Thursday, 21 February 2013

BreakThrough Prize...when big companies meet life science

Given the worldwide economic crisis, we have been looking in recent years at a consistent cuts on traditional sources of research funding (with the notable exception of China I think).
So we have to search for new ways to get the money we all need to accomplish good research. In recent times something new emerged, such as crowd-funded projects and big prizes funded by private corporations willing to contribute to human knowledge (with a consistent saving on tax by the way...).
In this perspective, I've found the new "Breakthrough" Prize really interesting. Founded by some of the biggest personality on the Internet and Genetic test markets, it will reward 3M US$ each year, to be divided between 11 top researchers, recognizing excellence in research aimed at curing intractable diseases and extending human life. The winners are also recruited to be part of the selection committee for the next year prize.

This bunch of money is gently provided by the Breakthrough Prize in Life Sciences Foundation, a not-for-profit corporation dedicated to advancing breakthrough research, celebrating scientists and generating excitement about the pursuit of science as a career. 
Among its member there are: 
Art Levinson, chairman of the Board of Apple and chairman of Genentech;
Mark Zuckerberg, founder and CEO of Facebook (who don't know this one anyway?);
Sergey Brin, co-founder of Google;
Anne Wojcicki, co-founder of 23andMe;
Yuri Milner, founder of Mail.Ru group, a leading European Internet company.

Giving the names providing the funds, the winners should fulfill the following criteria:
  • At least one published paper must have the title starting with a big G and visual doodle abstract to explain the whole idea.
  • Your results have to be available to the community...but for 0,79cent on Apple-store.
  • Author facebook profile must have at least 500 friends and 1000 likes on fb.
  • And don't forget, you have had produced a breakthrough research!
Winner of this first edition are:
-- Cornelia I. Bargmann
-- David Botstein
-- Lewis C. Cantley
-- Hans Clevers
-- Napoleone Ferrara
-- Titia de Lange
-- Eric S. Lander
-- Charles L. Sawyers
-- Bert Vogelstein
-- Robert A. Weinberg
-- Shinya Yamanaka

Wednesday, 20 February 2013

AGBT 2013...ready...GO!

The 2013 edition of AGBT (Advances in Genome Biology & Technology) is at its start on Marco Island. As usual it will be the main stage for announcements on new technologies and applications from the genomic community and any company working in the field.

There is excitement in the net for this new AGBT edition and a lot of words have already been spent in the various blogs about the main topics proposed in the 2013 meeting agenda. See for example posts on CoreGenomic, Omics! Omics! or MassGenomics.

Big announcements of new platforms seem missing this year, after breaking news of the past editions (do you remember Ion Proton and Oxford Nanopore?), and the whole conference is focused more on new applications than on new technology. However there still space for innovation, like the Positional sequencing presented by NabSys. According to what revealed by Keith Robison on Omics! Omics!, who have had a preview of the platform, this sysyem provides similar information to the optical mapping systems of OpGen and BioNano Genomics. However, by employing electronic detection and oligonucleotide probes to define genomic landmarks, Nabsys promise to deliver much more accurate measurements of position the possibility to tune the resolution of a map by adjusting the complexity of that probe pool. The initial application will be mainly small genome scaffolding, but the NabSys system looks promising also for structural variant detection.

Looking at the agenda there are several interesting talks:
  • Eric Boerwinkle, from University of Texas, reports on CHARGE Consortium results on the use of WGS and WES together with deep phenotyping to dissect genetic basis of complex traits.
  • Russ Altman, Stanford University, talks about pharmacogenomics in the NGS era, an ever-green topic.
  • Christine Eng, Baylor College of Medicine, reports on their experience on Clinical Whole Exome Sequencing. See also an interesting interview with Sharon Plon of the Baylor College talking about this topic.
  • In the clinical field Jonathan Berg, from The University of North Carolina at Chapel Hill, discuss the practical management of genomic incidental findings, which is a really interesting issue to be solved when managing WES clinical applications.
  • There are several talks discussing new applications for single-cell DNA and RNA sequencing, with particular focus on cancer cells, and Dagan Wells, from University of Oxford, reports also about Single Cells Sequencing on Human Embryos to Reveal Aneuploidy and Mutations of the Nuclear and Mitochondrial Genomes.
  • Epigenomics and data analysis are also wide covered and I want to point at an interesting talk from Gabe Rudy, Golden Helix, on the difficulties of getting Meaningful Analysis Results from genomic data. He reports the case of a trio study conducted on himself, his wife and their son using data from 23andMe.

As a side note, it seems that global economic crisis have exerted its effects also on Marco Island since there are no gold or platinum sponsors for this year edition...but I hope that this will not limit the fun&science experience for all the participants!

Don't forget to follow all the AGBT news in real-time on Twitter: the official hashtag is #AGBT2013, but don't miss the tweets from genomics addicts present at the conference (some of them are authors of our favorite blogs, so check out the list!).

A last curiosity, AGBT has always been innovative also in terms of communication with extensive coverage on the net (lot of participants directly report their experience on blogs, Twitter and other social networks), so this year the organizers have provided clear indication on what is "twittable" and what has to be kept secret!  This is digital revolution!

2012 NGS Market Survey by CLC Bio

As in 2011, CLC Bio has provided an extensive survey of the NGS market also for 2012. The picture is constructed based on responses from 708 individuals in 73 countries: about 24.6 percent work in the US, 73 percent of respondents work in academic research while 9 percent work in industry, another 9 percent in government, and 6 percent work in not-for-profit organizations, according to the survey.

Illumina’s HiSeq and MiSeq emerged as the most diffused instruments, used by about 34.6 percent and 21.3 percent of respondents. Meanwhile, Roche’s 454 sequencers got 21.2 percent of the votes and Life Technologies’ Ion Torrent Personal Genome Machine got 11.5 percent of the responses.
Talking about applications, Whole Genome Sequencing, RNA-Seq Expression analysis and de novo sequencing stay on top with about 40%, followed by amplicon sequencing. Instead, Whole Exome Sequencing seems quite limited in use with only 12%, that is quite unexpected in my opinion.

See the complete survey on CLC website for further details!

Friday, 15 February 2013

Breaking News: Bigfoot genome finally published

It's not April 1st yet, however something a little bit weird has been reported on several web sites.
Let's start from the beginning: back in November 2012 a team of researchers (experts in genetics, forensics, imaging, and pathology led by Dr. Melba S. Ketchum) claimed that through a DNA study they were able to sequence three complete Bigfoot (also known as Sasquatch) nuclear genomes and determined that the species is a human hybrid. The scientists said that Bigfoot is a human relative that arose roughly 15,000 years ago and is a hybrid of modern Homo sapiens and an unknown primate species.
A few days ago a paper describing the genome sequence was published on an online journal called De Novo (apparently the team performing the study had some trouble publishing their results so they decided to... buy an existing journal and renamed it). Unfortunately the scientists are trying to charge $30 to anyone wanting to view their research paper. Fortunately somebody was able to get their hands on a copy of the paper and found out that...
You can read more about it in this Ars Technica article.
Below is the abstract of the paper that, strange enough, cannot be found in PubMed.

Ketchum, M. S., Wojtkiewicz, P. W., Watts, A. B., Spence, D. W., Holzenburg, A. K., Toler, D. G., Prychitko, T. M., Zhang, F., Bollinger, S., Shoulders, R., Smith, R. 

Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies

DeNovo Scientific Journal, 2013, Vol. No. 1

One hundred eleven samples of blood, tissue, hair, and other types of specimens were studied, characterized and hypothesized to be obtained from elusive hominins in North America commonly referred to as Sasquatch. DNA was extracted and purified from a subset of these samples that survived rigorous screening for wildlife species identification. Mitochondrial DNA (mtDNA) sequencing, specific genetic loci sequencing, forensic short tandem repeat (STR) testing, whole genome single nucleotide polymorphism (SNP) bead array analysis, and next generation whole genome sequencing were conducted on purported Sasquatch DNA samples gathered from various locations in North America. Additionally, histopathologic and electron microscopic examination were performed on a large tissue sample. vel non-human DNA.