DNA fingerprinting relies on short, repetitive stretches of non-coding DNA that vary widely from person to person. These sections, called short tandem repeats (STRs), are the gold standard in forensic identification. Rather than reading all three billion base pairs of someone’s genome, analysts zero in on 20 specific locations where repeating patterns differ enough to distinguish one individual from virtually every other person on the planet.
Why Non-Coding DNA Makes Fingerprinting Possible
Over 99.9% of human DNA is identical from person to person. Scanning the entire genome to find the unique 0.1% would be impractical, so forensic scientists focus on non-coding regions. These stretches don’t carry instructions for building proteins and have no known biological function, but they accumulate variations freely because mutations in them don’t affect survival. That freedom to mutate is exactly what makes them useful: non-coding regions are where the most person-to-person differences pile up.
Short Tandem Repeats: The Core of Modern Profiling
Short tandem repeats are tiny DNA segments where a core unit of two to six letters (nucleotides) repeats back to back. One person might have the sequence AGAT repeated 8 times at a particular spot on a chromosome, while another person has it repeated 12 times. Because everyone inherits one copy from each parent, you carry two versions of each STR location. The combination of repeat lengths across multiple locations creates a profile that is, for all practical purposes, unique.
STRs replaced an older type of marker called variable number tandem repeats (VNTRs), which have longer repeating units (roughly 20 to 100 base pairs). VNTRs were used in the earliest DNA fingerprinting work in the 1980s, but they required larger, higher-quality DNA samples. STRs work with far less material and can be amplified reliably even from degraded evidence.
The 20 CODIS Core Loci
The FBI’s Combined DNA Index System (CODIS) originally required analysis of 13 STR locations when it launched in 1997. In January 2017, seven additional loci were added, bringing the current standard to 20 core STR loci. The full set includes locations scattered across different chromosomes: CSF1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045.
Those names refer to standardized positions on specific chromosomes. Each one was chosen because it shows high variability across human populations, making it especially good at telling people apart. When all 20 loci are analyzed together, the probability of two unrelated people sharing the same profile is astronomically small. Even with fewer markers, court cases have cited random match probabilities as low as one in 19 billion.
How These Sections Are Isolated and Read
The technique that makes STR profiling practical is the polymerase chain reaction (PCR). PCR uses specially designed primers, short synthetic DNA sequences that match the regions flanking each STR locus, to selectively copy only those target sections. The process cycles through three steps repeatedly: heating the DNA to separate its two strands, cooling it so the primers attach to their matching targets, then warming it again so an enzyme builds new copies. After 25 to 30 cycles, even a tiny sample yields millions of copies of just the STR regions analysts care about.
In forensic labs, the primers carry fluorescent tags that get incorporated into the copies. When the amplified fragments are sorted by size, each STR locus produces a pair of peaks (one from each parent’s chromosome) on a graph called an electropherogram. The pattern of peaks across all 20 loci is the DNA profile.
The Amelogenin Gene for Sex Determination
Alongside the 20 STR loci, forensic profiles include one gene-based marker: amelogenin. This gene exists on both the X and Y chromosomes but differs slightly in size between them. When amplified, a sample from a female (XX) produces one fragment size, while a male sample (XY) produces two distinct fragment sizes. This gives analysts a built-in check on the biological sex of the DNA source, and it also serves as a quality control step, confirming that the amplification worked correctly.
Mitochondrial DNA for Degraded Samples
When nuclear DNA is too damaged or scarce for STR analysis, such as in old bones, hair shafts without roots, or heavily decomposed remains, forensic scientists turn to mitochondrial DNA (mtDNA). Each cell contains hundreds to thousands of mitochondria, each with its own small circular genome, so mtDNA survives conditions that destroy nuclear DNA.
The sections analyzed are called hypervariable regions, found within the control region of the mitochondrial genome. Two of these, HV1 and HV2, accumulate mutations faster than the rest of the mitochondrial genome and carry the most variation between individuals. Current forensic guidelines recommend sequencing the entire control region, though HV1 and HV2 remain the most commonly examined stretches. Mitochondrial DNA was used to confirm the identity of the remains of the Russian Romanov royal family by matching profiles to living maternal relatives, including Prince Philip.
One important limitation: mtDNA is inherited only from the mother, so it cannot distinguish between siblings or anyone sharing the same maternal lineage. It narrows down identity rather than confirming it uniquely.
Y-Chromosome STRs for Male Lineage
Y-chromosome STRs (Y-STRs) work the same way as autosomal STRs but are located on the Y chromosome, meaning only males carry them. They are especially useful in sexual assault cases where the evidence contains a mixture of male and female DNA. Standard autosomal STR analysis can struggle with heavily unbalanced mixtures because the dominant contributor’s DNA masks the minor contributor’s profile. Y-STRs bypass this problem by targeting only male-specific DNA.
Like mtDNA, Y-STRs trace a single lineage (father to son) and cannot distinguish between men in the same paternal line. They complement autosomal STRs rather than replacing them.
SNPs as a Supplementary Tool
Single nucleotide polymorphisms (SNPs) are single-letter variations at specific positions in the genome. They aren’t the primary tool for forensic identification, but they fill gaps that STRs alone can’t cover. SNPs are useful for highly degraded DNA because the target fragments are extremely short, for predicting ancestry and physical traits like eye or hair color, and for resolving complex mixtures. Some newer approaches combine SNPs and STRs into linked markers (SNP-STRs), which target a small genomic region containing both types of variation. This pairing helps analysts tease apart mixed DNA samples that would otherwise be unreadable using standard methods alone.
SNP-STR markers that align with existing CODIS loci have the added advantage of being searchable against national databases, making them practical for real casework rather than just research settings.