Monthly Archives: March 2015

Health Care Sector Update for 03/20/2015: BIIB,PRTA,THRX

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Top Health Care Stocks

JNJ +0.76%

PZE +0.54%

MRK +0.33%

ABT +0.60%

AMGN +0.43%

Health care stocks were notching strong gains Friday with the NYSE Health Care Sector Index climbing more than 0.9% and shares of health care companies in the S&P 500 also rising almost 0.9% as a group.

In company news, Biogen Idec ( BIIB ) jumped to an all-time high Friday morning after interim results from Phase Ib testing of its aducanumab drug candidate indicated the experimental drug treatment reduced amyloid plaque in the brains of patients with prodromal or mild Alzheimer's disease.

Statistically significant declines of amyloid plaque were seen in both the 3 milligrams and the 10 milligrams per kilogram study arms, the company said, adding the drug also demonstrated an acceptable safety profile and positive results on radiologic and clinical measurements.

"This is the first time an investigational drug for Alzheimer's disease has demonstrated a statistically significant reduction on amyloid plaque as well as a statistically significant slowing of clinical impairment in patients with prodromal or mild disease," said Dr. Alfred Sandrock, chief medical officer at BIIB. "Based on these results, we are advancing the aducanumab clinical program to Phase 3 with plans to initiate enrollment later this year."

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Health Care Sector Update for 03/20/2015: BIIB,PRTA,THRX

The Race to Build a Search Engine for Your DNA

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Photo: Andrew Brookes/Corbis

In 2005, next-generation sequencing began to change the field of genetics research. Obtaining a persons entire genome became fast and relatively cheap. Databases of genetic information were growing by the terabyte, and doctors and researchers were in desperate need of a way to efficiently sift through the information for the cause of a particular disorder or for clues to how patients might respond to treatment.

Companies have sprung up over the past five years that are vying to produce the first DNA search engine. All of them have different tacticssome even have their own proprietary databases of genetic informationbut most are working to link enough genetic databases so that users can quickly identify a huge variety of mutations. Most companies also craft search algorithms to supplement the genetic information with relevant biomedical literature. But as in the days of the early Web, before Google reigned supreme, a single company has yet to emerge as the clear winner.

Making a functional search engine is a classic big-data problem, says Michael Gonzalez, the vice president of bioinformatics at one such company, ViaGenetics, which was expected to relaunch its platform in March. Before doctors or researchers can use the data, genomic data must be organized so that humans can read and search it. The first step toward that is to put it in a standard form called the variant call format, or VCF. As raw data, a persons complete sequenced genome would take up about 100 gigabytes, so a database that adds the genomes of even 10 patients per day would quickly get out of hand. But VCF files are more compact, requiring only a few hundred megabytes per genome, which helps researchers find the specific variants they want to search in a fraction of the time. Unlike a fully sequenced genome, VCF files point only to where a persons genetic data deviates from the standardthe genome originally compiled by the Human Genome Project in 2001.

With VCF, sifting the genomes themselves for pinpoint mutations isnt the challenge for search engine companies. Most of these companies are allocating their resources toward efforts to seamlessly compile supplementary information about a specific mutation from other databases across the Web, such as the biomedical research archive PubMed or various troves of electronic medical records. Many of these tools have finely tuned algorithms that prioritize the results by credibility or relevance. You want to be able to pull together the information known about a mutation in that position [of the genome] and quickly make an assessment, says David Mittelman, the chief scientific officer for Tute Genomics, based in Provo, Utah, another company designing a genetic-search engine.

In an effort to expand the information that can be attached to a genome under examination, ViaGenetics, based in Miami Beach, Fla., is making its newly updated platform useful for researchers who want to collaborate across institutions. With ViaGenetics tools, researchers can make their data available to other users, so other people can come across these projects, request access, and form a collaboration, Gonzalez says. It helps people connect the dots between different researchers and institutions. This is especially helpful for smaller labs that may not have very extensive genome databases or for researchers from different universities working to decode the same mutation.

Although the genomic-search industry is now focused on serving scientists, that might not always be the case. Mittelman envisions that Tute Genomics could eventually serve consumers directly. People are already demanding information about their genomes just to understand themselves better, Mittelman says, but most companies dont yet consider the average person to be their primary customer. In order to make that shift, the tool will have to be even more intuitive and user-friendly. Fire-hosing someone with data thats not easy to interpret, or using terminology thats not standardized, has the potential to confuse people, he says. Privacy is also a major concern for the average user; the information that Tute users upload isnt stored permanently, Mittelman says, but users will need extra reassurance if the platform becomes available to the lay public.

And a further evolution of the industry is in the offing. Both ViaGenetics and Tute are hoping to be able to run the entire process in-housefrom the initial DNA sequencing to the presentation of final searchable results to users. The market for analyzing and interpreting genomic data is very fragmented, like the computer industry in the 1990s, where you had to go to separate providers to buy a video card or a motherboard and then try to put it together, Mittelman says. Soon this field will consolidate, as the computer industry did.

This article originally appeared in print as A Google for DNA.

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The Race to Build a Search Engine for Your DNA

Letting go of the (genetic) apron strings

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Researchers explore the shift from maternal genes to the embryo's genes during development

A new study from Princeton University sheds light on the handing over of genetic control from mother to offspring early in development. Learning how organisms manage this transition could help researchers understand larger questions about how embryos regulate cell division and differentiation into new types of cells.

The study, published in the March 12 issue of the journal Cell, provides new insight into the mechanism for this genetic hand-off, which happens within hours of fertilization, when the newly fertilized egg is called a zygote.

"At the beginning, everything the embryo needs to survive is provided by mom, but eventually that stuff runs out, and the embryo needs to start making its own proteins and cellular machinery," said Princeton postdoctoral researcher in the Department of Molecular Biology and first author Shelby Blythe. "We wanted to find out what controls that transition."

Blythe conducted the study with senior author Eric Wieschaus, Princeton's Squibb Professor in Molecular Biology, Professor of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, a Howard Hughes Medical Institute investigator, and a Nobel laureate in physiology or medicine.

Researchers have known that in most animals, a newly fertilized egg cell divides rapidly, producing exact copies of itself using gene products supplied by the mother. After a short while, this rapid cell division pauses, and when it restarts, the embryonic DNA takes control and the cells divide much more slowly, differentiating into new cell types that are needed for the body's organs and systems.

To find out what controls this maternal to zygotic transition, also called the midblastula transition (MBT), Blythe conducted experiments in the fruit fly Drosophila melanogaster, which has long served as a model for development in higher organisms including humans.

These experiments revealed that the slower cell division is a consequence of an upswing in DNA errors after the embryo's genes take over. Cell division slows down because the cell's DNA-copying machinery has to stop and wait until the damage is repaired.

Blythe found that it wasn't the overall amount of embryonic DNA that caused this increase in errors. Instead, his experiments indicated that the high error rate was due to molecules that bind to DNA to activate the reading, or "transcription," of the genes. These molecules stick to the DNA strands at thousands of sites and prevent the DNA copying machinery from working properly.

To discover this link between DNA errors and slower cell replication, Blythe used genetic techniques to create Drosophila embryos that were unable to repair DNA damage and typically died shortly after beginning to use their own genes. He then blocked the molecules that initiate the process of transcription of the zygotic genes, and found that the embryos survived, indicating that these molecules that bind to the DNA strands, called transcription factors, were triggering the DNA damage. He also discovered that a protein involved in responding to DNA damage, called Replication Protein A (RPA), appeared near the locations where DNA transcription was being initiated. "This provided evidence that the process of awakening the embryo's genome is deleterious for DNA replication," he said.

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Letting go of the (genetic) apron strings

Scientists urge caution in using new CRISPR technology to treat human genetic disease

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BERKELEY

A group of 18 scientists and ethicists today warned that a revolutionary new tool to cut and splice DNA should be used cautiously when attempting to fix human genetic disease, and strongly discouraged any attempts at making changes to the human genome that could be passed on to offspring.

Among the authors of this warning is Jennifer Doudna, the co-inventor of the technology, called CRISPR-Cas9, which is driving a new interest in gene therapy, or genome engineering. She and colleagues co-authored a perspective piece that appears in the March 20 issue of Science, based on discussions at a meeting that took place in Napa on Jan. 24. The same issue ofSciencefeatures a collection of recent research papers, commentary and news articles on CRISPR and its implications.

Given the speed with which the genome engineering field is evolving, our group concluded that there is an urgent need for open discussion of the merits and risks of human genome modification by a broad cohort of scientists, clinicians, social scientists, the general public and relevant public entities and interest groups, the authors wrote.

Doudna, director of UC Berkeleys Innovative Genomics Initiative, was joined by five current and two former UC Berkeley scientists, plus David Baltimore, a Nobel laureate and president emeritus of the California Institute of Technology, Stanford Nobelist Paul Berg and eminent scientists from UC San Francisco, Stanford, Harvard and the universities of Wisconsin and Utah. Several of these scientists are currently involved in gene therapy to cure inherited diseases.

Such warnings have been issued numerous times since the dawn of genetic engineering in 1975, but until now the technology to actually fix genetic defects was hard to use.

However, this limitation has been upended recently by the rapid development and widespread adoption of a simple, inexpensive and remarkably effective genome engineering method known as CRISPR-Cas9, the scientists wrote. The simplicity of the CRISPR-Cas9 system enables any researcher with knowledge of molecular biology to modify genomes, making feasible many experiments that were previously difficult or impossible to conduct.

Correcting genetic defects

Scientists today are changing DNA sequences to correct genetic defects in animals as well as cultured tissues generated from stem cells, strategies that could eventually be used to treat human disease. The technology can also be used to engineer animals with genetic diseases mimicking human disease, which could lead to new insights into previously enigmatic disorders.

The CRISPR-Cas9 tool is still being refined to ensure that genetic changes are precisely targeted, Doudna said. Nevertheless, the authors met to initiate an informed discussion of the uses of genome engineering technology, and to identify proactively those areas where current action is essential to prepare for future developments. We recommend taking immediate steps toward ensuring that the application of genome engineering technology is performed safely and ethically.

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Scientists urge caution in using new CRISPR technology to treat human genetic disease

Scientists Urge Temporary Moratorium On Human Genome Edits

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A new technology called CRISPR could allow scientists to alter the human genetic code for generations. That's causing some leading biologists and bioethicists to sound an alarm. They're calling for a worldwide moratorium on any attempts to alter the code, at least until there's been time for far more research and discussion.

It's not new that scientists can manipulate human DNA genetic engineering, or gene editing, has been around for decades. But it's been hard, slow and very expensive. And only highly skilled geneticists could do it.

Recently that's changed. Scientists have developed new techniques that have sped up the process and, at the same time, made it a lot cheaper to make very precise changes in DNA.

There are a couple of different techniques, but the one most often talked about is CRISPR, which stands for clustered regularly interspaced short palindromic repeats. My colleague Joe Palca described the technique for Shots readers last June.

Why scientists are nervous

On the one hand, scientists are excited about these techniques because they may let them do good things, such as discovering important principles about biology. It might even lead to cures for diseases.

The big worry is that CRISPR and other techniques will be used to perform germline genetic modification.

Basically, that means making genetic changes in a human egg, sperm or embryo.

Those kinds of changes would be passed down for generations. And that's something that's always been considered taboo in science.

One major reason that it's considered off limits, ethically, is that the technology is still so new that scientists really don't know how well it works.

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Scientists Urge Temporary Moratorium On Human Genome Edits

Engineering humans: Utah professor joins group urging caution

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While it holds promise for eradicating genetic diseases, the technology also has big implications for the human genome: A person whose DNA is edited would pass the altered genes on to his or her future children.

There's also a fear the technology could be used in unethical ways, such as "engineering" a baby to look a certain way, or to be athletic or intelligent.

"One of the concerns is that some people may want to use the technology to make trivial or cosmetic changes, rather than using it to prevent devastating diseases," said Carroll, distinguished professor of biochemistry at the University of Utah School of Medicine.

The paper Carroll co-signed is expected to amplify discussion in the scientific community, which last week heard from another group of researchers who recommend that the new technology never be used on human embryos.

Changing the genome could have unpredictable effects on future humans, and that's unacceptable, the group says.

Instead, that group, led by Edward Lanphier, chief executive of the biotechnology company Sangamo Biosciences, suggests research focus on somatic, or non-reproductive cells.

CRISPR-Cas9, was developed in the lab of Jennifer Doudna, the University of California-Berkeley scientist who organized the Napa meeting.

Hundreds of papers in the past two years have proven the usefulness of the new tool in research involving mammals.

"The applications to humans are potentially just around the corner," Carroll said.

CRISPR-Cas9 allows more subtle, precise changes in DNA than was possible with technologies used in genetically modified organisms (GMOs), he added. Such genetic engineering typically involves introducing new genes into an organism.

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Engineering humans: Utah professor joins group urging caution

Lumber Liquidators Scandal with Dr Mitch Gaynor on Fox Business – Video

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Lumber Liquidators Scandal with Dr Mitch Gaynor on Fox Business
Subscribe to the GeneChanger YouTube: http://goo.gl/jOPcep Dr Mitch Gaynor, Medical Oncologist at Cornell Medical Center Author of "Gene Therapy Plan" on Fox Business. The Gene Therapy...

By: Mitchell Gaynor M.D.

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Lumber Liquidators Scandal with Dr Mitch Gaynor on Fox Business - Video

Scientists Call for a Summit on Gene-Edited Babies

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Nobel Prize winners raise alarm over genetic engineering of humans.

A group of senior American scientists and ethics experts is calling for debate on the gene-engineering of humans, warning that technology able to change the DNA of future generations is now imminent.

In policy recommendations published today in the journal Science, eighteen researchers, including two Nobel Prize winners, say scientists should accept a self-imposed moratorium on any attempt to create genetically altered children until the safety and medical reasons for such a step can be better understood.

The concern is over a rapidly advancing gene-editing technology, called CRISPR-Cas9, which is giving scientists the ability to easily alter the genome of living cells and animals (see Genome Surgery). The same technology could let scientists correct DNA letters in a human embryo or egg cell, for instance to create children free of certain disease-causing genes, or perhaps with improved genetics.

What we are trying to do is to alert people to the fact that this is now easy, says David Baltimore, a Nobel Prize winner and former president of Caltech, and an author of the letter. We cant use the cover we did previously, which is that it was so difficult that no one was going to do it.

Many countries already ban germ line engineeringor changing genes in a way that would be heritable from one generation to the nextonethical or safety grounds. Others, like the U.S., have strict regulations that would delay the creation of gene-edited children for years, if not decades. But some countries have weak rules, or none at all, and Baltimore said a reason scientists were speaking publicly now was to keep people from doing anything crazy.

The advent of CRISPR is raising social questions of a kind not confronted since the 1970s, when the ability to change DNA in microrganisms was first developed. In a now famous meeting in 1975, in Asilomar, California, researchers agreed to avoid certain kinds of experiments that were then deemed dangerous. Baltimore, who was one of the organizers of the Asilomar meeting, says the scientists behind the letter want to offer similar guidance for gene-engineered babies.

The prospect of genetically modified humans is surprisingly close at hand. A year ago, Chinese researchers created monkeys whose DNA was edited using CRISPR (see 10 Breakthrough Technologies 2014: Genome Editing).

Since then,several teams of researchers in China, the U.S., and the U.K. have begun using CRISPR to change the DNA of human embryos, eggs, and sperm cells, with an eye toward applying the technology at in vitro fertility (IVF) clinics. That laboratory research was described by MIT Technology Review earlier this month (see Engineering the Perfect Baby).

Last week, in Nature, representatives of an industry group, the Alliance for Regenerative Medicine, recommended a wider moratorium that would also include a cessation of such laboratory studies, which it termed dangerous and ethically unacceptable (see Industry Body Calls for Gene-Editing Moratorium).

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Scientists Call for a Summit on Gene-Edited Babies

Brunch Hate Reads: NYC Kids Choose Multi-Million Dollar Apartments For Their Parents

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We here at Brunch Hate Reads have seen every permutation of terrible in the weekend pages of the NY Times, from the hungover futurism consultants who are so over Brooklyn to the 22-year-old creative souls just trying to find a multi-million dollar place to hang their giant portraits of themselves. We've definitely seen some shit in our daybut we're happy to report we haven't become jaded by all the mason jar trend pieces. As we learned from a piece today, we still have the capacity for dumb-struck awe at their ability to hold up a mirror to modern New York and only notice 1% of the reflection.

This one really is a doozy.

Before we go any further, you should get yourself a glass of champagne and read the PSA below.

PSA: The NY Times has a weakness for self-parodying trend-baiting, masochistic Millennial obsessing, and the perverse lifestyles of the filthy rich. If a reporter with the Real Estate, Style or Weekend sections approaches you about a story, just smile gently and run in the opposite direction. No one is forcing you to become representative of everything that everyone hates about New Yorkers.

The NY Times Presents: Brunch Hate Reads is proud to bring you the story of .1%ers who have trained their children to help them buy multi-million real estate around NYC. "In New York, teens and preteens are becoming savvy connoisseurs of real estate," the Times writes.

No, they are not. There is nothing savvy about being able to functionally use a website.

Here are a few real sentences from the article:

Still, for a lark the couple strolled over to check out their sons find, which, in addition to the pool and an expansive terrace, had bedazzling views of the Hudson and the Palisades. We looked at each other and said, This is unbelievable, Mrs. van Merkensteijn recalled. The idea that you could own a place like this in New York City was amazing.

Skye came along to the closing a few months later.

"They choose where they and their parents are going to have dinner or where theyre going to go on vacation," Stuart Moss, an associate broker at Corcoran, told the Times. "So why shouldnt it extend to where theyre going to spend several million dollars for a residence?" Maybe because (follow us with this one) they are... children? I know this sounds crazy, but maybe children shouldn't be responsible for millions of dollars and major household decisions? We know rich people live entirely different lives than everyone else, but mixing money & kids generally hasn't worked out in the past.

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Brunch Hate Reads: NYC Kids Choose Multi-Million Dollar Apartments For Their Parents

Orbital Insight Raised $8.7 Million To Use AI To Analyze Satellite Data

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Satellite tracking of development at Olympic stadium in China. (Credit: Digitalglobe/Orbital Insight)

Orbital Insight, a company that provides data analytics of satellite imagery, announced this week that it had closed an $8.7 million Series A round led by Sequoia. Bloomberg Beta, Google Ventures, citizen.vc and Lux Capital also participated in the round. Sequoia partner Bill Coughran of Sequoia will be joining the board of Orbital Insight as part of the deal.

Orbital Insight was founded by Dr. James Crawford, an artificial intelligence researcher and entrepreneur who has experience building intelligent systems for NASA and other organizations. He was also previously the Engineering Director of Google Books, an experience that helped lead to the idea for his new company.

What this company really is is a Google Books like pipeline that is, an automated AI pipeline designed for understanding and processing satellite imaging at scale, Crawford explained to me.

The past few years have seen an explosion of satellite imaging companies. Older companies like DigitalGlobe continue to put up satellites and produce reams of detailed data. However, theyve been joined by a number of startups such as Planet Labs, Skybox and more who are putting up a myriad number of satellites.

The result of this influx is that between the various companies watching the planet from above, its possible to see changes being made in particular parts of the globe over time, and to track and monitor those changes. Those changes, in turn, can be used to inform decision makers and investors about the status of the economy, agriculture production, and more.

To analyze these images, Orbital Insight has developed machine learning programs that can be taught to find and analyze data points of interest. During its seed phase, for instance, the company used a human to tag cars in parking lots while the program observed it. After a few hundred tags, the program learns to identify cars in other parking lot images without the human being involved.

This wasnt an idle exercise, either. Once Orbital Insights deep learning program learned how to count cars, the company was able to determine a mathematical relationship between the number of cars in parking lots of retail stores in a quarter to the stores revenues that quarter. That type of information is definitely valuable to investors. But for the company, its a proof of concept that will allow it to pursue other kinds of data.

This funding round is geared towards utilizing satellite images to find other sources of useful data. One project, for example, is examining the shadows of buildings in China over time. Using those shadows and a little trigonometry, the company aims to be able to figure out the rate of construction in China to see if its speeding up or slowing down.

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Orbital Insight Raised $8.7 Million To Use AI To Analyze Satellite Data