A novel method for profiling short tandem repeats (STR) in personal genomes has promised to bring the procedure into the 21st century.
The lobSTR technique is carried out over three stages, and can accurately and simultaneously profile over 100,000 STRs from a human genome in one day. It works on the fact that each person’s set of STRs are different from everyone else’s.
LobSTR harnesses concepts from signal processing and statistical learning in order to avoid gapped alignment and to address specific noise in STR calling. The technology creates a DNA fingerprint by scanning the entire genome to identify the STRs and identifying which nucleotide pattern is repeated within those stretches of DNA.
It then makes a note of the non-repeating sequences flanking either end of the STRs before removing any noise, to produce an accurate description of the STRs’ configuration.
The new technology works at speeds and with reliability that far supersedes the performance of mainstream algorithms for STR profiling. It is also capable of accurately and efficiently describing thousands of STRs in one genome, which has opened up many new research opportunities.
Yaniv Erlich, a fellow at the Whitehead Institute for Biomedical Research said: “lobSTR found that in one human genome, 55 per cent of the STRs are polymorphic, they showed some difference, which is very surprising.
“Usually DNA’s polymorphism rate is very low because most DNA is identical between two people. With this tool, we provide access to tens of thousands of quickly changing markers that you couldn’t get before, and those can be used in medical genetics, population genetics and forensics.”
The researchers will now look to characterise the amount of STR variation in individuals and populations, said Ms Gymrek, author of the paper which has been published in Genome Research. Through this process, they could find information on the normal range of STR alleles at each locus, which would be useful in medical genetics studies aimed at determining if a given allele is normal or pathogenic.