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Predicting cancer relapse: Study finds high-throughput sequencing bests flow cytometry
Wednesday, May 16, 2012
A study led by researchers at Fred Hutchinson Cancer Research Center has found that a next-generation, high-speed DNA-decoding technology called high-throughput sequencing can detect the earliest signs of potential relapse in nearly twice the number of leukemia patients as compared to flow cytometry, the current gold standard for detecting minimal residual disease. The results of the study, led by Hutchinson Center computational biologist Harlan Robins, Ph.D., are reported in the May 16 issue of Science Translational Medicine.
“The ability to predict disease relapse sooner with high-throughput sequencing would give hematologists the option to treat cancer recurrence earlier, offering a greater chance of survival. Longer term, this technology potentially also could be used to initially diagnose leukemia and lymphoma much earlier than we can today,” said Robins, an associate member of the Hutchinson Center’s Public Health Sciences Division and corresponding author of the paper.
For the study, Robins and colleagues compared the effectiveness of high-throughput sequencing versus flow cytometry to detect minimal residual disease in 43 patients diagnosed with acute T lymphoblastic leukemia, a type of blood cancer that is most common in children under age 7. By sequencing the patients’ T-cell receptor genes before and 29 days after chemotherapy, the researchers were able to precisely measure their presence in the blood and provide a more accurate prediction of leukemia relapse.
“The high-throughput sequencing detected minimal residual disease in nearly double the number of patients than flow cytometry ? 22 versus 12 patients, respectively,” Robins said.
Minimal residual disease, or MRD, a major predictor of cancer relapse, is when a small number of cancer cells survive treatment and persist in patients. Until recently, MRD was undetectable.
Flow cytometry, the primary method for detecting MRD in the United States, counts the number of cells in the blood with cancer-specific protein markers on their surface. While it is considered the gold standard, flow cytometry comes with a number of limitations:
This study ? the first use of high-throughput sequencing, or HTS, to detect minimal-residual disease in a clinical trial setting ? found it to be at least 20 times more sensitive than flow cytometry in detecting MRD.
“Our research indicates that HTS offers many advantages over flow cytometry,” Robins said. “Since HTS can detect any pre-identified clone and is performed in a centralized lab, it consistently generates reproducible and reliable results regardless of cancer type, using the same process for disease detection and tracking. Furthermore, HTS is highly automated, cost-effective and objective, whereas flow cytometry is more time consuming, relies on the skill of the operator and is therefore subject to human error.”
The Hutchinson Center has patents pending on core technologies employed by Robins and colleagues in conjunction with high-throughput DNA-sequencing used for this study. These core technologies have been licensed exclusively to Adaptive Biotechnologies, a Seattle biotechnology company Robins co-founded that offers commercial DNA sequencing and analysis.
Robins and colleagues discovered how to adapt traditional high-throughput technology to sequence only variable regions of the human genetic code: the T- and B-cell receptors ? a critical component of the human adaptive immune system. These receptors are short strands of DNA that constantly rearrange to allow the immune system to fight viruses, infection or disease.
“This discovery was critical to our understanding of how patients mount immunological responses against cancer, autoimmune disorders and infectious diseases,” said Robins, whose Hutchinson Center research focuses on the genetics of the immune system ? particularly how it responds to pathogens and the aging process.
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Fred Hutchinson Cancer Research Center: http://www.fhcrc.org
Thanks to Fred Hutchinson Cancer Research Center for this article.
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What are the things you hate and love about being a step parent?
I hate not being able to be a part in major decisions even though the kids still partially resident at our house. All because im not a bio parent?? Its my home time and expenses too! Were supposed to count by being supportive, loving, and good role models but not heard?? We dont get credit for all we do.
I love that the kids by THIER choice call me ?mom? and their real mom by her name, they have alot more respect for me as i do for them. We communicate.
Big john- i do apreciate they call me mom but if i see them as my own and hey see me as their mom, if im a pivotal part in their life, i should have some kind of a say somewhere.
HUbby does listen but it gets really fustrating when all three of us have a different opinion. His ex is very threatened by the kids and my relationship, you figure she would be happy that there is someone there that treats them good and loves them.
Best answer: Answer by big John T
the worst thing about being a step parent is when you divorce if you are lucky as i am you still get to see the child so you said you dont get credit for what you do but then you turn around and say they call you mom and respect you by their choice that should be credit enough for what you do but you are right there bio mother is not going to pat you om the back and give you any credit and you should have some say in what goes on but it has to be done thru your husband the both of you should be talking about the decisions being made
Give your answer to this question below!
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By Tiffany in NeatoShop Features on May 15, 2012 at 10:01 am
Union Jack Bulldog Screen Wipe ? $9.95
Are you counting down the days to the summer Olympics? Make sure your screen is ready for viewing every magical moment with the festive Union Jack Bulldog Screen Wipe from the NeatoShop. This adorable screen cleaner has a soft chamois tummy and is perfect for cleaning and reducing static on monitors, laptops, and LCD screens.
Be sure to check out the NeatoShop for more fun Office & Desk items.
Link
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Shetland Arts has agreed a partnership with leading promoter DF Concerts & Events in the run-up to the opening of Mareel.
Meanwhile in a separate move local promoter Davie Gardner?s company Atlantic Edge Music Services will be responsible for programming 20 concerts in the music venue each year.
DF is one of Europe?s leading arts and concert promotion companies, bringing the best live music and events to audiences in Scotland. It works with a huge number and a diverse range of artists, from cutting edge unsigned talent to the music industry?s biggest acts, across club, arena, stadium and green field shows. The company also owns the legendary King Tut?s Wah Wah Hut in Glasgow and organises one the world?s most successful music festivals, T in the Park.
DF?s partnership with Mareel will see a number of high-profile gig dates in Shetland and give Mareel access to early discussions with agents who are planning to tour acts in the UK. The agreement will also place Shetland in line for acts keen to start their UK/European tour in Scotland and who are looking for exclusive warm-up dates.
Shetland Arts director Gwilym Gibbons said: ?I believe that our partnership between DF Concerts & Events and Mareel is a hugely exciting development in the life of this ambitious project.
?DF will bring a wealth of knowledge and experience to the success of Mareel and I believe Mareel will provide DF with a base in the UK?s most northerly music venue, in an extraordinary inspiring location that I hope in time will feel like a second home to their prestigious Glasgow-based venue King Tut?s Wah Wah Hut.?
DF chief executive Geoff Ellis said: ?We are delighted to be working with Shetland Arts on what will be a really exciting project. Mareel is a beautiful venue set in a stunning location and will offer touring artists a unique live experience. We look forward to announcing a great bill of acts over the coming months.?
Mr Gardner, the former music development officer with Shetland Arts Trust, has been involved with the isles music scene for many years, organising and promoting a number of highly successful concerts and festivals.
He set up Atlantic Edge Music Services in November 2006. The business offers management and agency services to established musicians and helps to introduce new and exciting musicians and musical acts. The company not only represents artists from Shetland and Orkney, but musicians from Scotland, Canada and Scandinavia.
Mr Gardner said: ?I?m delighted to have been asked by Shetland Arts to programme a series of events into the exciting and challenging project that is Mareel, as part of their overall monthly events programme.
?I also look forward to doing this in effective conjunction with others, both in and outwith Shetland, to ensure we deliver a dynamic, varied and popular programme that comfortably sits alongside other events in the venue and within the local community in general.?
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ScienceDaily (May 14, 2012) ? From human-made toxic chemicals such as industrial by-products to poisons that occur naturally, a water or food supply can be easily contaminated. And for every level of toxic material ingested, there is some level of bodily response, ranging from minor illness to painful certain death.
Biosensors have long been used to safeguard against exposure to toxic chemicals. Food tasters employed by the ancients acted as early versions of biosensors, determining if a meal had been poisoned. More modern examples include the use of fish, which may alter their swimming characteristics if a toxic material is introduced into to the water. But although current warning systems are more sophisticated, they require equipment and time that a soldier in the field or an adventurer in the wilderness do not have.
Now Prof. Yosi Shacham-Diamand, Vice Dean of Tel Aviv University’s Faculty of Engineering, along with Prof. Shimshon Belkin of the Institute of Life Sciences at the Hebrew University of Jerusalem, has married biology and engineering to produce a biosensor device called the “Dip Chip,” which detects toxicity quickly and accurately, generating low false positive and false negative readings. The Dip Chip contains microbes designed to exhibit a biological reaction to toxic chemicals, emulating the biological responses of humans or animals.
Converting biological response to electricity
The biological reaction is converted into an electronic signal that can be read by the user. When perfected for commercial applications, the chip might be easily plugged into a mobile device to determine toxicity, says Prof. Shacham-Diamand.
The new chips are based on genetically modified microbes developed in Prof. Belkin’s lab. When the modified microbes are exposed to toxic or poisonous materials, they produce a measurable biochemical reaction — and this is where Prof. Shacham-Diamand’s work begins.
“In my lab, we developed a method for communicating with the microbes, converting this biological response to electrical signals,” he explains. The device, which looks like a dip stick, immobilizes these specially-produced microbes next to the sensing electrodes. Once the microbes come into contact with a questionable substance they produce a chemical signal that is converted to an electrical current by an device that can interpret the signals, producing a binary “toxic” or “not toxic” diagnosis.
In the future, Prof. Shacham-Diamand hopes that smaller versions of the Dip Chips might be plugged into existing mobile electronic devices, such as cell phones or tablets, to give the user a toxicity reading. This would make it an economically feasible and easy-to-use technology for people such as campers or for military purposes.
Reading any toxic material
One of the chip’s advantages is its ability to identify toxicity as a biological quality instead of specific toxic chemicals. There are already excellent detectors to identify specific toxic materials, says Prof. Shacham-Diamand. The Dip Chip, however, is designed to alert the user to overall toxicity. And because the chip measures general toxicity, it will pick up on any and all toxic materials — even those that have not been discovered or invented yet.
Beyond their ability to find toxic chemicals in the field, these chips can also be put to use in the cosmetics or pharmaceuticals industries, says Prof. Shacham-Diamand. They could be used to detect the toxicity of new compounds, minimizing the controversial use of lab animals. Using the same technology, the researchers have also developed a larger-scale device which allows water to flow continuously over the sensor, making it appropriate for online, real-time monitoring of water supplies.
The results of their research have been published in a number of journals, including Electrochimica Acta and Sensors and Actuators B: Chemical.
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The above story is reprinted from materials provided by American Friends of Tel Aviv University.
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If you’ve been looking to get that web project off the ground but despise the idea of coding it, Adobe’s recently announced web design tool has just landed. Muse, the program that allows you to design websites without having to get your hands dirty with HTML5 is now available. The kit behaves more like a layout program (like InDesign) instead of a web publishing / programming tool, allowing those who are more design-minded to feel right at home. As you might expect, the software is available with an annual $49.99 per month Creative Cloud subscription alongside CS6 heavyweights like Photoshop and Illustrator. If Muse is all you’re after, you can snag it alone for a $24.99 month-to-month fee or $14.99 for a twelve-month commitment. Need to see it in action before you open your wallet? No worries. Hit the coverage link below for a look at what the application can do.
Adobe Muse is ready to let you design websites without the coding headaches for $15 a month originally appeared on Engadget on Mon, 14 May 2012 14:44:00 EDT. Please see our terms for use of feeds.
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If you’ve ever baulked at the price of Leica’s rebadged Panasonic cameras, then spare a thought (or some change) for the anonymous buyer of this 1923 0-Series snapper. Vienna’s WestLicht Photographica auctions flogged the prototype for €2.16 million ($2.77 million) and is now the most expensive camera ever sold — beating this $1.9 million 0-Series from last year. If you’d like to see the surprisingly relaxed way the auctioneer handles the recession-baiting sale, head on past the break for the footage.
[Thanks, Rakesh]
Continue reading You think your Leica’s expensive? This one cost $2.8 million (video)
You think your Leica’s expensive? This one cost $2.8 million (video) originally appeared on Engadget on Mon, 14 May 2012 09:49:00 EDT. Please see our terms for use of feeds.
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Rumor has it that the next iPhone will eschew Google's Maps backend in favor of Apple's own. Rene over at iMore, who has a good handle on how the minds in Cupertino operate, has a great overview of Apple's supposed current strategy that you really should read to try to make sense out of this one. The short version — Apple wants to shed Google's services. Not because users have a problem using them, but because they don't want Google to profit. Instead of offering an additional choice with their own version of a maps app, they are just going to replace what users know and love with something that generates less profit for Google. Smart business move, but a pretty foul dump on the users.
They're going to need some real magic to pull this one off. In the current version, Apple builds the UI and Google provides the mapping data. Google is really good at mapping stuff. The rumored version-in-waiting is supposed to add a 3D view, becoming the new killer feature for the next version of iOS. The problem is, users don't care about 3D map view (or anything 3D on their mobile devices) — they care about features, ease-of-use, and integration. Apple can certainly take care of the integration part, and even give it some of that good old fashioned Apple magic in the UI department. But that still isn't going to cut it. Google has the one big thing™ when it comes to maps and navigation — search data.
When you tap the button and tell your phone to find 1313 Mockingbird Lane, there's this unfathomably huge pool of data Google has at it's disposal to populate that map. Need to know where the closest Starbucks is? Ask Siri, or just look at the Google Maps app. Apple can't replicate this without years of it's own data. Users will be left with an app with a pretty front-end, that's actually a step backwards in functionality. Apple will either have to offer a sub-par maps experience, or use Google anyway. And the first person who says Bing has to stay late and clean the chalkboard. That's two steps backwards.
Google creates the web services people want and use — even people with iPhones. This is a space where Apple is going to find it's difficult to compete, and fickle users may just look elsewhere. Of course, you'll find just as many bloggers telling tales of how great this is, and that Apple invented Maps. It's going to be interesting to watch this one play out.
Source: iMore
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