In-silico selection of targeted anti-cancer therapies

The Biomedical Genomics group led by Núria López-Bigas at the Pompeu Fabra Unviersity have recently published a paper in Cancer Cell describing the landscape of anti-cancer targeted therapeutic opportunities across a cohort of patients of twenty eight of the most prevalent cancers. They first looked for all the driver mutations (mutations that ’cause’ the cancer) for each individual cancer, then collected information on all the existing therapeutic agents that target those mutations, and finally, combining both datasets, came up with anti-cancer targeted drugs that could potentially benefit each patient. You can read more about this paper on their blog post. Coinciding with the publication of that paper, the … Continue reading In-silico selection of targeted anti-cancer therapies

Improving the prediction of cancer causing mutations

Cancer is generally caused by a combination of many specific mutations, called drivers. But cancer cells contain many other mutations that are not the cause of the cancer, but rather a consequence (passenger mutations). Also, high-throughput genome projects are identifying a huge number of somatic variants. Which ones are cancer-causing? How to distinguish the needle in the haystack? A new computational method recently published in Genome Medicine by the research group led by Núria López-Bigas at the GRIB (UPF-IMIM), can help. Called transformed Functional Impact Score for Cancer (transFIC), it improves the assessment of the functional impact of tumor nonsynonymous … Continue reading Improving the prediction of cancer causing mutations

Genomic high-throughput sequencing data: what to trust

Does your research imply having to deal with a huge amount of high-throughput data? Are you worried about the interpretation of your Illumina sequencing data? Illumina’s Genome Analyzer (GA) and HiSeq instruments are currently the most widely used sequencing devices. If you use them or are thinking of using them, you might be interested in having a look at the latest paper coming from Heinz Himmelbauer and his colleagues at the CRG ultrasequencing unit and published in Genome Biology. Find out about the errors and biases they report to make sure your data analysis is of the highest quality! Reference: Minoche AE, … Continue reading Genomic high-throughput sequencing data: what to trust

Molecular and healthcare information, a necessary marriage

The first keynote speaker at the XI Bioinformatics Symposium was Søren Brunak, director of the Centre for Biological Sequence Analysis (CBS) in Denmark. He gave an interesting overview on the need to integrate the very detailed molecular information we have with the phenotypic data we can get from the healthcare sector. He explained the best source of this type of data are the electronic patient records (EPR or EMR – for medical records), which are very well established in his country as well as other small European countries such as the Netherlands, but not at all in bigger countries such … Continue reading Molecular and healthcare information, a necessary marriage

How to integrate your experimental data in a nice image

SVGmap is a configurable image browser for experimental data, a  new tool developed by the biomedical genomics group of the GRIB (UPF-IMIM) at the PRBB. According to the group “it is useful to create browsers for individualized high-quality images which change the color of some regions according to some values”.  It has recently been published in Bioinformatics. You can read more about it at Núria López-Bigas’ laboratory blog: http://bg.upf.edu/blog/ Continue reading How to integrate your experimental data in a nice image