Posts tagged: Genome Medicine

SRST2: a new tool for genomic epidemiology

Generic pink bacteria (cropped)

“We began this project because we needed more reliable methods to do our own research work, which involves detecting resistance genes and other genetic markers in thousands of bacterial genomes, but we quickly saw that it had direct and important implications for diagnostic labs.”

In this Q&A, Michael Inouye and Kathryn Holt, authors of a Software article recently published in Genome Medicine, tell us about the development of the software SRST2. SRST2 is a read mapping-based computational tool that allows fast and accurate detection of genes, alleles and multi-locus sequence types from whole genome short sequencing reads.

Why did SRST2 need to be developed?

“Genomic surveillance is being adopted by diagnostic and public health labs all over the world, as …

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For the ‘greater good’ would you share your biological data? Science’s need for study participants’ consent

Cote picture

Last week the National Institutes of Health released its genomic data sharing policy. From next year, study participants will need to give researchers permission to re-use and share their data. But, what about many older studies that were obtained years before re-use of samples was envisaged? Michele Cote and colleagues from Wayne State University and the Karmanos Cancer Institute, USA, wondered what would happen if people from a 15-year old lung cancer study were re-contacted and asked to share their de-identified data.

Fifteen years ago when I embarked upon a career in medical research as a project coordinator, the world of high-throughput genomics was in its infancy.  The Human Genome Project was nearing completion, but most …

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Large hypomethylated blocks could be a universal cancer ‘signature’

Figure 1 Many of the methylation changes at single probes between cancer and normal 
are far from CpG islands. Irizarry et al. Genome Medicine

In this guest post, Dr Andrew Teschendorff of University College London and the CAS-MPG Partner Institute for Computational Biology, Shanghai, examines a new Genome Medicine study.

In an exciting research article published today in Genome Medicine, Rafa Irizzary and colleagues provide evidence for a gradual systems-level deregulation of the epigenome in stages prior to the onset of cancer and which later is seen to progress further in cancer. Thus, these insights could potentially lead to a clinical test with the ability to predict cancer risk in cells that are not yet malignant.

The authors focused on a specific epigenetic mark, known as DNA methylation, a molecular modification of DNA which can regulate the activity of nearby …

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A new test to predict breast cancer risk

Image credit: Danvasilis/Wikimedia Commons

A simple blood test is currently in development that could help predict the likelihood of a woman developing breast cancer, even in the absence of a high-risk BRCA1 gene mutation, according to research published today in Genome Medicine. So what was found, and what could this mean for future cancer prevention and treatment?

Breast cancer is the most common cancer in the UK, and it’s highly likely you’ll know someone close to you who’s been affected by it.

My partner’s mother, soon to be my mother-in-law, was diagnosed with breast cancer nearly three years ago. What was particularly scary for all of us when we found out about her diagnosis, was that her sister had died of the same disease around …

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Cancer epigenomics and the new holy grail – turning cancer into chronic disease

DNA methylation


Genome Medicine introduces a new series on Cancer epigenomics - the first articles include an editorial from Guest Editor Stephan Beck, a comment from Christoph Bock and a Q&A from Andrew Feinberg, as well as research from Christoph Plass and colleagues.

Recently, Cancer Research UK reported that 50% of people currently diagnosed with cancer will survive for at least 10 years. This compares to just 25% in the early 1970s, when the then US President Richard Nixon signed the National Cancer Act, initiating a ‘war on cancer’ and paving the way for major national and international funding. A cure for the different types of cancer is still elusive, but the achievements of the Human Genome Project and subsequent large-scale cancer-focused …

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Personalizing care in coronary heart disease


A new paper published in Genome Medicine today describes research with the potential to ‘personalize’ treatment for patients with heart disease.


Determining whether or not certain treatments or interventions are right for a particular patient is a tricky business. Much of the time it is about weighing up the benefits versus potential side effects which may be unpleasant for the person being treated. It can ultimately be a matter of life and death.

Personalizing treatment for patients is now talked about for many different conditions, from cancer to arthritis, from heart disease to dental cavities. In essence, and as I’m sure most readers can glean from the name, it entails making treatments more tailored to the …

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Less talking and more doing: the return of secondary genomic findings to patients

woman concentrating (Flickr, RelaxingMusic, CC)

A study published today in Genome Medicine describes a framework for returning ‘secondary’ or ‘incidental’ genomic findings to patients. We take a look at what the implications of this could be, both for patients and clinical researchers.

Close your eyes and imagine for a moment you’re a patient trying to decide whether to enroll in a genome sequencing project at the hospital where you’ re receiving treatment.

As part of the enrolment process it will be explained to you that information in your genome, unrelated to your disease, that might reveal you are at risk of developing another condition could be found. The so-called ‘incidental’ or ‘secondary’ genomic findings. The following questions might cross your mind: would I like to …

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Patient preferences – does offering choice improve treatment outcomes?


If you had a condition that could be treated with a single operation that carries risks, or with a series of physiotherapy sessions, which has fewer risks but will take longer, which would you choose?

A post last week on our blogs looked at participatory medicine and what the meaning of ‘participation’ in this context is. Clearly, an element of patient participation is their ability to express a choice in the type of treatment they’re offered.

The choice is down to individual preference, personal needs, circumstances and motivation. These perspectives are becoming increasingly recognised by clinical and policy decision makers and should pave the way for improved patient satisfaction, in addition to outcome and cost-effectiveness of medical care.

The …

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The face of medicine is changing – are we ready for the new era?

doctor and patient

The news last month that genetic testing company 23andMe has suspended its marketing activities after intervention by the US Food and Drug administration (FDA) has again raised a related issue that’s been under debate now for several years. Should non-medically trained members of the public be offered the power to peer into their own genome?

Participatory medicine, where the patient is actively involved in their healthcare, is fast becoming a reality. The ideal of this new concept is that the clinician and patient are part of the same team, with patients feeling empowered by more available information, and taking a more active and responsible role.

In reality of course, things get a bit more complicated. For example, say I ordered …

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The H3Africa Consortium: leading the genomics revolution in Africa for Africans


Within the past three years, there has been increasing interest in understanding the wealth of human genetic diversity that exists across the planet. I spent much of my research career studying intra-African genetic variation, and since joining the Genome Medicine team in 2013 I have retained a key interest in this area of research.

The importance of including African populations within evolutionary and clinical research should not be underestimated; Africa is the most diverse continent on Earth, from a human genetics perspective, and with respect to its disease burden. A key aim of the genomics revolution is to translate biomedical research findings into clinical practice; personalised medicine, in particular, is a strategic goal of translational genomics research. …

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