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Bio Saga

Saturday, December 14, 2013

New Informatics Approach Combines Metabolic, Regulatory Networks to Elucidate Cells' Activities

A new paper written by researchers from the Institute for Systems Biology describes a computational approach for studying regulatory activities in cells that relies on integrated networks of transcriptional and metabolic data.

The study, published in PLOS Computational Biology earlier this month, describes software called the Gene Expression and Metabolism Integrated for Network Inference (GEMINI) which uses an integrated model of network and metabolic data to explore growth phenotypes in Saccharomyces cerevisiae .

GEMINI builds on work from the same researchers published in 2010 in the Proceedings of the National Academy of Sciences. That paper describes the Probabilistic Regulation of Metabolism (PROM), which provides a mechanism for integrating transcriptional regulatory networks and metabolic networks in a single in silico model and using it to make predictions about phenotypes such as flux and growth rate.

While based on PROM, GEMINI is designed to tackle a slightly different question, as the PLOS Comp. Bio. paper explains. While PROM "solves the forward problem of combining disparate networks to predict phenotype" with GEMINI "we iteratively use PROM to aid in solving the more challenging inverse problem — guiding TRN structure prediction using the metabolic network and the emergent phenotype measurements," the researchers wrote. "In doing so, our new method serves as a tool to refine the inferred TRN and improve the predictive power of the integrated network models."

Nathan Price, ISB's associate director and co-author on both papers, explained that while PROM uses the integrated network to try to predict what happens when transcription factors are deleted, GEMINI says "we don't know what the gene regulatory network is perfectly so we are going to use the fact that we can link these two together to now look at where we make wrong predictions," 

"GEMINI says, [for example], 'I have a prediction that this transcription factor influences a gene that happens to code for a metabolic enzyme,'" Price said. "Because we can link these things together and make growth predictions, we can say, 'When we knock out that transcription factor in yeast, does it have the decrease in growth rate that we predict because of this regulatory interaction.'"

The developers claim that theirs is the first approach that integrates regulatory and metabolic data in this way and use it to study cell's activities. They write in PLOS Comp. Bio that it improves on previous strategies that have used primarily "proximal data such as gene co-expression and transcription factor binding" to reconstruct and study TRNs. While these methods, they said, can be used to quickly reconstruct TRNs, "the overwhelming combinatorics of possible networks limits identification of mechanistic regulatory interactions."
Their findings, the researchers conclude, "suggest that a metabolic constraint-based approach can be successfully used to help reconstruct TRNs from high-throughput data, and highlights the potential of using a biochemically-detailed mechanistic framework to integrate and reconcile inconsistencies across different data-types."
Metabolic networks are one of the better understood cellular systems, according to Price, making it the ideal starting point for studying at least those regulatory activities in which cell metabolism plays a role, such as growth rates.

"It's hard to just look at a transcriptome and say [for example] if I knock out a transcription factor, that is going to lead to the death of this tuberculosis cell," he said. "But as soon as you tie it on to metabolism, there are very … clear rules about what … leads to cell death in metabolism in a way that you don't see directly in gene regulatory networks."
For their next steps, Price and his colleague and co-author, Sriram Chandrasekaran, are trying to use GEMINI to study networks in cells other than yeast, such as human cell lines. He also said that they're exploring ways to integrate it with network inference algorithms with an eye toward creating a "model-guided platform for synthetic biology." A third potential application would be to use GEMINI to study regulatory-metabolic interactions associated with disease-specific cancers, as well as metabolic and neurodegenerative diseases, he said. 

Wednesday, December 11, 2013

Bioinformatics Workshop on 'Structural Bioinformatics' at BISR, Jaipur, India

January 10-12, 2014 
Birla Institute of Scientific Research, Statue Circle, Jaipur, India 
[link] 

Bioinformatics Centre at Birla Institute of Scientific Research, Jaipur is organizing a three-day Bioinformatics workshop on "Structural Bioinformatics". BISR is known for providing a high quality training in advance area of Biotechnology and Bioinformatics. 

This workshop will enable participants to learn tools & techniques that are being used to analyze biological structures i.e. proteins and DNA along with application in drug design. The workshop will feature morning lectures, demonstrations with evening hands-on session in Bioinformatics lab. 

The no. of participants is limited to 40 only. The participants of the course may be the UG/PG students, research scholars, faculty member and industry personnel with background in Biological Sciences and/or Information Technology. The workshop is self-contained and does not assume any special knowledge of the subject. 

REGISTRATION: 
Last date of registration is 1st January 2014. Application form and brochure may be downloaded from the website. For further details kindly visithttp://www.bisr.res.in or email to the convener at workshop.bisr[at]gmail.com.

Accelrys Acquires Qumas for $50M

Accelrys has bought Qumas, a provider of cloud-based and on-premise enterprise compliance software for regulatory and quality operations in regulated industries including the life sciences, for $50 million.
Accelrys said that the added intellectual property extends its informatics portfolio by providing document and process management compliance solutions that improve its ability to help customers reduce regulatory risks and quality costs, improve compliance, and increase operational efficiency across their product development lifecyles.

Operating from offices in Cork, Ireland and New Jersey, Qumas provides an electronic document management application with related research and development submission and QA documentation packages based on customer and industry requirements and best practices.
Its business process management applications include corrective action/preventive action, audit, change control, deviation, complaint, and more. For the last two decades, the company has been involved in integrating content, processes, people, and systems into enterprise compliance programs that eliminate the cost and complexity associated with managing paper-based, disparate or legacy document management applications.

As part of an integrated solution, Accelrys said that applications such as the Accelrys Electronic Lab Notebook, Accelrys Laboratory Information Management System, Accelrys Lab Execution System, and Accelrys Discoverant for Operational Intelligence will function as data sources and integration points for the compliance and quality business systems that Qumas’ solutions manage.
"Integrating QUMAS solutions into the Accelrys product portfolio will provide a single-vendor [scientific innovation lifecycle management] solution that is already in high demand for product lifecycle management into the critical compliance and quality management arena for science-based process industries," Accelrys President and CEO Max Carnecchia, said in a statement.
It also enables Qumas to extend its customer base in other business areas currently served by Accelrys, Qumas CEO Kevin O’Leary added.

Under the terms of the agreement, in consideration for acquiring all of the outstanding capital stock of Qumas, Accelrys agreed to pay to the company’s shareholders a total of approximately $50 million in cash, subject to working capital and other adjustments. The transaction is expected to be neutral to Accelrys' non-GAAP earnings per share for the year ending Dec. 31, 2013, with a $1 million to $2 million non-GAAP revenue contribution.

Qumas had revenues of $15.2 million for the year ended Dec. 31, 2012.
This is Accelrys' second acquisition for the year. In January, the company bought Vialis, a systems integration firm headquartered in Liestal, Switzerland, for up to $10 million.
In its most recent financial report, Accelrys posted a 1 percent bump in third quarter revenues for a total of $40.9 million for the three months ended Sept 30, compared to $40.5 million for the same period a year ago.

Wednesday, November 20, 2013

Bioinformatics Short Time Courses

Here are some bioinformatics courses, These are geared towards:

- Scientists, so they can think like a programmer and solve bottlenecks in data-based Biology
- Computer programmers, so they know how to solve bioinformatics problems for scientists
- Bioinformaticians, so they can advance their skills in newer application areas

Some of these courses include scripting and database management with Linux, Perl, R, Matlab and MySql, while others include learning to use software for analyzing data from Microarray, NGS, Metabolomics and Proteomics platforms. A course on High Performance Computing and Primer Design is also offered. A detailed roster of scheduled courses is available at:
http://www.bioinformatics.org/edu/calendar/view.php?view=upcoming

Additionally, through Bioinformatics.org, an instructor-led program in practical bioinformatics is being offered. The goal here is to provide attendees a broad overview of the bioinformatics landscape, while giving them hands-on experience with tools used in various application areas of bioinformatics such as NGS, Microarrays, Metabolomics and Proteomics. Details can be found at: 
http://www.bioinformatics.org/wiki/Educational_services#Trainer-Led_Program_in_Bioinformatics
 

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.

Wednesday, August 7, 2013

The Layoffs Continue...

PerkinElmer Reduces Headcount by More than 400 in 2012

PerkinElmer reduced its workforce by 62 employees during the first quarter as part of a restructuring plan,

PerkinElmer Lays off 265 in Second Quarter

PerkinElmer laid off 265 employees during the second quarter, the company said in its Form 10-Q today.

In the document filed with the US Securities and Exchange Commission, it said that the reduction in workforce was part of a restructuring plan to move some of its operations into a newly established shared service center and to realign operations, R&D resources, and production resources as a result of previous acquisitions.

During the company's recent second quarter earnings conference call, PerkinElmer Chairman and CEO Robert Friel said that the firm had consolidated three North American facilities, "and efforts are underway to consolidate two additional legacy Caliper sites, further simplifying our operational footprint and improving our R&D efficiency."

All 265 employees being laid off were notified by June 30.

The restructuring resulted in a charge of $9.9 million pre-tax charge recognized by PerkinElmer during the second quarter in its Human Health segment, and an $8.8 million pre-tax charge recognized in its Environmental Health segment.

It said that it anticipates recognizing an additional $600,000 in incremental restructuring expenses in the future, resulting from one-time termination benefits.

The layoffs in the second quarter, during which PerkinElmer said revenues rose 4 percent year over year, come on top of 62 layoffs in the first quarter. In 2012, it cut its headcount by 437.
The Waltham, Mass.-based company has about 7,500 employees worldwide. 

Wednesday, June 26, 2013

Don't Do It Just Because Angelina Jolie Did It


The nonprofit ECRI Institute has released a BRCA testing information guide for patients interested in learning more about the genetic risk of hereditary breast and ovarian cancer.

The guide comes in response to the growing concern and questions among women about the information their genes contain about the risk for cancer, after actress Angelina Jolie wrote an op-ed piece discussing her decision to get a double mastectomy as a result of carrying a BRCA1 mutation associated with heightened risk of hereditary breast and ovarian cancer. There are reports that Jolie's highly publicized and controversial decision has caused a spike among women asking their physicians for BRCA testing.

"People can get caught up in the headlines, which can lead to quick, uninformed decisions," says Vivian Coates, VP of information services and health technology assessment at ECRI Institute, in a statement. "Many women may find that after talking to their physicians about their risks for the BRCA gene mutation, the best course of action may actually be to do nothing."

Indeed, the US Preventative Services Task Force's 2005 guidelines recommend that women with a history of breast and ovarian cancer be referred for genetic counseling and be evaluated for BRCA testing. For those without a family history of cancer, the USPSTF does not recommend counseling or BRCA testing.

In addition to information about who should be tested, ECRI's guide also includes information on Myriad's BRACAnalysis, highlighting it as the "currently available test." ECRI characterizes BRACAnalysis as "highly accurate" and reimbursed by most insurance companies if the woman meets certain criteria for testing. The institute also mentions that other labs have indicated they will offer testing for BRCA mutations as the US Supreme Court recently ruled that patents on isolated gene sequences are invalid, but ECRI does not offer any details about these new tests.

Do you wish to know more? - BRCA Gene Mutation Consumer Guide

Friday, June 14, 2013

How to analyze data from Next Generation Sequencing (NGS) platforms

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                        BI231 NGS Data Analysis
                            June 24-28, 2013
                      Online at Bioinformatics.Org

                  http://www.bioinformatics.org/edu/AGGT

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OBJECTIVES:
This course teaches biologists how to analyze data from Next Generation Sequencing (NGS) platforms. Topics to be covered include the description of sequencing strategies and platforms, experiment types, data formats, and command line tools for various workflows, such as quantification of transcripts, alternative splice forms, copy number variants, single nucleotide polymorphisms, etc.

INSTRUCTOR:
Shailender Nagpal, M.Sc. is a data analysis consultant in the biotechnology and pharmaceutical industries and specializes in the interpretation of data generated from various platforms in drug discovery, such as genomics and proteomics.

CV: http://www.bioinformatics.org/wiki/Shailender_Nagpal

SYLLABUS:
The course is divided into 4 sessions, with WebEx meetings scheduled for 16:00 to 17:00 GMT (12:00 PM to 1:00 PM US EDT), Monday through Thursday (Friday will be a reserve day). Homework assignments will involve running computationally intensive tools.  Recorded lectures on Linux will also be provided.

Session 1:
Fundamentals of NGS technologies - strategies, platforms and types of experiments that can be done (whole genome, transcriptome, targeted, ChIP-Seq, etc.)

Session 2:
Data formats and overview of algorithms, workflows and command line tools

Session 3:
Whole genome sequencing workflow used for CNV and SNP discovery

Session 4:
Transcriptomics workflow for quantifying abundance of transcripts and alternative splicing junctions

REGISTRATION:
If you haven't already done so, please create an on-line account to access the educational section of our website (http://www.bioinformatics.org/edu/). You may register for the course directly by making a payment using the on-line registration form (use this form only for PayPal and credit card payments for the base tuition listed below.):

  http://www.bioinformatics.org/edu/AGGT

Tuition:
For-profit & government: $1,000 USD
Non-profit & self-pay: $600 USD

Additional discounts are available as follows:
* Professional members: 20% discount (please inquire)
* Limited scholarships may also be available for those in low-income economies (please inquire).

Optional:
A one month subscription to our high performance Linux server, pre-configured with the software used in this course: $50.

For alternative payment methods, please write to edu@bioinformatics.org.

FOR MORE INFORMATION:
For more information, please visit: http://www.bioinformatics.org/wiki/BI231_NGS_Data_Analysis or contact edu@bioinformatics.org.

Saturday, May 4, 2013

Qiagen Buys Ingenuity to Provide Software Complement to Molecular Testing Solutions


Qiagen said this week that it acquired Ingenuity Systems for $105 million in cash in order to offer its life science and clinical customers a complete and integrated workflow for its PCR- and next-generation sequencing-based molecular testing solutions — from sample preparation to data interpretation.

Under its new parent, Ingenuity will continue to operate out of its offices in Redwood City, Calif., and retain all 120 current employees, while CEO Jake Leschly takes on new responsibilities within Qiagen's life science business unit.

Ingenuity will also continue to develop and offer products under its existing licensing scheme. Its portfolio includes a knowledgebase of curated genomic variants; Ingenuity Pathway Analysis, its web-based application for modeling and analyzing biological pathways; Ingenuity Variant Analysis, which selects clinically relevant genomic variants from NGS data (BI 1/13/2012); and Ingenuity iReport, its software for reporting the results of gene expression experiments from RNA-seq, microarray, and qPCR platforms.

Qiagen plans to incorporate content from Ingenuity's knowledgebase into a curated database that it sells with wet lab assays offered through its GeneGlobe portal — which provides access to hundreds of PCR- and NGS-based assay panels for exploring pathways and diseases such as cancer, cardiovascular disease, and central nervous system disorders. In total, GeneGlobe offers more than 60,000 annotated molecular assays.

Also, Qiagen later this year plans to begin offering an integrated workflow that will provide its customers with kits for sample and library prep, target enrichment, and sequencing, as well as informatics support. Its software component will include solutions that are currently being developed with German software-development firm SAP for sequence read alignment and variant calling (BI 7/6/2012) and Ingenuity's variant analysis and interpretation tools.

Do you wish to know more?

Monday, April 15, 2013

Thermo Fisher to buy Life Technologies for $13.6B

Thermo Fisher Scientific Inc. has offered to pay about $13.6 billion to buy genetic testing equipment maker Life Technologies in a cash deal that will create a giant company serving research and specialty diagnostics.
The Waltham, Mass., company said Monday it has agreed to pay $76 in cash for each share of Life Technologies, which is based in Carlsbad, Calif.

Friday, March 8, 2013

FDA Approves Dako Assays as CDx for Genentech Breast Cancer Drug

Dako today said that the US Food and Drug Administration has approved two assays for use as companion diagnostics for a Genentech drug targeting HER2-positive metastatic breast cancer.

FDA simultaneously approved Dako's HercepTest and HER2 IQFISH pharmDx assays and Genentech's drug Kadcyla (ado-trastuzumab emtansine).

Kadcyla is for patients with HER2-positive metastatic breast cancer who have been previously treated with Genentech's Herceptin (trastuzumab) and a taxane chemotherapy.

Dako, an Agilent company, and Genentech, a Roche company, have been collaborating on the development of companion diagnostics for Genentech's drugs for a few years. In May 2012 the two firms inked a pact to collaborate on the FDA submission of Dako's assays for Kadcyla.

A month later the HercepTest and HER2 FISH pharmDx were approved by FDA as companion diagnostics for Genentech's breast cancer drug Perjeta (pertuzumab). In late 2011, FDA gave the thumbs up to Dako's HER2 CISH pharmDx kit as a companion diagnostic for Herceptin in the treatment of breast cancer patients.

And in 2010, the agency approved the use of HercepTest and HER2 FISH pharmDx to help guide treatment of patients with metastatic gastric or gastroesophageal junction adenocarcinoma with Herceptin. cancer

Thursday, January 31, 2013

Interesting story about Nicholas Tatonetti & his New Computational Tools to Study Drug Effects

Courtesy Genomeweb & Julia Karow
 
Studying for a dual degree in mathematics and molecular biology, Nick Tatonetti became interested in using computational models to study biology and make sense of its massive datasets. As a bioinformatics PhD student at Stanford, he developed new statistical models and computational approaches for analyzing drug effects and drug-drug interactions.

At Columbia, Tatonetti is now focusing on molecular mechanisms of drugs. "We can actually think of each time a patient is being given a drug as an experiment," he says. "When the drug goes into the human system, it interacts molecularly, and then phenotypes come out of this system," which can be connected to molecular mechanisms in new ways.

In particular, he is developing techniques that use clinical data to develop networks that highlight interactions between different systems in the human body, such as two organs. "And once we know that certain gene products or pathways are working together at a systems level, we can start integrating all of the molecular data we know to fill out a complete picture" and to predict phenotypes from, for example, RNA expression data or genotypes, he adds.

Paper of note

A study revealing a new drug-drug interaction by using a machine learning algorithm Tatonetti designed that scanned through millions of adverse event reports from the Food and Drug Administration appeared in Science Translational Medicine this year. That is his favorite paper, he says, "because it represents the most comprehensive innovations on both the algorithmic side and the evaluation side."

Looking ahead

Tatonetti says that over the next five years, there will be major advances in using genetic data in medicine. "It may not be that we need to store lots of genetic data in the clinical record, but that we need to understand the genetic data better so that we can provide results and suggestions to physicians," he says. Personalized medicine will not only involve genotypes, though, but also environmental exposures. Putting genetics into the context of these, he says, will increase its clinical impact.

And the Noble goes to…

If he were to win the Nobel, it would be for developing a new scientific approach, based on informatics methods and computational methodologies, that discovers a fundamental biological or medical truth. "Where that truth may be, in what system, in what disease, I could not say, but I love the idea that we're in the midst of changing the way that we do science," Tatonetti says. "That's what informatics is about, advancing the tools of the scientific method itself."

Tuesday, January 29, 2013

NextBio Teams Up with Emory, Aflac, to Locate Biomarkers for Pediatric Brian Tumors


NextBio said this week that it is partnering with Emory University’s Winship Cancer Institute and the Aflac Cancer Center to work on identifying biomarkers that can predict brain cancer metastasis in children, which will help clinicians determine which patients should receive radiation therapy.

The partners will use NextBio Clinical software to analyze and interpret molecular and genomic data collected from children with medulloblastoma, a childhood brain tumor that affects around 500 children in the US every year and accounts for 20 percent of all brain cancers in children below the age of 19.

Specifically, “this study will look at clinical and genomic data from real patients, as well as data from mouse models and frozen human tissue samples, and then will correlate these data sets with other data from the public domain,” Alpana Verma-Alag, NextBio’s head of clinical development, explained in a statement.

Tobey MacDonald, director of Aflac’s brain tumor program and associate professor of pediatrics at Emory, noted that there is currently no way to tell which patients have a higher risk of metastasis and as such all children suffering from medulloblastoma receive radiotherapy even though “it causes long term side-effects and toxicity in young growing brains.”

“[The] ability to perform genomic studies on patients and then to use NextBio Clinical’s correlation engine to compare the genomic profile of primary tumors with that of metastatic tumors, both across our data and across the large amount of data that NextBio has curated from the public domain, makes achieving our goal of improving outcomes for people with medulloblastoma seem nearer in sight,” he said in a statement.

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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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