There has been quite a backlash to the recent news that many cancers are due to “bad luck” of random mutations, which was proclaimed in headlines around the world, and based on a report published in the January 2 issue of Science.
The International Agency for Research on Cancer (IARC), the World Health Organization’s specialized cancer agency, put out a press release to say that it “strongly disagrees with the conclusion,” and warning that the message could harm cancer research and public health.
“We already knew that for an individual to develop a certain cancer there is an element of chance, yet this has little to say about the level of cancer risk in a population,” explained IARC director Christopher Wild, PhD. “Concluding that ‘bad luck’ is the major cause of cancer would be misleading and may detract from efforts to identify the causes of the disease and effectively prevent it.”
As previously reported by Medscape Medical News, the researchers, from Johns Hopkins University in Baltimore, reported that in about two-thirds (22 of the 31) of cancer tissue types they had investigated, the cancer could be largely explained by the bad luck of random mutations that arise during DNA replication in normal noncancerous stem cells.
However, many of the news stories reported a distorting simplification of the findings, and stated that two-thirds of all cancers are due to bad luck.
There has been fierce criticism of the way that the media reported the story, but an expert argues that journalists were misled.
The Science report was accomapnied by an editorial entitled “The Bad Luck of Cancer,” and the subheading added: “Analysis suggests most cases can’t be prevented.”
But the data do not support either of these ideas, noted George Davey-Smith, MD, a clinical epidemiologist at Bristol University, United Kingdom, in a BBC News report. He also noted that “in the press release [from the Johns Hopkins School of Medicine], the authors say they’ve come up with a method to quantify the contribution of these stochastic or chance factors, which their method doesn’t,” he adds.
“It’s both in the journal and in the press release so it’s just not fair to attribute the mis-reporting of this to journalists,” Dr Davey-Smith commented.
In reaction to the huge media uptake of the story, the study authors issued further comments in a Johns Hopkins University statement, which also included the press release that had been “ammended for clarity.” The public relations officer for Johns Hopkins University, Vanessa Wasta, MBA, noted that the press release was updated to change reference from “incidence” to “risk” as a clarification in the first paragraph, but pointed out to Medscape Medical News that the original news release contained no reference to “cases” or “all” cancers, but referred to “risk” many times.
Science ran a follow-up piece, entitled “A Science Reporter’s Reflections on a Controversial Story,” in which the author returned to the researchers for clarification. “We did not claim that two-thirds of cancer cases are due to bad luck,” said lead author Christian Tomasetti, PhD, an assistant professor of oncology at the Johns Hopkins School of Medicine and the Bloomberg School of Public Health. What the study argued, he explained, was that two-thirds of the variation in cancer rates in different tissues could be explained by random bad luck.
Dr Tomasetti also said that many scientists and statisticians had also needed clarification, and that the team is now working on a technical report with additional details.
The Medicines and Healthcare Products Regulatory Agency (MHRA) says the 23andMe spit test, which is designed to give details about a person’s health risks based on their DNA, can be used with caution.
But critics say it may not be accurate enough to base health decisions on.
The company, California-based 23andMe, stands by its test.
Backed by Google, the firm offered US customers details of health risks based on gene variants they carry.
But in November 2013, the US Food and Drug Administration (FDA) banned the company from marketing its service in the US, claiming 23andMe had failed to provide adequate information to support the claims it made about results.
A month later, the company stopped offering genetic tests related to health.
An MHRA spokesperson said it regulated such tests in the UK to make sure they met minimum standards.
23andMe’s mission is to ensure that individuals can personally access, understand and benefit from the human genome”
Anne Wojcicki Chief executive, 23andMe
“People who use these products should ensure that they are CE marked and remember that no test is 100% reliable so think carefully before using personal genome services.
“If after using the service, you have any questions or concerns you should speak to your healthcare professional.”
She added: “If you are concerned that you have an incorrect result due to a faulty product, you can report this to MHRA at email@example.com or 020 3080 7080.”
The UK Department of Health said it was behind the idea of using gene tests to guide patient care within the NHS, but echoed the MHRA advice on giving careful consideration before opting for services like the one offered by 23andMe.
23andMe chief executive Anne Wojcicki said: “The UK is a world leader in genomics and we are very excited to offer a product specifically for UK customers.”
Ms Wojcicki is separated from but still legally married to Sergey Brin, the co-founder of Google – which has invested millions in 23andMe.
The company had previously offered results on a customer’s risk for 254 diseases and conditions, including identifying genes linked to heart disease and breast cancer. There was also information on how individuals might respond to certain medicines.
Genetic testing is an important medical tool in certain situations, but for healthy people as a way to predict common complex diseases, it’s pretty useless”
But the FDA said the reliability of such tests had not been proven to its satisfaction. It was also worried that some customers could make life-changing decisions based solely on their results.
The UK Department of Health said the product launched in Britain was very different to the service halted by the US regulator.
“Many of the drug responses, inherited conditions and genetic health risks that were of concern in the US have been removed,” a spokesperson told BBC News.
In October, 23andMe said it would sell kits in Canada – these too contain only a handful of health-related results.
“I think a large part of it is trying to expand their markets,” said Professor Hank Greely, director of the Center for Law and the Biosciences at Stanford University in California.
“They may also want to make it clear to the public, to their investors, to their employees that they’re alive and kicking.”
23andMe said it does not share the genetic data with insurance companies or any other interested party without a person’s explicit consent.
“The science is soundest behind 23andMe’s ancestry reports, which are good, but the majority of the rest of the reports are generally based on very small shifts of risk, which are better served by simply living healthier and getting more exercise,” said Dr Ewan Birney – associate director of the EMBL-European Bioinformatics Institute in Cambridge and unconnected with 23andMe, although he has used one of its kits.
“Despite 23andMe’s careful use of language and explanation, there is an understandable concern that this type of genetic testing could cause inappropriate harm simply through people worrying excessively or becoming neurotic over these small increases in risk.”
In the UK, 23andMe is not the first to launch genetic testing. The NHS’s 100,000 genome project conducts full genome sequencing as opposed to genotyping, whichcompares common differences in known genes. The NHS’s project, which is set to complete its pilot stage by 2017 as part of analysing how best to use genomic data in health care, is “world leading”, said Birney.
“This government is developing the use of genomics for patient care within the NHS,” a Department of Health spokesperson said. “We welcome initiatives that help to raise awareness of genomics and those which enable people to take more interest in their personal health but we urge people to think carefully before using private genomic services as no test is 100per cent reliable.”
“For the curious and the scientists, 23andMe is fine, it’s fun and you can have a ball with your ancestry, but for the general population the NHS is truly working out how best to use this in a way that is world leading,” said Birney. “If you’re waiting for the technology to catch up with you, the NHS will deliver.”
What’s the plan?
Dr Marcy Darnovsky, executive director of the Center for Genetics and Society in California, said the UK and Canadian launches could be a way of placing pressure on the FDA by demonstrating that regulators in other countries found no fault with their product.
“Genetic testing is an important medical tool in certain situations, but for healthy people as a way to predict common complex diseases, it’s pretty useless,” she told BBC News.
“Most complex diseases and almost all the common ones – with some exceptions such as the BRCA 1 and 2 genes (implicated in breast cancer) – are multi-factorial with many genes and other biological, social and environmental causes.”
What happens to the data gathered by 23andMe also concerns some people. “It’s not entirely clear what their business plan is – whether they want to make money by selling kits to consumers, or whether they want to make most of their money by selling consumer data to other companies,” Prof Greely told BBC News.
But Ms Wojcicki believes the information provided to customers is empowering. “23andMe’s mission is to ensure that individuals can personally access, understand and benefit from the human genome,” she said.
Commenting on the announcement, Mark Thomas, professor of evolutionary genetics at University College London, said: “For better or worse, direct-to-the-consumer genetic testing companies are here to stay.
“One could argue the rights and wrongs of such companies existing, but I suspect that ship has sailed.”
Mutations in related DNA polymerase genes POLE and POLD1 were described in families with oligopolyposis and endometrial cancer by Ian Tomlinson’s group in Oxford. An elegant approach was employed using whole-genome sequencing in 15 selected patients with more than ten adenomas before age 60 years. Several had a close relative with at least five adenomas who could also have whole-genome sequencing performed. All tested patients had CRC or a first-degree relative with CRC. All had negative APC, MYH, and MMR gene mutation test results. No variants were found to be in common among the evaluated families. In one family, however, linkage had established shared regions, in which one shared variant was found (POLE p.Leu424Val; c.1270C>G), with a predicted major derangement in protein structure and function. In a validation phase, nearly 4,000 affected cases enriched for the presence of multiple adenomas were tested for this variant and compared with nearly 7,000 controls. In this exercise, 12 additional unrelated cases were found to have the L424V variant, with none of the controls having the variant. In the affected families, inheritance of multiple-adenoma risk appeared to be autosomal dominant. Somatic mutations in tumors were generally consistent with the otherwise typical chromosome instability (CIN) pathway, as opposed to MSI or CIMP. No extracolonic manifestations were seen. A similar approach, whole-genome testing for shared variants, with further “filtering” by linkage analysis identified a variant in the POLD1 gene, p.Ser478Asn alteration, c.1433G>A). This S478N variant was identified in two of the originally evaluated families, suggesting evidence of common ancestry. The validation exercise showed one patient with polyps with the variant but no controls with the variant. Somatic mutation patterns were similar to the POLE variant. Several cases of early-onset endometrial cancer were seen. The mechanism underlying adenoma and carcinoma formation resulting from the POLE L424V variant appeared to be a decrease in the fidelity of replication-associated polymerase proofreading. This in turn appeared to lead to mutations related to base substitution.
The study authors recommend consideration of POLE and POLD1 testing in patients with multiple or large adenomas in whom alternatives mutation testing is uninformative and surveillance akin to that afforded patients with LS or MAP. POLE and POLD1 mutation testing is being incorporated into the new multigene CRC susceptibility panels.
Venue: St Mark’s Hospital, London
Target Audience: All members of the Colorectal Cancer MDT (nurse specialists, oncologists, gastroenterologists, colorectal surgeons, pathologists), Geneticists, genetics counsellors
Learning Style: Lectures and case discussions
Learning Outcomes: On completion of this course, attendees will:
£150.00 – Consultants
£75.00 – Nurses, Trainees and other Healthcare Professionals
A project aiming to revolutionise medicine by unlocking the secrets of DNA is under way in centres across England. Prime Minister David Cameron has said it “will see the UK lead the world in genetic research within years”. The first genetic codes of people with cancer or rare diseases, out of a target of 100,000, have been sequenced. Experts believe it will lead to targeted therapies and could make chemotherapy “a thing of the past”. Just one human genome contains more than three billion base pairs – the building blocks of DNA.
This four-year project which will look at 100,000 genomes is being run by Genomics England,. The 100,000 Genomes Project is not simply a research project, nor is it a new way of caring for patients, or a transformation project to use genomic medicine to change how patients are treated in the NHS. It is all of these things.
Pilots have been set up at centres across England – including sites in Newcastle, Cambridge and London – and the first genome was sequenced on 30 May. The project has now passed the 100 genome mark, with the aim of reaching 1,000 by the end of the year and 10,000 by the end of 2015. The genome of a patient’s tumour will be scoured for differences with the genetic code of their healthy tissue. People with rare diseases, usually children, will have their DNA compared with that of close relatives. University scientists and a drug companies will be allowed to access the data for their research. They argue that understanding DNA will soon play a role in every aspect of medicine from cancer to cardiology.
Cancer is one of the main areas the project will focus on. Tumours are caused by mutations in DNA which lead to abnormal cells growing unchecked. Previous genetics research has shown how different cancers can be – for example that breast cancer is not one disease but at least 10 – each with a different cause, life expectancy and needing a different treatment. And the development of targeted drugs such as Herceptin, only given if a patient’s breast tumour has a certain mutation – has been possible because of genetics research.
Also included in the package announced today:
Genomics England anticipates that around 40,000 NHS patients could benefit directly from the research and that this work will pave the way for genomics-based medicine to become part of everyday practice throughout the NHS.
Our briefing highlights the lack of surveillance screening for younger people at higher risk of bowel cancer.
Genetic factors contribute up to 30% of bowel cancer cases, an estimated 8,000-12,000 cases each year.
Genetic factors mean a strong family history of bowel cancer, or genetic conditions such as familial adenomatous polyposis (FAP) or Lynch syndrome. People with long-term inflammatory bowel disease are also at higher risk.
People in higher risk groups are likely to develop bowel cancer much younger than the general population. Clinical guidance recommends that people in high-risk groups should be in a surveillance screening programme, which is proven to reduce deaths in these groups.
Recent evidence shows that:
Our briefing, “Never too young: Supporting people at higher risk of bowel cancer”, has five recommendations to improve services for people in high risk groups:
Full details of our findings and recommendations are in our full report available here.
The ability to sequence a human genome for just $1,000 has arrived, a US genetics company has announced.
San Diego-based Illumina says it is to release a new sequencing machine that can deliver five genomes in a day.
The race to unlock a human’s genetic blueprint for $1,000 has been underway for more than a decade.
The Archon X Prize had offered $10m to the first team that hit this target or came closest, until the contest was cancelled in August 2013.
The term was thought up as a symbolic landmark that would, in theory, light the fires of a long-anticipated revolution in personalised medicine.
Understanding how genes influence disease could lead to better treatments for patients.
The HiSeq X Ten high throughput genetic sequencing machine was announced at the annual JP Morgan Healthcare Conference in San Francisco this week.
In his presentation at the meeting, Illumina’s chief executive Jay Flatley said the HiSeq X Ten would improve on the scanning speed of its predecessor by a factor of six. This would offer the ability to sequence five whole human genomes in a single day, Bio-IT World reported.
He said the $1m sequencers (sold in a minimum of 10 units) would be able to deliver a genome for just under $1,000 (£610; 735 euros), consistent with calculations the National Human Genome Research Institute uses to estimate sequencing costs.
In his presentation, Mr Flatley said the world was “entering the supersonic age of genomics”.
Eric Lander, founding director of the Broad Institute, announced as one of the first customers, described this development as “tremendously exciting” and heralded it as “an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine”.
“The HiSeq X Ten should give us the ability to analyse complete genomic information from huge sample populations. Over the next few years, we have an opportunity to learn as much about the genetics of human disease as we have learned in the history of medicine.”
On his blog, Mick Watson, a computational biologist at the University of Edinburgh, checked the maths behind Illumina’s claims for the HiSeq X Ten.
“I think they might be right in claiming the $1000 genome – if you do 18,000 human genomes per year for four years on each X Ten system. That’s a lot of human genomes though,” he wrote.
The term “$1,000 genome” was coined in 2001 at a closed scientific meeting to discuss the future of biomedical research. A year later, it became the subject of a symposium in Boston hosted by entrepreneur and genome pioneer Dr Craig Venter.
In the last few years, the decline in the cost of genome sequencing had outpaced the famous Moore’s Law, which describes how computer processors double in complexity every two years. Nevertheless, the target proved difficult to reach, even with large sums of money on offer.
Dr Venter’s foundation offered $500,000 to the first team able to realise $1,000 genome sequencing.
This sum was subsequently rolled into the Archon X Prize competition which was to have awarded $10m to successful scientists. However, this contest was cancelled in August 2013 because the effort had, in the words of X Prize co-founder Peter Diamandis, been “outpaced by innovation”.
“What we realised is that genome sequencing technology is plummeting in cost and increasing in speed independent of our competition,” he explained in a column for the Huffington Post.
However, this breakthrough is, as scientists would say, ‘necessary but not sufficient’ to deliver the health benefits of genomics. As Illumina Director of Scientific Research Sean Humphray observes on the company blog, making genomes really useful requires ‘annotation, leveraging public databases using tools’ – that is, analysis to identify the individual sequence variants within that sequence and their potential scientific relevance.
Turning a genome sequence into a clinically useful diagnostic report requires even further interpretation, selecting from the many millions of individual variants only those of most probable and significant relevance to that person’s health, and delivering this information in a meaningful format for normal clinicians to understand and use. Illumina themselves have provided a potential vision of the future in the form of their personal genome sequence interface, MyGenome – delivered in glorious technicolour on an individual iPad – although a more utilitarian product would no doubt fit the bill for many health services.
Many more innovations and developments are still needed, not least in computing and bioinformatics, in order to move us from $1,000 genome to $1,000 clinical genome – but there’s little doubt that we can get there eventually.
Download Public Health Genomics briefing note for more information on the steps involved in whole genome analysis and clinical interpretation.
In new recommendations published in the , ASCO stated that family history of cancer in first- and second-degree relatives is critical to assessing for familial risk in patients with cancer. ASCO’s recommendations are the first to focus on family history taking specifically in oncology to help determine patients’ personal genetic risk for cancer.
Although the current standard in medical genetics, genetic counseling and research settings is a comprehensive recording of three generations, following a review of all available evidence, ASCO concluded that reported family history is most accurate in close relatives and loses accuracy in more distant relatives.
“Genetic factors are a key component of precision medicine because they can unlock important information that can help an oncologist determine the best course of individualized treatment, “ said ASCO President Clifford A. Hudis, MD, FACP. “An adequate family history is key to identifying those patients whose cancer may be associated with inherited genetic factors.”
For each relative with cancer, ASCO recommends recording type of primary cancer(s), age at diagnosis, lineage (maternal and/or paternal), ethnicity and results of any cancer genetic testing in any relative. Family history information should be recorded at a patient’s initial visit to the oncology provider, and be reassessed if new information about family members diagnosed with cancer becomes available.
Addressing Barriers to Implementation
In a separate analysis of data from ASCO’s Quality Oncology Practice Initiative QOPI®, results showed that of breast and colorectal patients with a first degree family history of cancer, 79.8 percent were documented in their chart and for those with a second degree family history of cancer, 64.6 percent were documented. These results document a greater opportunity for oncologists to maximize the potential of family history taking, and set a baseline for further quality improvement efforts.
To address barriers to implementation, ASCO recommends increasing patient education and awareness on the importance of a family history and the significance of a cancer risk assessment for patients and their family. Cancer.Net, ASCO’s patient website, will offer an article and infographic, as well as a cancer family questionnaire patients can download.
ASCO also notes that the increasing use of electronic health records (EHRs) can help providers overcome challenges to adopting these new recommendations.
ASCO will be providing a comprehensive update of cancer genetics including family history assessment at its annual meeting. For more information about ASCO’s prevention and genetics work, please click here.
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Lynch syndrome, familial adenomatous polyposis, and Mut Y homolog (MYH)-associated polyposis are three major known types of inherited colorectal cancer, which accounts for up to 5% of all colon cancer cases. Lynch syndrome is most frequently caused by mutations in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2 and is inherited in an autosomal dominant manner. Familial adenomatous polyposis is manifested as colonic polyposis caused by mutations in the APC gene and is also inherited in an autosomal dominant manner. Finally, MYH-associated polyposis is caused by mutations in the MUTYH gene and is inherited in an autosomal recessive manner but may or may not be associated with polyps. There are variants of both familial adenomatous polyposis (Gardner syndrome—with extracolonic features—and Turcot syndrome, which features medulloblastoma) and Lynch syndrome (Muir–Torre syndrome features sebaceous skin carcinomas, and Turcot syndrome features glioblastomas). Although a clinical diagnosis of familial adenomatous polyposis can be made using colonoscopy, genetic testing is needed to inform at-risk relatives. Because of the overlapping phenotypes between attenuated familial adenomatous polyposis, MYH-associated polyposis, and Lynch syndrome, genetic testing is needed to distinguish among these conditions. This distinction is important, especially for women with Lynch syndrome, who are at increased risk for gynecological cancers. Clinical testing for these genes has progressed rapidly in the past few years with advances in technologies and the lower cost of reagents, especially for sequencing. To assist clinical laboratories in developing and validating testing for this group of inherited colorectal cancers, the American College of Medical Genetics and Genomics has developed the following technical standards and guidelines. An algorithm for testing is also proposed.