Bio Saga Headlines

Bio Saga

Thursday, October 31, 2013

Senator Rand Paul (R-Ky.) Draws some inspiration from BioSaga Blog

GATTACA has always been one of my favorites; every now and then I have used it as a reference in many of my posts, this one being the recent! Genome From Birth - Dawn of the GATTACA era!

This is what Senator Rand Paul (R-Ky.) says in his latest public address;

Speaking at a Liberty University event in Virginia, Senator Rand Paul (R-Ky.) warned that genetic testing could lead to eugenics à la the 1997 movie Gattaca, reports the Associated Press.
"In your lifetime, much of your potential — or lack thereof — can be known simply by swabbing the inside of your cheek," Paul said. "Are we prepared to select out the imperfect among us?" He was campaigning in Virginia for gubernatorial candidate Ken Cuccinelli.

Other aspects of Paul's speech referring to the dystopian movie, though, resembled the Wikipedia entry on the movie, Rachel Maddow pointed out on her show on Monday. USA Today notes that Paul has not responded to those accusations.

Paul added that he was not against science, noting that he is a physician, and he praised the decrease in childhood mortality rates and the increase in life expectancy during the past 100 years, according to the video at USA Today.



Tuesday, October 29, 2013

Illumina to Acquire NextBio, Integrate Firm into Enterprise Informatics Business

Illumina today announced it signed a definitive agreement to acquire clinical software firm NextBio.

NextBio, based in Santa Clara, Calif., provides platforms to aggregate and analyze large amounts of phenotypic and genomic data for research and clinical applications. It currently has customers at more than 50 commercial entities and academic institutions.

By acquiring the firm, Illumina "will be able to offer customers enterprise-level bioinformatics solutions that accelerate the discovery of new associations between the human genome and disease, and ultimately, enable the application of those discoveries within healthcare," according to a company statement.

NextBio's platform allows customers to compare experimental data against existing data sets using a correlation engine, enabling them to discover new associations. It uses "highly scalable" software-as-a-service enterprise technology and is capable of analyzing petabytes of data.

Illumina plans to combine its BaseSpace cloud computing environment for next-generation sequencing data with NextBio's platform for integrating patient data.

The acquisition is expected to close by the end of October. No financial terms were provided.

Illumina will integrate NextBio into its newly-formed Enterprise Informatics business and will retain NextBio's co-founder Ilya Kupershmidt and Chief Technology Officer Satnam Alag.

Monday, October 28, 2013

Qiagen Acquires CLC Bio

Qiagen has acquired CLC Bio, a privately held bioinformatics software company headquartered in Aarhus, Denmark. The news was first reported on AllSeq's blog.


This is the second bioinformatics company that Qiagen has purchased this year. In May, it bought Ingenuity Systems for $105 million in cash to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions (BI 5/3/2013).

Qiagen has been making some interesting moves lately, slowly building an end to end sequencing solution. They’ve already established themselves as the market leaders in sample prep, but then they started acquiring the missing pieces. First they bought Intelligent BioSystems in June 2012, giving them access to a sequencing platform built with the clinical market in mind (fairly standard SBS chemistry, relatively fast runs and multiple flow cells to obviate the need for sample multiplexing). Then they acquired Ingenuity in April 2013, giving them another piece of the puzzle – the ‘genome interpretation’ part.

So they can isolate the DNA and RNA, they can prepare sequencing libraries (for Illumina and Ion Torrent, since their own ‘GeneReader’ isn’t out yet) and they can perform variant analysis on the data. The piece they’re still missing is the data analysis part (which generates the variant list that feeds into Ingenuity’s Variant Analysis™ program). So…

We’ve been hearing a couple of rumors that maybe they plugged that gap, specifically through the acquisition of CLC bio. We couldn’t find anything about this on the web, so we decided to just ask. We called up a couple of people at CLC bio and, after a little bit of “Er, um, why do you want to know?”, we got the official confirmation – CLC bio was acquired by Qiagen! They wouldn’t confirm exactly when this happened (probably sometime this summer) or for how much (for reference, Ingenuity was acquired for $105M). [Edit - CLC bio has made it clear that they will continue to support all major sequencing platforms in the future.]

We’re not sure why they aren’t talking about this more as it seems like a pretty big deal to us – Qiagen is rapidly building the end to end solution that no one other company seems to have. Illumina currently has a stranglehold on the high throughput market and controls at least half of the desktop market (with Ion Torrent picking up the other half). Is Qiagen’s ‘one stop shop’ solution going to be the key to shaking up the leaders? We’re not sure, but we can’t wait to find out!

Wednesday, October 23, 2013

The END of 454 Saga


Following Roche's disclosure last week that it will shut down 454 Life Sciences and stop supporting 454 sequencing instruments by 2016, customers are making plans to move their sequencing over to other platforms, if they have not done so already.

While Illumina, Life Tech's Ion Torrent, and Pacific Biosciences are eager to step in to fill the void, some customers say aspects of 454's technology cannot be replaced by other platforms at this point. Also, those customers who have started to use 454 for routine clinical applications need to revalidate their assays on a new platform.

Roche said last week that it will close down 454, which is based in Branford, Conn., and lay off about 100 employees over the next three years (GWDN 10/15/2013). By mid-2016, it will stop supporting the 454 sequencing platforms, the GS FLX+ and the GS Junior.

Roche's decision to pull the plug on 454 came to light less than a month after the company announced a deal with Pacific Biosciences, worth up to $75 million, to develop a sequencing system and assays for clinical diagnostics using PacBio's single-molecule real-time sequencing technology (IS 10/1/2013).

Earlier this year, Roche had already eliminated 60 positions at 454 as part of a reorganization that combined the 454 business in Branford and the NimbleGen business in Madison, Wis., into a new sequencing unit (IS 4/23/2013). That move was part of a larger restructuring that dissolved Roche Applied Science, the life science unit of Roche Diagnostics, and integrated its products into other units. At the same time, Roche cut its sequencing technology development collaborations with DNA Electronics and with IBM.
Dan Zabrowski, head of Roche's sequencing unit, told In Sequence last week that all 454 products, such as instruments, parts, reagents, consumables, and services for those products, will continue to be available to customers until mid-2016. These include the GS FLX and GS Junior Titanium reagent series, the XLR70 and the XL+ sequencing kits, and subkits for the GS FLX and FLX+ instruments. Also included will be existing and soon-to-be-launched GS Junior/+ sequencing kits and subkits.

Do you wish to know more?

Genome From Birth - Dawn of the GATTACA era!

Dawn of the GATTACA era! this was one of my old post. AND now this is what we hear from Robert Green

The idea of sequencing someone's genome at birth has been "has been around for a long time in a pie-in-the-sky way," Robert Green from Brigham and Women’s Hospital tells Carl Zimmer at Slate. But it is becoming more of a reality, Zimmer adds.
Green's BabySeq project recently received funding from the US National Institutes of Health to study how sequencing the genomes of some 240 healthy and ill infants affects their lives. They will be compared to a similar cohort of infants whose genomes will not be sequenced.
As the study is small, Zimmer notes that rare, deleterious mutations may not crop up. The project will, though, make the discussion of ethics in genomic medicine more concrete, he says.
“We’ll be grappling with them in real life, with real babies and real families and real clinicians and real laboratory results,” Green adds.

Friday, October 4, 2013

Search for Mutation-Sensitive Genome Sites Yields Tool for Finding Disease Players in Non-Coding Sequences

By considering sequence data for individuals assessed through the 1000 Genomes Project, a team led by researchers from Yale University and Wellcome Trust Sanger Institute came up with a computational method for prioritizing potential disease culprits — including those in non-protein-coding parts of the genome.

As they reported online today in Science, the researchers sifted through SNP profiles in coding and non-coding sequences in 1,092 genomes, focusing on functionally annotated areas. With the help of information from the ENCODE project, mutation databases, and other data sources, they narrowed in on sequences that seem especially sensitive to change.

The group tapped these mutation-sensitive sites to develop an approach called FunSeq, which proved useful for uncovering new apparent driver mutations using sequences from around 90 cancer genomes. These included almost 100 driver candidates in non-coding sequences, according to study authors, who noted that FunSeq is expected to help in tracking down crucial non-coding variants in other disease types as well.

"Our technique allows scientists to focus in on the most functionally important parts of the non-coding regions of the genome," co-senior author Mark Gerstein, a computational biology and bioinformatics researcher at the University of Yale, said in a statement. "This is not just beneficial for cancer research, but can be extended to other genetic diseases, too."
"Although we see that the first effective use of our tool is for cancer genomes, this method can be applied to find any potential disease-causing variant in the non-coding regions of the genome," the Sanger Institute's Chris Tyler-Smith, co-senior author on the study, said in a statement.

The ability to discern functionally important variants is critical for interpreting information in the human genome and finding changes that can produce disease, the researchers noted. But the consequences of many variants are unknown and tricky to define, especially those occurring outside of protein-coding sequences.

Conservation across multiple mammalian species can offer some clues to the importance of various sequences. For the current study, though, investigators turned to available human population data, reasoning that "signatures of purifying selection identified by using population-variation data could provide better insights into the importance of a genomic region in humans than evolutionary conservation."

Using polymorphism patterns determined for the 1,092 genomes profiled for the 1000 Genomes Project, the team searched for sequences that appear to be sensitive to alterations and subject to purifying selection.

"As expected," the researchers wrote, "we found that having variants from 1,092 individuals allowed us to detect specific functional categories under strong purifying selection with greater power than previously possible."

To further tease apart functionally important variants, researchers incorporated other types of data, too, including mutation information from the Human Gene Mutation Database, patterns found in one individual's genome sequence, interaction network data, and results from the ENCODE project.

By applying this type of analysis across hundreds of sequence categories, the team got a sense of the relative strength of selection working in different coding and non-coding sequences. For instance, some apparent transcription factor binding sites appeared especially sensitive to mutation, as did genes at the heart of interaction networks.
By formalizing their functional variant and mutation predictions into a computational tool known as FunSeq that focuses on regions of the genome that seem especially sensitive to change, the investigators demonstrated that they could identify around 100 non-coding driver mutations using information from 90 tumor genomes. Those included 21 breast cancer genomes, three medulloblastoma samples, and dozens of prostate cancers.

"This allows us to take a systematic approach to cancer genomics," Gerstein said. "Now we do not need to limit ourselves to the roughly [1 percent] of the genome that codes for proteins but can explore the rest of our DNA."

The study's authors noted that it should be feasible to gain insights into other types of disease risk by scrutinizing the same sorts of mutation-sensitive non-coding elements defined in the current analysis.

"Because they cover a small fraction of the entire genome (comparable to the exome), these regions can be probed alongside exome sequences in clinical study," they wrote, explaining that the variant sorting scheme may be further refined in the future by folding in additional population profiles and other types of genomic data.

Life Science and Informatics

What is this?
is this a new industry?
or a old wine in a new bottle?

Well Life Sciences and Informatics can be anything form computational biology, all omes and omics, core bioinformatics to curation and literature mining, database creation, in the area of biology, chemistry , bio-chem space.

There are number of companies in India and bangalore is the forefront as a major bio-cluster with 20 to 30 companies in this sphere.

now how good are these companies doing?
how good are they in terms of the international markets and how profitable is their business?
what do they do?
their clients?

These are some interesting things that could be discussed in this blog page...

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