Molecular markers

Short tandem repeat genotyping


Editorial Board Member: Josephine K. Dermawan, M.D., Ph.D.
Editor-in-Chief: Debra L. Zynger, M.D.
Nancy M. Joseph, M.D.
Sarah Umetsu, M.D., Ph.D.

Last staff update: 25 January 2024 (update in progress)

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PubMed Search: Short tandem repeat genotyping

Nancy M. Joseph, M.D.
Sarah Umetsu, M.D., Ph.D.
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Cite this page: Joseph NM, Ladwig NR, Umetsu S. Short tandem repeat genotyping. PathologyOutlines.com website. https://www.pathologyoutlines.com/topic/molecularshttandreptgenotyp.html. Accessed February 22nd, 2024.
Definition / general
  • Molecular technique that compares DNA from ≥ 2 samples to determine whether 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
    • Testing of suspected teratoma derived somatic neoplasms
Essential features
  • Like microsatellites, short tandem repeats (STRs) 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 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 2 alleles for every STR locus; 1 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 1 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
Pathophysiology
  • Specimen identity
    • If tissue is derived from 2 different individuals (i.e., 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: 1 maternal and 1 paternal allele at each locus
    • Digynic triploid, nonmolar pregnancy
      • Triploid: 2 maternal and 1 paternal allele at each locus
  • Complete mole
    • Monospermic complete mole (90% of complete moles)
      • 1 sperm fertilizes an ovum without maternal DNA, sperm subsequently divides to produce diploid genome
      • Diploid: 2 homozygous paternal alleles at each locus; no maternal alleles
    • Dispermic complete mole (10% of complete moles)
      • 2 sperm fertilize an ovum without maternal DNA
      • Diploid: 2 heterozygous paternal alleles at each locus; no maternal alleles
  • Partial mole
    • Dispermic partial mole (90% of partial moles)
      • Triploid: 1 maternal and 2 heterozygous paternal alleles at each locus
    • Monospermic partial mole (10% of partial moles)
      • Triploid: 1 maternal and 2 homozygous paternal alleles at each locus
Laboratory
  • Can be performed on formalin fixed paraffin embedded (FFPE) tissue
    • For hydatidiform mole diagnosis: requires separation of fetal / placental tissue (tissue of interest) from decidua (maternal tissue reference)
    • Performed on both samples
  • Multiplex polymerase chain reaction (PCR) 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
Pitfalls in interpretation
Uses by pathologists
Case reports
  • First trimester abortus; testing identifies tetraploid partial hydatidiform mole (Int J Gynecol Pathol 2012;31:73)
  • 19 year old woman with an ovarian mass; testing determines nongestational choriocarcinoma (Int J Gynecol Cancer 2007;17:254)
  • 44 year old woman and tissue sample from a 34 week placenta; testing was used to determine the uterine origin of tumors presenting in association with the placenta (Am J Surg Pathol 2018;42:807)
  • 57 year old woman; testing distinguishes uterine gestational from nongestational choriocarcinoma 22 years following pregnancy (Int J Surg Pathol 2008;16:226)
  • 62 year old woman; testing used to distinguish ectopic tissue from specimen contamination in a gallbladder specimen (Hum Pathol 2007;38:378)
  • 70 year old man; testing demonstrates specimen mix up in a gastric biopsy specimen (Am J Forensic Med Pathol 2004;25:113)
  • 9 women with ovarian mucinous neoplasms in association with teratomatous tissue; testing confirms teratomatous origin in all 6 cases in which testing was informative (Histopathology 2016;69:383)
Molecular / cytogenetics images

Contributed by Nicholas R. Ladwig, M.D.
STR locus

STR locus

STR PCR

STR PCR

Example: specimen identity testing

Example: specimen identity testing

Example: molar testin

Example: molar testing

Example: molar testing with low level maternal contamination

Example: molar testing with low level maternal contamination

Examples and interpretations

Example: STR genotyping of a uterine tumor

Sample pathology report
  • Products of conception, evacuation:
    • Consistent with nonmolar gestation with digynic triploidy (see comment)
    • Comment: The genetic profile of the villous tissue compared with the maternal tissue is consistent with a nonmolar gestation with digynic triploidy. PCR data analysis: villous tissue showing a digynic triploid genotype. 6 of 15 amplified STR loci were diagnostic for a digynic triploid genotype. The remaining amplified loci were consistent with this diagnosis. These pregnancies are nonmolar.
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. 1 peak matches and 2 peaks do not match
  2. 2 peaks match and 1 peak does not match
  3. All peaks match
  4. No peaks match
Board review style answer #1
A. 1 peak matches and 2 peaks do not match. 1 peak matches, corresponding to maternal DNA contribution; 2 nonmaternal peaks do not match, corresponding to 2 separate DNA contributions from sperm with different STR alleles. Answer C is incorrect because all peaks matching would support the tissue in question being of maternal origin without extra DNA contribution and might be expected in a specimen identity test of tissue that belongs to this patient. Answer D is incorrect because no peaks matching would support no maternal DNA contribution to the tissue in question and might be expected in a specimen identity test of tissue from another patient. Answer B is incorrect because 2 peaks matching the maternal sample corresponds to digynic triploidy, which represents a nonmolar gestation.

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Reference: Short tandem repeat genotyping
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