Molecular markers
Short tandem repeat genotyping
Authors: Nancy M. Joseph, M.D., Nicholas R. Ladwig, M.D., Nicholas Willard, D.O., Sarah Umetsu, M.D., Ph.D.
Editorial Board Member: Josephine K. Dermawan, M.D., Ph.D.
Editor-in-Chief: Debra L. Zynger, M.D.
Last author update: 2 April 2024
Last staff update: 2 April 2024
Copyright: 2018-2024, PathologyOutlines.com, Inc.
PubMed Search: Short tandem repeat genotyping
Table of Contents
Definition / general | Essential features | Pathophysiology | Laboratory | Pitfalls in interpretation | Uses by pathologists | Case reports | Molecular / cytogenetics images | Sample pathology report | Board review style question #1 | Board review style answer #1Cite this page: Joseph NM, Ladwig NR, Willard N, Umetsu S. Short tandem repeat genotyping. PathologyOutlines.com website. https://www.pathologyoutlines.com/topic/molecularshttandreptgenotyp.html. Accessed April 19th, 2024.
Definition / general
- Molecular technique that compares DNA from ≥ 2 samples to determine whether they share a common origin
- General uses include
- Paternity testing
- Donor cell engraftment in bone marrow transplant recipients
- 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
- Biparental, nonmolar pregnancy
- 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
- Monospermic complete mole (90% of complete moles)
- 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
- Dispermic partial mole (90% of partial moles)
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
- For tissue identity 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)
- In post-bone marrow transplant patients with high leukemic burden, can show allelic changes reflecting genomic changes in leukemia (e.g., loss of heterozygosity)
- Low level donor or recipient peaks can be hidden within canonical stutter peaks
Uses by pathologists
- Useful for resolving questions of mislabeled samples, specimen contamination or tissue floater (Arch Pathol Lab Med 2003;127:213, Adv Anat Pathol 2008;15:211)
- Diagnosis of hydatidiform moles in morphologically abnormal products of conception (Am J Surg Pathol 2008;32:445, Annu Rev Pathol 2017;12:449)
- Outperforms p57 immunohistochemistry alone for several reasons (Am J Surg Pathol 2009;33:805)
- Resolves equivocal p57 results
- Ability to diagnose partial moles that are not detected by p57 immunohistochemistry
- Outperforms p57 immunohistochemistry alone for several reasons (Am J Surg Pathol 2009;33:805)
- Determining the origin of tumors presenting in association with the placenta (Am J Surg Pathol 2018;42:807)
- Distinguishing gestational from nongestational choriocarcinoma (Int J Surg Pathol 2008;16:226)
- Confirming teratomatous origin of teratoma associated somatic neoplasms (Histopathology 2016;69:383)
- Quantitatively test the engraftment of donor cells in the bone marrow transplant recipients
- Longitudinally monitors the percentage of donor cells versus recipient cells
- Can evaluate bone marrow or sorted fractions of peripheral blood (e.g. CD3, CD33, CD56)
- Also used in conjunction with measurable residual disease techniques, such as flow cytometry and droplet digital PCR
- Can suffer from a lack of quantitative assay precision
- Longitudinally monitors the percentage of donor cells versus recipient cells
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
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.
- Posttransplant bone marrow with complete donor cell engraftment (100% donor cells)
- No molecular evidence of residual pretransplantation host cells is detected in the bone marrow specimen by our PCR based STR chimerism assay. This finding indicates complete donor cell engraftment.
- Peripheral blood with only partial engraftment in the lymphoid population
- Donor cells contribute approximately 80% of the total cell population in the CD3 enriched cell fraction of the peripheral blood specimen by our PCR based STR chimerism assay, while no molecular evidence of residual pretransplantation host cells is detected in its CD33 enriched cell fraction. These findings indicate complete donor cell engraftment in the myeloid lineage.
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 peak matches and 2 peaks do not match
- 2 peaks match and 1 peak does not match
- All peaks match
- 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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Reference: Short tandem repeat genotyping
