Illumina and Wellcome Trust Sanger Institute Announce Completed Genome for Endangered Tasmanian Devil
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Researchers from Illumina, Inc. and the Wellcome Trust Sanger Institute have used Illumina's next generation sequencing technology to create a draft genome sequence for the endangered Tasmanian devil, and will use this to find genetic mutations in the transmissible cancer that is ravaging its population.
The results open the door for new research to pick out those specific mutations that drive the cancer and will lay the foundation for ongoing work to trace the spread of disease and inform the development of preclinical tests, conservation strategies and disease therapies. The announcement is being made by Sanger Institute researcher, Dr. Elizabeth Murchison, at the AMATA 2010 Conference in Hobart, Tasmania, Australia.
The reference Tasmanian devil genome - approximately the same size as the human genome - was sequenced in eight days in one run on Illumina's HiSeq 2000, generating more than 80-fold genome coverage. Two cancer genomes of affected animals from different parts of Tasmania were sequenced at high coverage as well. Sequencing, de novo assembly and analysis of genetic variation of the three genomes has been undertaken jointly by scientists at the Wellcome Trust Sanger Institute and Illumina.
"We're excited about what this project means, not just for the future of this very rare and endangered species and this unusual cancer," said David Bentley, Chief Scientist at Illumina. "It is wonderful to see Illumina's next generation sequencing, with its emphasis on speed, accuracy and genome coverage, opening a world of new possibilities for scientists to get at the root causes and manifestations of disease."
The Tasmanian devil is the largest carnivorous marsupial and is native to the island of Tasmania. The species is at risk of extinction in the wild due to a transmissible facial cancer, which is spread between devils by the transfer of cancer cells by biting. The cancerous cells from the first devil then colonize the bitten animal, which usually dies within months of the appearance of symptoms. In the 14 years since the disease was first observed, the devil population has declined by more than 80 per cent.
Tasmanian devil facial tumor is almost unique in cancers of the animal kingdom in that it is transmitted by direct transplantation of cancer cells from animal to animal.
"This sequence is invaluable and comes at a crucial time," said Dr. Murchison. "By comparing our draft sequence with samples taken from many hundreds of devils suffering from this cancer, we can begin to look at the spread of the disease, quite literally, by identifying geographical routes and barriers in its transmission. This knowledge could ultimately shape the ongoing conservation efforts in Tasmania.
"It took 10 years to sequence the draft human genome; the devil took just two months using this new technology. We are entering a new era when genome sequencing can be applied to some of our most pressing problems in real time."
The next step will be to sequence many more Tasmanian devil facial tumor samples. By generating profiles of the mutations present in these cancers, the team hopes to improve understanding of the disease and its spread.
"This sequence is not only a boon to the efforts to protect this endangered species," said Professor Mike Stratton, Director of the Sanger Institute and joint head of the Cancer Genome Project. "We believe that this research, the first of its kind to look at this very unusual form of transmissible cancer, will also teach us important lessons about the evolution of cancers. What we are observing is not just a class of cancer that afflicts the Tasmanian devil; we are actually peering into the very same cancer that originated in just one devil, some 20 years ago - a cancer that has long survived its original host.
"In research terms, this is truly unique - it will provide an unprecedented window into the evolution of cancer," Prof. Stratton added.
The results open the door for new research to pick out those specific mutations that drive the cancer and will lay the foundation for ongoing work to trace the spread of disease and inform the development of preclinical tests, conservation strategies and disease therapies. The announcement is being made by Sanger Institute researcher, Dr. Elizabeth Murchison, at the AMATA 2010 Conference in Hobart, Tasmania, Australia.
The reference Tasmanian devil genome - approximately the same size as the human genome - was sequenced in eight days in one run on Illumina's HiSeq 2000, generating more than 80-fold genome coverage. Two cancer genomes of affected animals from different parts of Tasmania were sequenced at high coverage as well. Sequencing, de novo assembly and analysis of genetic variation of the three genomes has been undertaken jointly by scientists at the Wellcome Trust Sanger Institute and Illumina.
"We're excited about what this project means, not just for the future of this very rare and endangered species and this unusual cancer," said David Bentley, Chief Scientist at Illumina. "It is wonderful to see Illumina's next generation sequencing, with its emphasis on speed, accuracy and genome coverage, opening a world of new possibilities for scientists to get at the root causes and manifestations of disease."
The Tasmanian devil is the largest carnivorous marsupial and is native to the island of Tasmania. The species is at risk of extinction in the wild due to a transmissible facial cancer, which is spread between devils by the transfer of cancer cells by biting. The cancerous cells from the first devil then colonize the bitten animal, which usually dies within months of the appearance of symptoms. In the 14 years since the disease was first observed, the devil population has declined by more than 80 per cent.
Tasmanian devil facial tumor is almost unique in cancers of the animal kingdom in that it is transmitted by direct transplantation of cancer cells from animal to animal.
"This sequence is invaluable and comes at a crucial time," said Dr. Murchison. "By comparing our draft sequence with samples taken from many hundreds of devils suffering from this cancer, we can begin to look at the spread of the disease, quite literally, by identifying geographical routes and barriers in its transmission. This knowledge could ultimately shape the ongoing conservation efforts in Tasmania.
"It took 10 years to sequence the draft human genome; the devil took just two months using this new technology. We are entering a new era when genome sequencing can be applied to some of our most pressing problems in real time."
The next step will be to sequence many more Tasmanian devil facial tumor samples. By generating profiles of the mutations present in these cancers, the team hopes to improve understanding of the disease and its spread.
"This sequence is not only a boon to the efforts to protect this endangered species," said Professor Mike Stratton, Director of the Sanger Institute and joint head of the Cancer Genome Project. "We believe that this research, the first of its kind to look at this very unusual form of transmissible cancer, will also teach us important lessons about the evolution of cancers. What we are observing is not just a class of cancer that afflicts the Tasmanian devil; we are actually peering into the very same cancer that originated in just one devil, some 20 years ago - a cancer that has long survived its original host.
"In research terms, this is truly unique - it will provide an unprecedented window into the evolution of cancer," Prof. Stratton added.
