Medical genomics in infectious disease and cancer

Interrogating genome data to identify biomarkers and create new diagnostic tools

In the global fight against antibiotic-resistant bacteria, otherwise known as superbugs, the development of a point-of-care diagnostic tests is considered crucial.

So important that a £10million prize, The Longitude Prize, has been set as a reward for its discovery. Similarly, the US Department of Human Health is sponsoring a $US20m Antimicrobial Resistance Diagnostic Challenge.

IMB's Coin Group use genomic and transcriptomic tools to uncover biomarkers for rapid characterisation of pathogenic bacterial infections.

Research overview

“Identifying that a patient has a pathogenic bacterial infection, correctly characterizing the type of bacterial infection, and rapidly identifying the presence of antibiotic resistant genes, are imperative to prescribing the correct antibiotic,” said Group Leader Associate Professor Coin. 

“The current testing process is long, up to 48 hours, and often returns an inconclusive result. Patients are therefore often given a broad-spectrum antibiotic which can be 'hit-and-miss.' 

“We are developing an approach which allows clinicians to identify the type of bacterial infection and the presence of antibiotic resistance genes within 6 hours, or a single hospital shift.”

The technology utilises nanoparticles which can bind to and extract bacteria from a biological fluid, such as blood. By concentrating bacterial cells, the group can extract and sequence bacterial DNA, using a portable sequencing device the size of a mobile phone.

The team has developed streaming algorithms which enable them to identify the presence of resistance genes from sequence data in 'real-time.'

The research team is also applying genomics tools to create a diagnostic tool for cancer.

“We can sequence the blood to examine the cell-free DNA released by the tumour cells into the blood stream when they die. We then try to reconstruct the solid tumour genome to help with early cancer detection, to monitor response to treatments, check for relapse and detect specific mutations to treat with the correct drug.”

Research projects

Develop genomic tools for rapid diagnosis of bacterial infection using host and bacterial biomarkers

One of the major reasons for delay in diagnosis of infectious disease as well as the identification of antibiotic drug resistance is the time taken to culture and isolate the bacteria. To address this problem, we will develop a culture-free long-read sequencing meta-genomics pipeline for profiling clinical samples. We couple techniques for isolating bacteria direct from clinical sample with portable, real-time sequencing and streaming bioinformatics.

Develop genomic tools for diagnosis of the presence of a solid tumour and for prediction of tumour subtype and likely treatment response from circulating tumour DNA

We will develop genomic and bioinformatics tools for tumour detection and profiling from circulating tumour DNA present in the blood in multiple cancers. We have already developed bioinformatics algorithms for accurate copy number and loss-of-heterozygosity profiling in tumours with as little as 10% cellularity. We have also successfully applied these tools to publicly available datasets consisting of DNA extracted from blood plasma (containing an estimated 20-30% of circulating tumour DNA); normal cellular DNA, primary tumour DNA and metastatic tumour DNA, indicating the applicability of this tool to characterising copy number alterations in circulating tumour DNA.

Characterisation of complex structural variation in bacterial and human genomes

There is substantial genomic variation in the human genome, which remains extremely difficult to assay globally using existing genomic technologies. Many of these variants, such as repeat variation as well as recurrent copy number variation and recurrent inversions, mediated by non-allelic homologous recombination, are not well tagged by single-nucleotide variation, and hence their effects on phenotype remain largely unexplored. In depth characterisation of this class of variation is beginning to uncover moderate effect size variants. We are developing approaches which combins target sequence capture, followed by long read sequencing using the Oxford Nanopore Technologies sequencers and real-time bioinformatics analysis of sequence data to genotype inversions and repeats.

Research training opportunities

Research title: Population and medical genomics

Summary of research interests: The initial sequencing of plant and animal genomes, including the human genome, has led to remarkable discoveries about the genomic relationships between species and into evolutionary history and processes. We are now entering a population sequencing era in which thousands of genomes from these species are being sequenced. This data will enable us to map genomic variation within species, and assess the phenotypic impact of this variation. My group is particularly interested in mapping genomic structural variation, including copy number variation, repeat variation and balanced structural variation such as translocations and inversions. We are developing algorithms for mapping this variation from long read sequence data.

Traineeships, honours and PhD projects include

  • Developing streaming algorithms for meta-genome assembly identification and genotyping of tandem repeats and inversions from long read sequence data
  • Mapping structural variation in multiple plant and animal genomes
  • Investigating population differentiation and positive selection of structural variation in humans.

Contact: Associate Professor Lachlan Coin
+61 7 3346 2649
l.coin@imb.uq.edu.au


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Featured publications

  • Kaforou, Myrsini, Herberg, Jethro A., Wright, Victoria J., Coin, Lachlan J. M. and Levin, Michael (2017) Diagnosis of bacterial infection using a 2-transcript host RNA signature in febrile infants 60 days or younger. Journal of the American Medical Association, 317 15: 1577-1578. doi:10.1001/jama.2017.1365

  • Shimizu, Chisato, Eleftherohorinou, Hariklia, Wright, Victoria J., Kim, Jihoon, Alphonse, Martin P., Perry, James C., Cimaz, Rolando, Burgner, David, Dahdah, Nagib, Hoang, Long T., Khor, Chiea Chuen, Salgado, Andrea, Tremoulet, Adriana H., Davila, Sonia, Kuijpers, Taco W., Hibberd, Martin L., Johnson, Todd A., Takahashi, Atsushi, Tsunoda, Tatsuhiko, Kubo, Michiaki, Tanaka, Toshihiro, Onouchi, Yoshihiro, Yeung, Rae S. M., Coin, Lachlan J. M., Levin, Michael and Burns, Jane C. (2016) Genetic variation in the SLC8A1 calcium signaling pathway is associated with susceptibility to Kawasaki disease and coronary artery abnormalities. Circulation: Cardiovascular Genetics, 9 6: 559-568. doi:10.1161/CIRCGENETICS.116.001533

  • Herberg, Jethro A., Kaforou, Myrsini, Wright, Victoria J., Shailes, Hannah, Eleftherohorinou, Hariklia, Hoggart, Clive J., Cebey-Lopez, Miriam, Carter, Michael J., Janes, Victoria A., Gormley, Stuart, Shimizu, Chisato, Tremoulet, Adriana H., Barendregt, Anouk M., Salas, Antonio, Kanegaye, John, Pollard, Andrew J., Faust, Saul N., Patel, Sanjay, Kuijpers, Taco, Martinon-Torres, Federico, Burns, Jane C., Coin, Lachlan J. M. and Levin, Michael (2016) Diagnostic test accuracy of a 2-transcript host RNA signature for discriminating bacterial vs viral infection in febrile children. The Journal of the American Medical Association, 316 8: 835-845. doi:10.1001/jama.2016.11236

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Engagement and impact

The Coin Group has contributed to identification of biomarkers which distinguish a bacterial versus viral infection. This is a significant discovery to aid in the international fight against antibiotic resistant bacteria – superbugs.

For febrile patients in intensive-care units suffering from bacteraemia and sepsis, it is of critical importance to identify the pathogenic agent and its antibiotic drug resistance profile rapidly, as there is a 6% rise in mortality associated with every hour delay in the administration of antibiotics. Researchers in the Coin Group are working with clinicians to test new approaches to rapidly identify antibiotic resistance.

The group has also been working on sequencing cell-free DNA from cancer patients, and developing algorithms for characterising copy number variation in the tumour genome from circulating tumour DNA. This has several applications including early detection for people with high genetic risk.

Partners and collaborators

Coming soon.

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Associate Professor Lachlan Coin

Associate Professor Lachlan Coin

Group Leader, Genomics of Development and Disease Division
Deputy Director, Centre for Superbug Solutions

  +61 7 3346 2649  
  l.coin@imb.uq.edu.au
  IMB Researcher Profile
  Centre for Superbug Solutions
  @ljcoin

 


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  Group Leader

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  • Mr Son Nguyen

    Higher degree by research (PhD) student & Research Officer
    Institute for Molecular Bioscience
  • Ms Miranda Pitt

    Higher degree by research (PhD) student & Research Officer
    Institute for Molecular Bioscience
  • Mr Haojing Shao

    Higher degree by research (PhD) student
    Institute for Molecular Bioscience
  • Mr Chenxi Zhou

    Higher degree by research (PhD) student & Research Officer
    Institute for Molecular Bioscience
  • Mr Hyun Jae Lee

    Higher degree by research (PhD) student
    Institute for Molecular Bioscience
  • Ms Janice Reid

    Honours student
    Institute for Molecular Bioscience
  • Ms Dilys Li

    Honours student
    Institute for Molecular Bioscience

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