29th April 2008

Seeing the enemy up close

New-technology DNA sequencing boosts cancer genome research

cancer

Rearrangements in small cell lung cancer genome. Mapping to the base-pair level of an acquired insertion of sequence from a homogeneously staining region on chromosome 12p13 into chromosome 2q22. The insertion was evident on spectral karyotype (SKY image), and a paired-end read spanned the breakpoint. Confirmatory PCR and sequencing showed a small 127-bp fragment (shard) from chromosome 2 inverted at the breakpoint. FISH using a probe (RP11-444J21) from the chromosome 12p13 amplicon adjacent to the breakpoint (green) and a probe (RP11-58C7) from the chromosome 2q22 region (red) generated a fusion signal (yellow), confirming that the breakpoint identified corresponded to that seen on the spectral karyotype.

A massive, new-technology DNA sequencing project has uncovered more than 100 novel rearrangements of the DNA of lung cancer cells. The study shows that new sequencing methods are able to capture these changes rapidly and to reveal changes that were not feasible using existing methods. The research, published in Nature Genetics, has set the standard for analysis of cancer genomes.

In the study, the team from the Wellcome Trust Sanger Institute generated more than 60 million sequences from random, short fragments from two lung cancer samples. They describe more than 100 rearrangements to the level of single letters of DNA code (base-pair level) in lung cancer genomes. In addition, they characterized more than 300 normal variations in the genome.

"New-sequencing technologies are comparable to the introduction of more powerful microscopes - we are able to see each potential sequence change in cancer genomes at a the base-pair level, in much, much greater detail than before, even in the face of a vastly disorganised structure," says Dr Andy Futreal, co-Leader of the Cancer Genome Project at the Wellcome Trust Sanger Institute.

" This study demonstrates the enormous potential of massively parallel DNA sequencing to understand the complexity of cancer genomes and raises the prospect of a harvest of new cancer genes. The field of cancer genomics will be transformed. "

Dr Andy Futreal

"The emerging picture is remarkable; a genome ravaged during evolution of cancer. Each genome contains many, many mutations, some of which are drivers of the cancer, but many of which are passengers, incidental changes acquired during the erosion of the form and structure of a normal genome on the way to cancer."

Prior technologies offered three approaches: to look at changes of one or a few letters in DNA code; to look at larger chromosomal rearrangements visible under a light microscope; or to look at a very small subset of the genome on a clone by clone basis. The new method used by the team fragments the entire cancer genome and uses new-technology sequencing to extract DNA sequences from each end of the fragments, and can uncover DNA changes invisible to older technologies.

The researchers looked at two lung cancer samples and compared them to the Reference Genome Sequence produced by the Human Genome Project. Where the ends of the random fragments did not map to the correct location on the Reference Genome, the team studied the anomalies at the base-pair level in both tumour and normal DNA from the same patient, thus defining the subset that were acquired during cancer development.

Significantly, they identified more than 100 differences (somatic rearrangements) that occur in the cancer cells. The cancer genome is tattered, with many amplified regions, duplications and small fragments of DNA - genomic shards - inserted into novel locations.

"This, the first comprehensive view of cancer genomes at this level of resolution, emphasizes the bewildering array of forces sculpting the cancer genome," says Professor Mike Stratton from the Cancer Genome Project. "We found multiple instances of genes being broken, duplicated and/or moved about the genome, some of which could alter gene activity - suggesting that there may well be a new set of genes important in cancer that are altered by these sorts of processes."

"In addition, we were able to characterise more fully the labyrinth complexity of amplification of MYC, a well-known cancer gene, to a level of detail never before seen."

In the ten years since its inception, the Cancer Genome Project has led the world in uncovering variants in genomes of cancer cells. Some research has been taken to clinical trial, but the vast panorama of changes in cancer genomes remains to be explored. A genome-wide view of the type in this study provides the needed information about networks of players in cancer development, about their genesis and their interaction in these complex diseases.

"This study demonstrates the enormous potential of massively parallel DNA sequencing to understand the complexity of cancer genomes and raise the prospect of a harvest of new cancer genes," explains Dr Futreal. "The field of cancer genomics will be transformed."

The Wellcome Trust Sanger Institute has made a significant investment in new sequencing technologies and this is the first human disease to be reported from the new platforms. The Institute is a leading contributor to the recently announced International Cancer Genome Consortium, which will examine the genomes of around 50 different cancer types.

Notes to Editors

Publication details

  • Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.

    Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR and Futreal PA

    Nature genetics 2008;40;6;722-9

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The Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute, which receives the majority of its funding from the Wellcome Trust, was founded in 1992. The Institute is responsible for the completion of the sequence of approximately one-third of the human genome as well as genomes of model organisms and more than 90 pathogen genomes. In October 2006, new funding was awarded by the Wellcome Trust to exploit the wealth of genome data now available to answer important questions about health and disease.

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The Wellcome Trust

The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.

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