Posts tagged: Genome Biology

Reading the new map of breast cancer

- 0 Comments
Dr Nick Peel of Cancer Research UK on the classification of breast cancer

Research published today in Genome Biology could improve treatments, and the targeting of treatments, for breast cancer. In this guest post, Cancer Research UK’s Dr Nick Peel describes the history of the findings and what they could mean for future research.

Just over two years ago a landmark study took our knowledge of breast cancer to a new level.

An international team of scientists, led by Professor Carlos Caldas and his team at the Cancer Research UK Cambridge Institute, mapped the genetic landscape of breast cancer in unprecedented detail, redefining it as 10 distinct diseases.

But as with many of these vast genetic explorations, the study revealed as much unexplored terrain as it mapped – exposing the complexity …

Read more

‘Prostate cancers’ not ‘prostate cancer’ – revealing the many faces of ‘one’ disease

- 0 Comments
Iain Frame

New research published today in Genome Biology shows that RNA sequencing could lead the way towards more personalized treatments for prostate cancer. In this guest post, Dr Iain Frame, Director of Research at Prostate Cancer UK discusses what this could mean for patients and health services, and what more is needed to provide effective support and treatment for men with prostate cancer.

We are used to hearing and talking about prostate cancer as a single disease.  Albeit a disease with its tigers and pussycats – the tigers being the aggressive cancers that move out of the prostate gland to other parts of the body, and the pussycats being those cancers that may never cause any harm and won’t go …

Read more

On a personal note: cancer genomics and personalized medicine

- 2 Comments
Special issue GB cover-page-001

When I was three years old my grandma passed away after a long fight with cancer. I should disclaim quickly: it never affected me greatly, since I was too young to remember anything. I know, though, that that experience was a gruelling one for my mum, who cared for our grandma during the therapy – battle with cancer ain’t pretty in general, and it was even worse then.

It would of course be easy to blame the health system of the communist regime in which we lived at the time but the truth is that the treatment strategy was pretty much the same all over the place: surgery, radiotherapy, chemotherapy. It doesn’t work? Let’s try harsher treatment. And the understanding …

Read more

Microbial monitoring: health forensics for the modern age

- 0 Comments
Metadata plot

A new paper published in Genome Biology today uses smartphone tracking and additional observations to piece together a staggering amount of information about the research subjects and their individual microbiomes. In this guest post, Jack A Gilbert, Associate Professor at the University of Chicago and Group Leader at Argonne National Laboratory, delves into this promising new avenue of research and data collection.

At the beginning of September 2013 I weighed about 205lbs (92kg). I decided to do something about my weight, for my health and for the sake of my family and of course I approached this plan as a scientist. For me that meant parameterizing my inputs and outputs so I could control what I was doing to …

Read more

Word of caution: a new method to study RNA-seq biases

- 2 Comments
Shaury Nash CC BY-SA

As next generation sequencing methods quickly become ubiquitous tools of genomics, more and more effort is directed to understand what are the limitations of these approaches. These limitations present themselves quite often in the form of coverage biases.

Last year Genome Biology published a study from David Jaffe and colleagues that looked at coverage biases in DNA sequencing. The authors used a suite of computational tools for bias assessment and applied them to a number of commonly used technologies. It turned out that, for instance, PacBio coverage is the least biased; and that high- and low-CG regions and long runs of homopolymers are very prone to coverage biases. They emphasized that the presence of such biases may lead to …

Read more

Genome regulation: it’s the geometry, stupid!

- 0 Comments
Transcription factories (from Cope et al.)

The emerging realization that cells modify the three dimensional arrangement of DNA in order to regulate the genome is changing the way that scientists think about how and when genes are expressed. A new study in Genome Biology goes so far as to show that information about the shape of the genome is sufficient on its own to accurately classify cells according to leukemia subtype.

Traditional genomics studies have examined the genome as a linear DNA sequence. According to this viewpoint, each gene is surrounded by adjacent sequence – in particular the region of the genome immediately upstream – that regulates its expression: when the gene is turned off and on, and to what degree.

It has long been known that …

Read more

It’s in your genes: a new method for cancer drug response prediction

- 0 Comments
source: flickr;  viZZZual.com (CC BY)

One of the greatest challenges of current medicine is predicting how a patient will respond to a given drug. In an ideal world, where time, money and – most importantly – the patient’s well-being and survival are not an issue, we would simply either keep trying different treatments until hitting the jackpot, or perhaps harvest the patient’s cells and try a range of treatments in vitro. The problem is, of course, that the world is not ideal and such in vitro testing is usually not practical and, in general, especially in the case of many of the most debilitating diseases, patients often don’t have time to waste.

It is then not really surprising that many researchers have been …

Read more

Methylating much?

- 0 Comments
source: flickr, calciostreaming (CC BY)

Our readers might have gotten distracted this month by discussions on whether it is right or wrong for Illumina to limit researchers’ use of their kit, and so we are here to help you regain focus: after a deliberately thematic issue on the RBPome, we have just published an accidentally thematic issue on DNA methylation.

Useful tools

This month Genome Biology publishes three tools that many working on DNA methylation should find quite handy.

Mark Robinson (of edgeR, which he published together with another of this issue’s authors, Gordon Smyth) and company present a new method, BayMeth, for the effective quantification of data generated with DNA-methylation-capture-seq techniques (MBD-seq, MeDIP-seq and so on). So if you …

Read more

Why mosquitoes resist – a new molecular marker sheds light on insecticide resistance

- 0 Comments
Mosquito

This guest blog is written by Vera Unwin. With an MSc in Medical Parasitology and experience as a Parasitology Research Technician, Vera regularly writes for Bugbitten, our blog on parasites and vectors.

Insecticides are fundamental to vector control programs for vector borne diseases. Malaria is one of the most dangerous of these diseases, with an estimated 627,000 deaths per year. Reducing transmission by targeting mosquito populations is an integral strategy for controlling this disease. Such programs are heavily reliant on the use of insecticides- in the form of Insecticide Treated bed Nets (ITNS) and Indoor Residual Spraying (IRS)- to decrease mosquito populations and so lower transmission of the disease.

 

The widespread use of insecticides has inevitably …

Read more

Uniform diversity: a genome-wide study of PRC1 ortholog localization

- 0 Comments
Poly-combs! /source: Sean McMenemy (CC BY)

Polycomb-group proteins are a well-characterized family of proteins involved in chromatin remodeling. In mammals, Polycomb-group proteins form two multiprotein complexes: Polycomb repressive complex 2 (PRC2), which represses gene expression, and PRC1.

PRC1, unlike its highly conserved sister, is a masterpiece of variety. It comprises the subunits Polycomb (Pc), Posterior sex combs (Psc), Polyhomeotic (Ph) and Sex combs extra (Sce) – but in humans there are five orthologs of Pc, six of Psc, three of Ph and two of Sce, which can, in theory, give rise to up to 180 different versions of PRC1. And while we don’t know for sure how many versions of PRC1 are to be found in human cells, one thing is clear: there doesn’t …

Read more