Twenty years ago, at the Institute for Genomic Research (TIGR) in Rockville, Maryland, Claire Fraser became one of the first scientists in the world to take part in sequencing an entire genome.
In 1995, she was part of a large team that produced the whole genome of Haemophilis influenzae, the first free-living organism ever sequenced. That project was also the first appearance of whole genome shotgun assembly, a now widely-used method by which a genome is split into random fragments, then reassembled by a computer.
Fraser would go on to become TIGR’s president, leading the teams who sequenced the bacteria behind syphilis and Lyme disease, and eventually the first plant genome, Arabidopsis thaliana.
When the genome of H. influenzae was first sequenced, 14 Sanger sequencing machines had to run every day for three months to generate all the DNA data, and a custom-built software program, TIGR ASSEMBLER, took 30 hours to stitch the genetic fragments back together. Today, as director of the Institute for Genome Sciences (IGS) at the University of Maryland in Baltimore, Fraser oversees a battery of sequencers and a bioinformatics core that can turn out thousands of times that amount of sequence in a single day. What hasn’t changed is her interest in the agents of infectious disease, a research area that has been embraced by the genomics revolution.
Twenty-first century genomics, a field that has transformed our understanding of biology at an incredible pace, has coincided with a period when chronic disease consumes the attention of the biomedical community. With the worst infectious diseases largely eliminated from the developed world, and conditions like cancer and heart disease overwhelming healthcare resources, the highest-profile genomic projects have mainly focused on the genetic factors behind chronic illness. But for billions of people around the globe, infectious disease is still a daily reality, and emerging problems like antibiotic resistance threaten to reverse a century of gains even in the wealthiest countries. In this environment, pathogen researchers are still racing to catch up with data-hungry approaches, like population genetics, transcriptomics, and metagenomics, which are almost routine in other fields.
Read the full, original story: The genomics of infectious disease