We are all individuals

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  • Published: Apr 19, 2010
  • Author: Jon Evans
  • Channels: Electrophoresis
thumbnail image: We are all individuals

By separating short stretches of DNA known as Alu sequences on an electrophoresis microchip, US researchers have come up with a new approach to DNA fingerprinting.

DNA fingerprinting identifies individuals based on the 0.5% of their genome that is unique; in conventional DNA fingerprinting, this is done by analysing short tandem repeats (STRs). These are found in non-coding regions of the genome and consist of repeated sequences of DNA bases, with each sequence ranging in length from two to 16 base pairs.

So far, scientists have discovered over 10,000 separate STRs in the human genome. The useful thing about them is that while the repeated DNA sequence in each STR is the same in every individual, the number of times the sequence is repeated differs. Thus, the pattern of repeats in a small selection of STRs can provide a unique fingerprint of an individual.

In practise, identifying this fingerprint involves using the polymerase chain reaction to amplify the repeated DNA sequences of around 10 STRs and then separating these sequences by gel electrophoresis. This produces a distinct pattern of thick and thin bands, representing the separated STR sequences, with thicker bands indicating a greater number of repeats.

As this pattern is unique for an individual, it can be used to identify the perpetrator of a crime, and as these patterns will be more alike between direct relations than between strangers, they can also be used to determine paternity. Furthermore, a related technique, which amplifies a single gene that differs in length between the X and Y sex chromosomes, can be used to determine gender.

But conventional DNA fingerprinting can't reveal much more about an individual. However, STRs are not the only repetitive, non-coding DNA sequences that differ between individuals, and some of these could potentially provide more information. Take the Alu sequences, which are a family of one million DNA sequences, each of which comprises around 300 base pairs, and which have been estimated to make up over 10% of the human genome.

Different people possess slightly different collections of Alu sequences and scientists have shown that specific patterns of Alu sequences are related to characteristics such as gender and ethnicity. For instance, Alu sequences known as AluSTXa and AluSTYa are only found on the X and Y sex chromosomes respectively and thus can be used to determine gender. Meanwhile, sequences known as RC5 and A1 are only found in individuals of African descent, while a sequence known as PV92 is more often found in Asian individuals.

Steven Soper and his colleagues at Louisiana State University in Baton Rouge decided to build on these findings and develop a microchip electrophoresis-based method for identifying seven different Alu sequences, including AluSTXa, AluSTYa, RC5 and A1, in order to determine gender and ethnicity. This involved etching a single separation channel, 100µm deep, 50µm wide and 5cm long, into a polymer microchip and utilising laser-induced fluorescence to detect the separated sequences.

After optimising the separation parameters for the seven Alu sequences, Soper and his team tested their method on DNA extracted from five different cells lines, for which the gender and ethnicity of the original donor were known.

By detecting AluSTXa and AluSTYa, Soper and his team found they could accurately determine gender for each of the cell lines. What is more, they were able to distinguish between male and female DNA in mixed samples, as are often collected from crime scenes. Accurately determining gender in such mixed samples is often tricky when using conventional techniques.

Ethnicity was a bit more difficult, however, with Soper and his colleagues finding that the presence or absence of a single Alu sequence was not sufficient for determining an individual's ethnic group. However, they were able to tell whether DNA from the cell lines contained one, two (if present on each of a pair of chromosomes) or no copies of each of the Alu sequences. It turned out that this record for all five Alu sequences was unique for each cell line, indicating that with a bit more work such records could be used to determine ethnicity.



The views represented in this article are solely those of the author and do not necessarily represent those of John Wiley and Sons, Ltd.

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