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Forensic Genetics

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Leanne Tonge

FZ3011 Assignment 1

FZ3011 Forensic Genetics


Short Tandem Repeat Polymorphisms


STRs, also known as microsatellites or simple sequence repeats (SSR), are 2-6bp DNA sequences tandemly repeated units flanked by unique sequence. They are usually between 100-300 bp long. They are classified based on the structure of the number of core repeats (base pairs):

  • Dinucleotide - 2
  • Trinucleotide - 3
  • Tetranucleotide - 4
  • Pentanucleotide - 5 (Russell, 2006).

They are also divided into categories depending on the type of repeats:

  • Simple – contain the exact same sequence and length with non-consensus alleles.
  • Compound – contain repeats of two or more adjacent simple repeats (non-consensus).
  • Complex – can be of several repeat blocks, varying sequences or intervening sequences.
  • Hypervariable - complex repeats with numerous non-consensus alleles, e.g. STR loci SE33 or ACTBP2.
  • Microvariants – contain alleles with incomplete repeat units, e.g. allele 9.3 at TH01 locus (Butler, 2005).


They are scattered throughout the genome and occur approx. every 10,000 nucleotides (Butler, 2005).

Methods of Detection

  • Fluorescently labelled primers in PCR products are passed through Capillary Electrophoresis. As labelled PCR products migrate through the gel towards the anode on the laser they separate based on their size. Fluorescence is measured from exciting a dye molecule and detecting the light emitted from the excited dye. Automated and simple process, accurate but more expensive. Peaks seen in electropherograms allow for an easier interpretation of the data. E.g. ABI PRISM 3730xl has 96 capillaries and analyses 4000 a day.
  • Polyacrylamide Gel Electrophoresis (PAGE) – used to separate between 20-500 nucleotides long with a single base pair resolution (Butler, 2005).

Uses in Forensic Science

They are highly polymorphic in a population so they are unique to an individual. As they are small and very useful in the forensic sense – many crime scene samples are trace evidence and sometimes very degraded. As the size of an STR is generally small they are analysed using PCR.  PCR can distinguish homozygotes and heterozygotes and define the copy number of each repeat (Russell, 2006), producing DNA profiles for comparison. The UK developed the National DNA Database in which STRs profile are stored for comparisons.

STR typing is less expensive than other methods and can be automated to a degree (PCR) so it is faster and less labour-intensive. STRs are interpreted using population genetics and produce allele frequencies for each of the loci found (Klug, 2006).

There are multiplexing kits available to use for forensic purposes, SGM Plus is the most widely used in forensic science today. This kit amplifies 10 loci for comparison, giving a 1: 3.3 trillion probability. The kit also incorporates the amelogenin loci, which tells us the sex of the profile, useful if identification is needed for missing persons or if bodies are visually unrecognisable (Goodwin, 2007). The multiplexing kits are highly polymorphic (10-50 alleles or more) and are highly discriminatory.

A major problem when interpreting STRs is when stutter artefacts are present – this disguises the results and give misrepresentation of the data. Other problems include allele drop-out/in, spikes, pull up peaks etc (Clayton, 1998).

MiniSTRs have recently been developed which produces a product of 200bp, which brings STRs more inline with SNPs.  The future of STRs can only improve the quality and effectiveness as it has rapidly improved since it began.

Single Nucleotide Polymorphisms


  • A SNP is a single base pair change (mutation) at the SNP locus and account for 85% of human genetic variation.
  • They are bi-allelic meaning they have two possible alleles and three possible genotypes, e.g. SNP locus has A and B alleles. The genotypes could be AA, BB or AB.


Millions of SNPs occur in an individual and in the human genome they occur in every 1000 nucleotides. The majority of SNPs occur in non-coding regions, called non-coding SNPs, but also occur in coding regions (Butler, 2005). There are abundant, over 10 million SNPs in the human genome, which have been placed in a database for comparison ad to provide information (Goodwin, 2007).

Method of Detection

There is no single method for SNPs, there are lots of methods and they can be mixed and matched.

  • Microarray (also known as DNA chips, GeneChip arrays and Oligonucleotide arrays) is a grid of DNA molecules of known sequences, fixed on a solid substrate, either on silicon chip or glass (Russell, 2006). DNA chips can test hundreds or thousands of genes in a single assay. DNA is amplified using PCR, the product is tagged with fluorescent dyes, denatured and placed into the microarray. The fragments that exactly match the probe will bind. It is then scanned by a laser and where the fields have bound it will fluoresce producing patterns of dots on the chip (Klug, 2006).
  • Primer extension assay – target sequence is amplified using PCR. A primer hybridises to the target adjacent to the SNP and is labelled by Taq polymerase ddNTP with fluorescent dyes. Then a analysed by capillary electrophoresis (Goodwin, 2007).
  • Allele specific hybridisation – where the primer only extends if it is 100% complementary to the template sequence.

Uses in Forensic Science

The PCR product from SNPs can be as small as 100bp, which means that it will yield better results when analysing degraded DNA – STR amplicons are 300-400bp. Size base separation is not needed so the process can be almost completely automated.

There are no stutter artefacts associated with SNPs so interpretation is much easier. Allele specific primer extension in mtDNA SNP assay was used in a 40 year old missing person case. They couldn’t identify the exact family but found familiar alleles to 4 of the 60 samples taken for comparison (Sturk, 2008).  

SNPs have a much lower mutation rate than STRs and become fixed in a population. SNPs and Y-SNPs can potentially provide information relating to ethnic origin and physical traits (from coding regions), which is vital information when dealing with missing persons and human remains that are unidentifiable. This can be especially useful if physical characteristics and ethnicity could lead to a suspect or missing persons, like in mass disasters.

There are some potential problems when looking at mixed samples due to SNPs being bi-allelic and having three possible genotypes (Butler, 2005). They hold limited information; between 50-80 SNPs are required to match the same levels of discrimination of STRs (Goodwin, 2007).

I don’t think SNPs will supersede STRs due to the differential uses they both have. E.g. STRs are excellent at analysing mixtures and SNPs are more superior at analysing degraded samples.


  • Butler J, 2005, Forensic DNA Typing: Biology, Technology and Genetics of STR Markers, 2nd Edition, Elsevier Academic Express: London.
  • Clayton T et al, 1998, Analysis and Interpretation of mixed forensic stains using DNA STR profiling, Forensic Science International, 91 (1), Pg 55-70.
  • Goodwin W, 2007, An Introduction to Forensic Genetics, John Wiley & Sons Ltd: West Sussex.
  • Klug W, et al, 2006, Concepts of Genetics, 8th Edition, Pearson Education Inc: NJ.
  • Russell P, 2006, I-Genetics A Molecular Approach, 2nd Edition, Pearson Education Inc: CA.
  • Sturk K et al, 2008, The Application of mtDNA SNPs to a Forensic Case. Forensic Science International: Genetics Supplement Series, 1 (1), pg 295-297.

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