Short-tandem repeat markers

Genetic markers

These are specific known locations on chromosomes.

Focus on markers in Non-coding regions of DNA

Most genetic markers are repeated DNA sequencing where highly polymorphic for distinguishing one person from another.

Satellite DNA

Very long arrays of tandem repeats. Not typically used in forensic analysis due to their size and complexity

Minisatellites (VNTRs)

Repeats units of 6-50 base pairs. Used in early DNA fingerprinting but largely replaced by STRs due to the need for large DNA quantities and difficulties with degraded samples.

Microsatellites (STRs)

Repeat units of 2-6 base pairs. The Gold standard in modern DNA typing

Dinucleotide, Trinucleotide, tetranucleotide, pentanucleotide

________: 2bp repeats common but prone to stutter artifacts

_________: 3bp repeats, relevant in medical genetic.

___________: 4bp repeats Preferred in forensic- low stutter rates and cleaner profiles

________: 5 bp repeat used in some expanded kits

Simple repeats, compound repeats

______ ______- units of identical length and sequence with non-consensus alleles

_____ _________- two or more adjacent simple repeats with several repeat blocks of variable unit length

TH01 9.3 allele is a classic example of a microvariant- an allele that contains an incomplete repeat unit.

Allelic ladder

It is a critical quality control tool that consists of a mixture of the common alleles present in the human population. Must be within ± 0.5 bp

1. Purpose: serve as a calibration standards. It can accurately assign allele designations by comparing fragment migration times.

2. Construction: they are constructed by combining PCR products from multiple individuals who collectively possess all known common alleles at a locus.

3. Genotyping Accuracy: Without these, small variations in electrophoretic conditions could cause allele miscalls. The ladder ensures that every run is internally calibrated, maintaining consistency,

13, 20

Core STR Markers is a common set of standardized markers must be used

in 1997, the FBI selected __ core CODIS loci as the national standard

in 2017, expended to __ core loci to improve international compatibility and increase discrimination power

Non-Nucleotide Link

1. 5’ Fluorescent Dye: A fluorescent label is attached at the 5’ end of the primer

2. HEO Linker Units: Non-nucleotide HEO units are added between the dye and the primer sequence. Each unit shifts apparent migration by about 2.5 bp.

3. Primer Sequence

4. Labeled PCR Product: Lebel and mobility modifiers creating a predicable size shift.

STR References, microvariant, trialleltic

The National Institute of Standard and Technology (NIST) maintains STRBase.

___ ___________: Comprehensive sequence and allele frequency data for a commonly used forensic STR loci.

_________ Alleles: Documentation of rare off ladder STR alleles and their population frequency

_______ patterns: Recording of three alleles appear in a single individual due to duplication

Additional tools: Mutation rate data, concordance studies between kits.