Molecular markers

Short tandem repeat genotyping

Editor-in-Chief: Debra L. Zynger, M.D.
Nancy M. Joseph, M.D.
Sarah Umetsu, M.D., Ph.D.

Last author update: 1 October 2018
Last staff update: 17 February 2023 (update in progress)

Copyright: 2018-2019,, Inc.

PubMed Search: Short tandem repeat genotyping [title]

Nancy M. Joseph, M.D.
Sarah Umetsu, M.D., Ph.D.
Page views in 2022: 309
Page views in 2023 to date: 78
Cite this page: Joseph, NM, Ladwig, NR, Umetsu, SE. Short tandem repeat genotyping. website. Accessed March 22nd, 2023.
Definition / general
  • Molecular technique that compares DNA from two or more samples to determine if they share a common origin
  • General uses include:
    • Paternity testing
    • Forensic pathology (identity testing or DNA fingerprinting)
    • Specimen identity testing (determine origin of tissue floater or specimen mix up)
    • Diagnosis of hydatidiform molar pregnancy
Essential features
  • Like microsatellites, are repetitive stretches of DNA composed of typically 5 - 50 repeats of a short base unit that commonly ranges from 1 to 6 nucleotides in length
    • Spread throughout genome
    • Often occur in noncoding regions
    • Some short tandem repeat (STR) loci are polymorphic, meaning many different alleles exist in the population
    • For any STR locus, the only difference between alleles is the number of repeats, with the repeating unit being constant
  • Multiple (10 - 15) polymorphic STRs are typically chosen for identity testing to increase the genotype specificity from person to person
    • Individuals inherit two alleles for every STR locus, one allele from each parent
    • For polymorphic STR loci, most individuals are heterozygous at most loci
    • Because the same allele can be inherited from both parents at any given locus, most commercial kits evaluate at least 13 loci, with one including the amelogenin sex locus for sex determination
  • Identity of a specimen can be determined by comparing the STR lengths of multiple loci between a known and unknown tissue sample
  • Specimen Identity:
    • If tissue is derived from two different individuals (ie: tissue floater in block / slide or specimen mix up), the degree of polymorphism at STR loci predicts that the alleles at the majority of loci tested would not match between tissue samples
  • Normal gestation or hydropic abortus (nonmolar):
    • Biparental, nonmolar pregnancy:
      • Diploid: one maternal and one paternal allele at each locus
    • Digynic triploid, nonmolar pregnancy
      • Triploid: two maternal and one paternal allele at each locus
  • Complete mole:
    • Monospermic complete mole (90% of complete moles)
      • One sperm fertilizes an ovum without maternal DNA, sperm subsequently divides to produce diploid genome)
      • Diploid: two homozygous paternal alleles at each locus; no maternal alleles
    • Dispermic complete mole (10% of complete moles)
      • Two sperm fertilize an ovum without maternal DNA
      • Diploid: two heterozygous paternal alleles at each locus; no maternal alleles
  • Partial mole:
    • Dispermic partial mole (90% of partial moles)
      • Triploid: one maternal and two heterozygous paternal alleles at each locus
    • Monospermic partial mole (10% of partial moles)
      • Triploid: one maternal and two homozygous paternal alleles at each locus
  • Can be performed on formalin fixed paraffin embedded tissue
    • For hydatidiform mole diagnosis: requires separation of fetal / placental tissue (tissue of interest) from decidua (maternal tissue reference)
    • Performed on both samples
  • Multiplex PCR (polymerase chain reaction) with primers aligned to DNA flanking each STR locus tested (see Molecular images)
    • As the number of repeats in the STR locus increases, the length of the PCR product from that locus increases
    • PCR products at each locus are displayed on an electropherogram
      • Lateral position of peak is determined by fragment size / length
      • Vertical height of peak is roughly determined by quantity of DNA (note: the assay is not truly quantitative)
        • Height of the peak can be useful for identifying low level contamination of samples
Uses by pathologists
Pitfalls in interpretation
  • For tissue identify testing: microsatellite instability (MSI) high tumors can show unexpected allelic discordance (Hum Pathol 2014;45:549)
  • In the diagnosis of hydatidiform moles: a nonmolar pregnancy from a donated egg would show allelic discordance with the decidua and could be misinterpreted as a complete hydatidiform mole (Int J Gynecol Pathol 2014;33:507, Int J Gynecol Pathol 2018;37:191)
  • Examples:
    1. Specimen identity testing
      • Interpretation: samples show different allele patterns at all four loci displayed, consistent with the specimens being from different patients
    2. Molar testing
      • Interpretation: placenta specimen has a single nonmaternal allele at every locus; this pattern is consistent with a monospermic complete mole (a single sperm is duplicated to form the diploid zygote)
    3. Molar testing with low level maternal contamination
      • Interpretation: placental specimen shows one maternal and one paternal peak at each loci, consistent with a nonmolar gestation
        • In addition, in the placental specimen, a third, smaller peak is present in both loci (alleles 13 and 29) which each correspond to maternal alleles
        • These peaks are likely due to a small amount of maternal decidua present in the placental sample
    4. STR genotyping of a an inflammatory myofibroblastic tumor (IMT) associated with the placenta
      • Interpretation: decidua (maternal tissue) and uterine IMT show an identical pattern at all loci displayed, while the placental villi (fetal tissue) and IMT show a different pattern at 3 of 4 loci (D8S1179, D21S11 and CSF1PO)
        • This finding confirms that the IMT was of maternal origin
Case reports
Molecular / cytogenetics images

Contributed by Nicholas R. Ladwig, M.D.

STR locus


Examples and interpretations

Board review style question #1
If short tandem repeat (STR) genotyping was performed on a dispermic (diandric triploid) partial mole, what would be the expected result when the placental tissue is compared to maternal decidua?

  1. All peaks match
  2. No peaks match
  3. One peak matches and two peaks do NOT match
  4. Two peaks match and one peak does NOT match
Board review style answer #1
C. One peak matches and two peaks do NOT match

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Reference: Short tandem repeat genotyping
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