Editing Microsatellite (section)

===Limitations===
Repetitive DNA is not easily analysed by [[DNA sequencing|next generation DNA sequencing]] methods, which struggle with homopolymeric tracts.<ref>{{cite journal | vauthors = Tytgat O, Gansemans Y, Weymaere J, Rubben K, Deforce D, Van Nieuwerburgh F | title = Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling | journal = Genes | volume = 11 | issue = 4 | pages = 381 | date = April 2020 | pmid = 32244632 | pmc = 7230633 | doi = 10.3390/genes11040381 | s2cid = 214786277 | doi-access = free }}</ref> Therefore, microsatellites are normally analysed by conventional PCR amplification and amplicon size determination. The use of PCR means that microsatellite length analysis is prone to PCR limitations like any other PCR-amplified DNA locus. A particular concern is the occurrence of '[[null allele]]s':
* Occasionally, within a sample of individuals such as in paternity testing casework, a mutation in the DNA flanking the microsatellite can prevent the PCR primer from binding and producing an amplicon (creating a "null allele" in a gel assay), thus only one allele is amplified (from the non-mutated sister chromosome), and the individual may then falsely appear to be homozygous. This can cause confusion in paternity casework. It may then be necessary to amplify the microsatellite using a different set of primers.<ref name="Jarne 1996"/><ref name="Dakin">{{cite journal | vauthors = Dakin EE, Avise JC | title = Microsatellite null alleles in parentage analysis | journal = Heredity | volume = 93 | issue = 5 | pages = 504–9 | date = November 2004 | pmid = 15292911 | doi = 10.1038/sj.hdy.6800545 | doi-access = free }}</ref> Null alleles are caused especially by mutations at the 3' section, where extension commences.
* In species or population analysis, for example in conservation work, PCR primers which amplify microsatellites in one individual or species can work in other species. However, the risk of applying PCR primers across different species is that null alleles become likely, whenever sequence divergence is too great for the primers to bind. The species may then artificially appear to have a reduced diversity. Null alleles in this case can sometimes be indicated by an excessive frequency of homozygotes causing deviations from Hardy-Weinberg equilibrium expectations.