the study and drafted the manuscript. YS, AS, and MY collected the clinical data. YK, YS, and KH performed the molecular genetic studies. YS and KH contributed to the statistical analysis. SM performed the pathological examination of the resected tumor tissue. YK, YS, AS, KH, and MY reviewed and approved the final version of the manuscript. All authors read and approved the final manuscript.
Competing interests {#FPar4}
===================
The authors
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