Fragment Analysis Applications

Analysis of DNA fragments enables a variety of applications, from cell line
authentication to detection of aneuploidy. While sequencing techniques, such as next-generation sequencing (NGS) also enable these applications, researchers choose fragment analysis for features such as detection of multi-repeat regions, a faster turnaround time, and a higher sensitivity and resolution.

Misidentification of cell lines produces misleading results, confusion, and added costs to research. Many journals and funding agencies now require researchers to ascertain that the cell lines they use are authentic. Fragment analysis can provide a simple, inexpensive, and highly specific genetic “fingerprint” of a cell line.

Sanger sequencing is the gold standard for sequencing single genes, confirming gene variants, detecting repeat sequences, copy number variation, and single nucleotide changes. Perfect for smaller-scale projects and for confirmation of NGS results, Sanger sequencing can complement your laboratory's techniques and lead to efficient SARS-CoV-2 research.

Microsatellite markers are polymorphic DNA loci containing repeated nucleotide sequences, typically 2 to 7 nucleotides per repeat unit. The length of the repeated unit is the same for the majority of the repeats within an individual microsatellite locus, but the number of repeats for a specific locus may differ, resulting in alleles of varying length, which can be analyzed with fragment analysis by capillary electrophoresis.

The CRISPR-Cas9 system, the easiest, most precise, and most widely adopted genome editing technology, is based on the components of a simple bacterial immune system. In any genome editing experiment, the repair process is not completely efficient or accurate. Fragment analysis can be used to screen primary transformed cultures to determine editing efficiency.

Relative fluorescent quantitation or quantitative fluorescence PCR (QF-PCR) is a technique used in a variety of fragment analysis applications that requires accurate peak height or peak area comparisons across multiple samples. Research applications that utilize this technique include evaluating loss of heterozygosity (LOH), aneuploidy assays, and detecting large chromsomal deletions.

Single-nucleotide polymorphism (SNP) genotyping is a measure of genetic variation. SNP genotyping is used to research differences in genetic traits, susceptibility to disease, and response to drug therapies. A robust tool for SNP analysis is the Applied Biosystems™ SNaPshot™ Multiplex Kit. The kit allows multiplexing during single base extensions of up to 10 primer–template combinations in a single-tube, single-capillary format.

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