Month: April 2015


The War Against Cancer

This is the second part of a guest blog post written by Dave Dubin. Read the first part here. Let’s see how far we’ve come… Since 2007, we have written, made appearances, and held events in order to bring awareness to what I have gone through with the goal of reaching a younger audience, including women.  Every conference we’ve attended has talked about the under-fifty age group, whose numbers are increasing every year, as well as genetics and genetic testing, even genomics.Soccer is a worldwide game, with as many women participating as men, and it encompasses all ages and levels of ethnicity and socioeconomic background.  We have had events with women’s and men’s professional soccer teams from the National Women’s Soccer League, Major League Soccer, North American Soccer League and college teams. My voice has been used to narrate videos and I’ve moderated a webinar about knowing your family history. Today, cancer is as much about finding the proverbial “needle in the haystack” as it is about curing and prevention. Immunotherapy is a big topic. If a group of individual family members all get a certain genetic mutation, and only two of the three siblings are affected by the disease, […]

DNAdigest interviews GA4GH

This week I am extremely excited to introduce you to Julia Wilson, Associate Director at the Wellcome Trust Sanger Institute. In this interview Julia tells us more about the Global Alliance for Genomics and Health (GA4GH), the current projects and working groups, the recently published first Road Map and the 3rd GA4GH plenary meeting in June that we all are so excited about. Julia Wilson, Associate Director at the Wellcome Trust Sanger Institute Could you please give a short introduction to the Global Alliance for Genomics and Health? The Global Alliance for Genomics and Health (Global Alliance) was formed less than two years ago when key players in the field of genomics came together to discuss how we could help accelerate the use the potential of genomics to advance human health. Since then the Global Alliance brings together almost 300 institutions from 30 different countries. Member institutions are very varied and include those working in research, healthcare delivery, disease advocacy, and information technology. It is pretty unique being a mix of academic and commercial partners. The partners in the Global Alliance are working together to enable genomic data sharing. This involves developing new software and creating a framework of harmonized approaches for the responsible, voluntary, […]


Open Knowledge announce plans for OpenTrials

OpenTrials will collect information about all clinical trials around the world Before any drug goes on the market, it usually takes several years of clinical trials to make sure that the drug is safe to use and is effective against the disease. In reality, some drugs are better than others and many drugs have severe side effects in particular groups of patients. Patients, doctors, researchers and policy makers often rely on the results of clinical trials to make informed decisions about which drugs are best. For multiple reasons, only about half of all clinical trial results are published. Positive results are published twice as often as negative results. And very often not all important details about the methods and findings are published. It is therefore exciting news that Open Knowledge announced the development of OpenTrials – an open, online database of information about the world’s clinical research trials. Open Trials will collect information from different existing sources and provide a clear picture of the data and documents on all trials conducted on medicines and other treatments around the world. The project is designed to increase transparency and improve access to research. It will be directed by Dr. Ben Goldacre (@bengoldacre), an internationally known leader on clinical transparency. You can take a look at his […]

Pickard family

Family Trio Sequencing – Genetic Clues in Autism

This is a guest blog post written by KT Pickard (@kthomaspickard) and Kimberly Pickard (@kimberlypickard), Co-founders of StartCodon. Amazingly, the cost of whole genome sequencing is now 100,000 times less expensive than it was a dozen years ago. If the Tesla Model S followed this trajectory, you could buy one today for less than $1 USD. This super logarithmic decline puts genomics on par with desktop publishing or 3D printing—it has become something that you can affordably do yourself. My wife, Kimberly, and I were excited about the prospect of having our genomes sequenced. Our daughter has autism, and like many parents of special needs children, we were eager to explore the underlying causes of her condition. We “got genomed” last year by enrolling in Illumina’s Understand Your Genome program. We received our whole genome sequencing (WGS) data, as well as limited predisposition and carrier screening for a number of Mendelian traits. As many DNAdigest readers know, the cost of WGS continues to drop in price, almost to the $1,000 genome that Illumina announced last year. Kimberly and I were intrigued to learn that we were both carriers of some rare genetic variants. Could our genetic idiosyncrasies be contributing to our […]


A patient advocate for cancer research

This is the first part of a guest blog post written by Dave Dubin. Read the second part here. 1997 seems so far away.  I’m 29, still a strapping 200 plus pounds, playing soccer, managing the business, recently married with first house and first son.  As much as “family history of colon cancer” is written all over the chart, I’m sent away by my primary physician when I have symptoms.  A few months later, symptoms of blood in the stool and cramping don’t go away.  A gastroenterologist finally confirms stage three colon cancer.  I have what will become the first of several surgeries at Mt Sinai Hospital in Manhattan, and the start of what would become much more than a patient-doctor relationship with Gastroenterologist Blair Lewis and Brian Katz, my surgeon. Three years after my surgery, my older brother develops colon cancer.  Since he started getting screened by Blair Lewis after my episode, his is caught earlier.  Brian Katz is his surgeon as well, and since laparoscopic surgery is now more prevalent at Mt Sinai, his is less invasive and scars are smaller.  No chemo.  I notice how my parents have a difficult time watching their son go through this.  […]

DNAdigest interviews Transcriptomine

This week I would like to introduce you to Dr Neil McKenna who is a principal investigator of the Nuclear Receptor Signaling Atlas consortium. In the following A&Q session you will learn about the tool Transcriptomine which gives the research community ready access to transcriptomic datasets – some background, future plans for improvement as well as step-by-step process for you to start using it for your research. Dr Neil McKenna, principal investigator of the Nuclear Receptor Signaling Atlas consortium 1. Could you please give us an introduction to Transcriptomine? Eukaryotic signal transduction involves small extracellular signaling molecules (ESMs) – hormones and growth factors, for example – and transcription factors (TFs), which bind DNA and regulate the expression of target genes. Transcriptomine is an effort to compile, organize and consistently annotate transcriptomic datasets involving ESMs or TFs, and to expose these to the research community so that they can make more effective use of them for their research. 2. What is your role in the project and how does you background support it? Transcriptomine draws together the talents of a scientific curation and annotation team, with a strong background in signal transduction research, and a web development and information technology team. Financial support for Transcriptomine is […]

Genomic Data

Genomic Data Sharing – Ethical and Scientific Imperative

This is a guest blog post writen by Mahsa Shabani (@Mahsashabani). Genomic data sharing has become an ethical and scientific imperative in the recent years. Funding organizations, research institutes and journals among others, endorsed the significance of data sharing practices to the progress of research and an optimal use of community resources. Consequently, researchers all around the world are extensively involved in the data sharing process, ranging from data production to data use. As sharing practices do involve individuals’ data, the associated ethical and legal concerns should receive thorough attention in order to respect individuals’ rights and maintain public trust. Sharing data via controlled-access public databases has been seen as an answer to the identified concerns at the moment. Data Access Committees (DACs) constructed locally or in a central fashion control access to these datasets according to defined criteria. Evaluating the qualification/eligibility of data users, ethical and scientific grounds of proposed uses and oversight on downstream data uses are considered as the main responsibilities of DACs. While the structure, membership and procedure of access review vary across DACs, some similarities in approaches and mechanisms are observed. A requirement of preparing a summary of data use and signing a data access agreement […]

Anna Middleton

Involving participants in genomics research

Guest post by Dr Anna Middleton, Senior Staff Scientist, Wellcome Trust Sanger Institute. This blog post was originally published by the Nuffield Council on Bioethics. The blog post is based on the talk Dr Middleton gave at the launch of the Council’s report: The collection, linking and use of data in biomedical research and health care: ethical issues. My career has explored, from multiple different perspectives, the impact of genomics on people. Genomics refers to the study of a person’s 20,000 or so genes. Given the almost infinite ways that people can be genetically different to each other, genomic research often needs to be done on a very large scale in order to be able to interpret the significance of findings, particularly a rare genetic change. So, Big Data and Genomics go hand in hand. To give you an example, I’m currently part of the Deciphering Developmental Disorders (DDD) project at the Sanger Institute which seeks to offer cutting edge genomic testing to 12,000 children from the NHS with severe, complex, physical and/or intellectual disability. These children have exceptionally rare conditions that their doctors may never have seen before. Using an online database that contains large sets of health and biological […]

DNAdigest interviews COS

DNAdigest readers, this week I am happy to present you to the Centre for Open Science (COS). Our interviewee is Tim Errington, who is the project manager of the Reproducibility Project: Cancer Biology, part of COS. Take a look at what exactly this non-profit technology company is all about and how it will improve research practices. Tim Errington, Project Manager of the Reproducibility Project: Cancer Biology 1. You are a part of the Centre for Open Science team. Please, tell us what the mission and the interests of the company are? Our mission is to increase the openness, integrity, and reproducibility of scientific research.  We support shifting incentives and practices to align more closely with scientific values. We work on this through three main activities: metascience activities to research scientific practices, community activities to foster open science, and providing infrastructure support through the Open Science Framework (OSF). 2. Why do you think OPENNESS, INTEGRITY and REPRODUCIBILITY of scientific research are of such a great importance for the community? Openness and reproducibility are core scientific values. They refer to increasing transparency of research data, methods, materials, and workflow, and to increase inclusivity so that everyone has opportunity to access and contribute to […]