Short tandem repeats of human genome are intrinsically unstable in cultured cells in vivo

Short tandem repeats (STRs) are a class of abundant structural or functional elements in the human genome and exhibit a polymorphic nature of repeat length and genetic variation within human populations. Interestingly, STR expansions underlie about 60 neurological disorders. However, "stutter" artifacts or noises render it difficult to investigate the pathogenesis of STR expansions. Here, we systematically investigated STR instability in cultured human cells using GC-rich CAG and AT-rich ATTCT tandem repeats as examples. We found that triplicate bidirectional Sanger sequencing with PCR amplification under proper conditions can reliably assess STR length. In addition, we found that next-generation sequencing with paired-end reads bidirectionally covering STR regions can accurately and reliably assay STR length. Finally, we found that STRs are intrinsically unstable in cultured human cell populations and during single-cell cloning. Our data suggest a general method for accurately and reliably assessing STR length and have important implications in investigating pathogenesis of STR expansion diseases.