Genomic instability and chromosomal abnormalities can occur spontaneously after extended passages of cultured stem cells. The cause of genomic instability is unclear; however it is widely known that these aberrations can occur in response to several factors, including adaptation to cell culture conditions, viral infection, mitotic stress or DNA damage. Molecular techniques, such as STR, SNP and resequencing analysis are complementary tools to karyotyping analysis and. can be used to routine analyze changes in gene copy number or point mutations in nuclear and mitochondrial DNA.
- Short tandem repeat markers (or STR's) can be used to estimate macroscopic changes in chromosome number (aneuploidy or trisomy). The AmpFℓSTR® Identifiler® PCR Amplification Kit is a multiplex STR kit which contains 15 loci and 1 sex determination marker (Amelogenin) and is compatible with Applied Biosystems capillary electrophoresis instruments, such as the 3130 Genetic Analyzer.
- Single nucleotide polymorphisms (SNP) analysis can be used to detect copy number variation (CNV) or loss of heterozygosity (LOH) at target loci, like oncogenes or tumor suppressor genes. Applied Biosystems offers over 4.5 million TaqMan® SNP Genotyping Assays for human and mouse genomes. Use the SNPbrowser™ Software to view SNPs by gene or putative function, and order assays.
- The resequencing method can be used to monitor the accumulation of mutation in nuclear or mitochondrial genes. The VariantSEQr™ Resequencing System can be used to discover novel genomic variants, such as fine microdeletions, duplications or inversions in nuclear DNA. The mitoSEQr™ Resequencing System can be used to identify sequence variants in the control region or the entire human mitochondrial genome.