Identity Testing

Identity testing uses highly polymorphic short tandem repeat (STR) markers to compare DNA profiles between samples. The clinical genetics laboratory applies STR identity testing in four main contexts: maternal cell contamination (MCC) testing of prenatal specimens, parentage (paternity/maternity) testing, specimen identity confirmation (sample mix-up resolution and tumor/normal pairing), and as a foundation for chimerism monitoring and forensic identification. STRs are chosen because they are abundant, multi-allelic, easy to multiplex, and produce a discriminating profile from very small DNA inputs.

• STRs (microsatellites) are tandemly repeated 2-6 bp motifs with high heterozygosity (typically 0.7-0.9), making them ideal for distinguishing individuals.
• CODIS (Combined DNA Index System) is the FBI-maintained forensic database. The expanded CODIS core panel includes 20 autosomal STR loci plus amelogenin (sex marker). Most clinical identity panels overlap heavily with CODIS markers.
• Typical clinical panels test 13-16 autosomal STRs plus amelogenin, with a random match probability on the order of 1 in 10^15 or rarer for unrelated individuals.

Required when a prenatal sample is processed for genetic analysis. The concern is that maternal cells (decidua in CVS, blood-tinged amniotic fluid, maternal tissue in products of conception) may overgrow or contaminate the fetal sample, leading to a false maternal genotype reported as fetal.

• When to perform: routinely on CVS, amniocentesis, and POC samples sent for molecular or cytogenetic analysis (especially when sequencing or microarray is being run on direct or cultured cells).
• Method: 13-15 STR markers compared between the maternal blood sample and the fetal specimen.
• Expected fetal result: at each marker, one allele matching the mother and one paternal allele (the non-maternal allele). If only maternal alleles are present at multiple loci, the sample is presumed contaminated with maternal cells.
• Quantitative MCC: peak height ratios estimate the percentage of maternal contamination. Thresholds (often >5-10%) trigger reporting caveats or rejection of the result.
• Critical for: confirming fetal origin before reporting carrier or affected status, especially when the result has reproductive consequences.

STR-based comparison of alleged father, mother, and child to test biologic parentage.

• At each locus, the child must inherit one allele from the mother and one from the biologic father (Mendelian inheritance). Any non-maternal allele in the child must be present in the alleged father; otherwise that locus is an exclusion.
• Combined paternity index (CPI): the product of paternity indices across all tested loci. Larger CPI = stronger support for paternity.
• Probability of paternity (W): derived from CPI assuming a 50% prior. Reporting standards (AABB) require W > 99.0% for an inclusion; two or more locus exclusions for an exclusion (a single mismatch can reflect mutation).
• Prenatal paternity testing is feasible from CVS, amniocentesis, or cell-free fetal DNA in maternal plasma (NIPP).

• Tumor/normal pair verification: in somatic cancer panels, STR comparison confirms that the tumor and germline samples come from the same patient before reporting somatic-only variants.
• Sample mix-up resolution: when results are inconsistent with clinical context (for example, an unexpected sex chromosome configuration or implausible variant), STR comparison to a fresh patient sample resolves whether a mix-up occurred.
• Pre- and post-transplant samples: baseline STR profile of donor and recipient.

• Post-transplant chimerism monitoring: after allogeneic hematopoietic stem cell transplant, STR analysis of peripheral blood (or sorted lineages) quantifies the percentage of donor versus recipient DNA. Increasing recipient signal can herald relapse or graft loss.
• Forensic identification: CODIS STRs are the regulatory standard for criminal databasing, mass disaster victim identification, and missing persons. Y-STRs and mitochondrial DNA supplement when male-lineage or maternal-lineage testing is needed.

Biological chimerism

Two genetically distinct cell lines in one person, arising without a transplant. STR identity testing is the diagnostic tool.

• Tetragametic chimerism: fusion of two zygotes, or a zygote plus a separately fertilized polar body. Presents as a 46,XX/46,XY difference of sex development with ambiguous genitalia, or as patchy skin pigmentation along the lines of Blaschko, or heterochromia. Test several tissues (blood, buccal, cultured skin fibroblasts, and gonadal tissue when available), because a single tissue can look entirely normal.
• Twin-to-twin blood chimerism: shared placental vasculature in dizygotic twins seeds each twin's marrow with the other's stem cells. Blood shows a mixed profile while skin fibroblasts are pure. A recognized cause of confusing blood-based results, including a paternity test that appears to exclude a true father.
• Fetomaternal microchimerism: fetal cells persist in the mother for decades and maternal cells persist in the child. Ordinarily below the detection limit of a clinical STR panel, but relevant to more sensitive assays.
• Chimerism is not mosaicism. Chimerism is two cell lines from two zygotes; mosaicism is two cell lines from one zygote diverging after fertilization. STR profiling separates them: a chimera can show three or four alleles at a single locus, because two independent genomes are present, while a mosaic cannot.