This year’s conference kicked off with an interesting Data Science panel that included Tanya Cashorali (TCB Analytics), Jerald Schindler (Alkermes), John Reynders (Alexion Pharmaceuticals), and Lihua Yu (H3 Biomedicine). Without a doubt, data science is important and involves much more than big data, including the entire workflow of data creation, to insight generation, and decision-making. One key message that came across is that not all data is big data, and that we need improvements in data collection and infrastructure support for data analysis and management. Other key take-home messages: breaking down data silos, educating about responsibility, being responsible to not act independently on data, creating an environment that motivates everybody within a team to share, not rewarding bad data behavior, and being insensitive to data sharing to get more out in return. The big issue here is the culture. If the culture rewards Continue reading
The National DNA Day commemorates the 1953 Nature publication of the Structure of DNA by James Watson, Francis Crick, Maurice Wilkins, Rosalind Franklin, and colleagues. It has been….
Image credits: Zen Sutherland
- 65 years since the publication of the Molecular Structure of Nucleic Acids
- paper by Watson, Crick, and colleagues like Wilkins and Franklin,
- 41 years since the release of the Sanger sequencing methodology,
- 31 years since the launch of the first automated DNA sequencer by Applied Biosystems which eventually enabled the completion of the Human Genome Project in 2001,
- 12 years since the launch of the Solexa Genome Analyzer, the first second-generation sequencing platform, which supported the sequencing of 1 GB of data in a single run,
- 4 years since the $1,000 Genome has become a reality via Illumina’s introduction of the HiSeq X Ten platform and a 10,000-fold reduction in price relative to the cost of the human genome in 2004,
- 3 years since the completion of the 1,000 Genomes Project and the start of the 100K Genomes Project and many other projects taking off.
This year’s ACMG conference in Charlotte, North Carolina, included a very well received first installment of TED-style talks which reflected on the evolution and impact of healthcare. All three talks delivered by Kaylene Ready (Director of Inherited Cancer and a Genetics Counselor, Counsyl), Christian Schaaf (Professor Clinical Genomics, University of Cologne), and Wendy Chung (Associate Professor of Pediatrics, Columbia University Irving Medical Center) were inspirational, and were considered a great addition to ACMG 2018. Takeaways and key messages included: “treat every patient like patient No. 1, always keeping them at the center of the work, and us working as mediators rather than as a barrier”. Image credit: @DeniseCalvert13
Some statistical numbers were eye-opening and challenging as it comes as no surprise that the community currently lacks genetic counselors (GCs), with fewer than 4,000 GCs and 2,000s medical geneticists in the US which translates to one geneticist per ~60,000 people. With new genetic tests generated every day, GCs need to take on the role of mediators. New operational solutions were discussed to address this shortcoming, and as such Kaylene Ready proposed the exploration of chatbots as alternatives to GC service delivery. While certainly an interesting suggestion, we will have to see whether the field with its customers (i.e. patients) is ready to discuss challenging genetics findings with a computer. As a result, it was suggested to decouple Continue reading
For this month’s “Company Spotlight” blog series we are reviewing Genohm with an interview with Nick Beckloff, Director of US Operations at Genohm. Genohm is a 50-person company headquartered in Lausanne, Switzerland. I took this opportunity to learn more about Genohm, and SLIMS (Sample Laboratory Information Management System), their sample and data management software offering intended to address today’s challenges of managing the sample and data throughput in clinical, NGS, and other types of labs.
The following summarizes questions and answers from my dialogue with Nick Beckloff.
EB: Tell us more about Genohm – what need are you trying to address and what products/services do you offer?
NB: Genohm’s mission is to reduce the complexity of life in the lab by offering a software package that distills the important aspects of a LIMS while providing functionality across many relevant spectra. We offer a flexible and customizable solution Continue reading
This year’s meeting was in every way very much what was expected: a great set of science talks, a never ending networking event, and last but not least a product launch point. Instead of summarizing what has been written up by many other great writers and bloggers on a daily basis, here just a few highlights accompanied by the announcements that went hand-in-hand with this event. For convenience purpose, and to have it all in one place, I listed the different blog posts reflecting on AGBT 2015.
A great resource of the different AGBT activities and highlights can be found in the following blog posts written by Genohub, Pacific Biosciences, Golden Helix, DeciBio bloggers, Bio-IT World, and NextGeneSeq Report. Continue reading
Given the exciting times we are living in right now, sometimes it feels like we have hit the data jackpot. Consider the fields of biology and health care, which are changing rapidly and churning out big data thanks to constantly evolving technology developments. Even just a couple of years ago, we would never have imagined the phenomenal pace of progress in this area.
Being able to contribute to some of these efforts is enormously valuable — but also challenging as the information flow never ceases. With the availability of big data, many new initiatives in research and health care, the reduced (and continuously dropping) cost of sequencing and its accompanying Continue reading