19 September 2016
Researchers at the Garvan Institute of Medical Research are successful recipients of a $220,000 Research Equipment Grant from Cancer Institute NSW (CINSW), enabling the purchase of the Chromium Genome Solution from 10x Genomics Inc. This transformative new technology, which has only recently become commercially available, will expand the range of genetic changes that are detected by whole genome sequencing, giving researchers across NSW a more comprehensive view of the genomes of cancer cells than ever before.
As a normal cell progresses to being cancerous, it acquires a host of changes to its genome, ranging from small mutations that affect only a few DNA base pairs or ‘letters’ to complex structural rearrangements – which involve the large-scale relocation of long stretches of DNA from one part of the genome to another. The Chromium Genome Solution will make it easier to interpret these complex rearrangements of the genome.
“We know that during cancer progression, large structural rearrangements of the genome can be just as important as small mutations,” says Dr Mark Cowley, a Team Leader in Garvan’s Kinghorn Centre for Clinical Genomics and one of the chief investigators on the successful CINSW grant proposal.
“Until now, though, it has been difficult to see complex rearrangements in our genomic sequencing readouts – they often fly under the radar of existing sequencing technologies.
“The Chromium platform changes that. In effect, the technology makes large-scale, complex genome rearrangements more visible to next-generation sequencing platforms – meaning that researchers can capture accurate information about the whole spectrum of genomic changes in a single sample.”
The technology will propel a wide range of research projects in cancer and other diseases at Garvan. Among other projects, it will support the Institute’s researchers in:
- exploring the extensive genomic differences between cancer cells in diverse tumour types
- investigating gene expression in individual cancer cells,
- sequencing the tumour and normal genomes of 400 Australian children with high-risk cancer (the Lions Kids Cancer Genome Project)
The Chromium Platform will also support Dr Cowley’s efforts to develop a clinical diagnostic test for FSHD (facioscapulohumeral muscular dystrophy), a severe form of muscular dystrophy that is caused by genomic changes not readily detected by next-generation sequencing. Dr Cowley’s project was recently funded by the FSHD Global Research Foundation.
“At Garvan, we’re fortunate to be operating the world’s leading next-generation genome sequencing platform, the Illumina HiSeq X Ten,” Dr Cowley says. “With the additional capabilities of the Chromium platform, in concert with single-cell genomics technologies that will be developed at the Garvan-Weizmann Centre for Cellular Genomics, Garvan will have a world-leading ability to characterise cancer genomes.”
The Chromium Genome Solution will be made available to researchers across NSW, through Garvan’s Kinghorn Centre for Clinical Genomics.
How does the new technology expand our understanding of genomic changes in cancer?
The Chromium platform will make it easier to interpret complex DNA rearrangements within the genome, and to understand the extensive genomic differences between cancer cells in a tumour.
Detecting large structural rearrangements in the genome using next-generation sequencing technologies is challenging, because they deal with ‘short reads’ – in other words, they break genomic DNA into very short fragments (450 bases), determine the sequence of each short fragment, then work out which fragment sits next to which.
This process of aligning short reads is computationally demanding, and is often incapable of detecting when structural rearrangements have occurred.
Dr Cowley says, “There are long-read sequencing technologies in existence that can detect structural rearrangements – but these are currently too expensive to use for routine sequencing in research or the clinic.”
“In contrast, the Chromium platform takes an intuitive approach that we call a ‘synthetic long read’ approach, and it gives us the best of both worlds: the obvious advantages of long sequencing reads, at the cost and quality of short sequencing.”
The Chromium Platform uses a novel ‘barcode’ strategy to mimic a long read approach at a fraction of the cost. Long stretches of DNA are broken up into short fragments for sequencing – but, unlike the short read approach, every short fragment from the same region of DNA is labelled with the same ‘molecular barcode’ before they are pooled with other fragments.
After sequencing, the fragments with the same ‘barcode’ can still be recognised as belonging together, making it easier to assemble and align the genomic sequence correctly – and, in the process, enabling structural rearrangements within the genome to be readily detected.