Forensic STRs

What is an STR?

Short Tandem Repeats (STRs) are regions of DNA where a short sequence of bases is repeated multiple times in a row.

Example:

ATCT ATCT ATCT ATCT ATCT

In this sequence:

• The same pattern (ATCT) appears repeatedly
• Each block has 4 bases
• The block is repeated 5 times consecutively

Because the sequence is repeated 5 times, this is called: Allele 5

This is a simplified example of a perfect repeat. At real loci, the allele number follows a length convention calibrated for each locus, and it does not always equal the number of blocks (see the counterexample below).

How to interpret an STR sequence

To determine the allele in a simple repeat, you need to answer: “how many times is the same sequence repeated?” In a simple repeat like this one, that number defines the allele.

Example

ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT

The same sequence appears 10 times. Allele designation = 10

Quick notation

For users already familiar with STR terminology:

Motif = ATCT

Repeat count = 5

Allele = 5

This is the standard way to summarize the same information.

When the sequence is not a full repeat

Some alleles include an incomplete repeat. In this example it is at the end, but it can also sit inside the repeat region.

Example:

ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT AT

• Full repeats: 9
• Remaining bases: AT (2 bases of a 4-base motif)

Allele designation = 9.2

How to read decimal alleles

• Integer = complete repeats
• Decimal = extra bases from a partial repeat

Examples:

• 12.1 → 1 base of an incomplete repeat
• 12.2 → 2 bases of an incomplete repeat

Practical interpretation: “number of full repeats + extra bases”. The suffix counts the extra bases; it does not say where they are. In TH01 9.3, for example, the missing base is inside the repeat region: [AATG]6 ATG [AATG]3.

A real counterexample. At D6S474, the GRCh38 reference allele has 5 + 12 = 17 repeat blocks (AGAT[5]GATA[12]), yet its harmonized designation is 16 (Bodner et al., 2024). Counting blocks gives the allele only at simple loci.

STR analysis in forensic practice (CE overview)

In forensic laboratories, STRs are commonly analyzed using Capillary Electrophoresis (CE).

• DNA fragments are amplified using PCR
• The size of each fragment is measured
• The allele is inferred from fragment length, using allelic ladders calibrated for each locus

Important: CE provides fragment size, not the underlying DNA sequence.

This means:

• The allele number reflects length
• Internal sequence variation is not observed

Sequence-level variation (brief note)

Different DNA sequences can produce the same allele number if they have the same length.

These are known as isoalleles.

• Same allele designation
• Different underlying sequence

(This is explored further in sequence-based STR analysis modules)

Summary

• STRs are repeated DNA sequences
• In simple loci, the allele corresponds to the number of repeats; each locus follows its own calibrated length convention
• Partial repeats are represented with decimals (e.g., 9.2); the decimal counts extra bases, not their position
• CE measures fragment size, not sequence
• Identical allele sizes may differ at the sequence level

References

1. Bodner M, Ballard D, Borsuk LA, King JL, Parson W, Phillips C et al. (2024). Harmonizing the forensic nomenclature for STR loci D6S474 and DYS612. Forensic Science International: Genetics, 70, 103012. https://doi.org/10.1016/j.fsigen.2024.103012