Monthly Archives: August 2017

August 16, 2017 Liquid biopsy for cancer. Credit: Victor Velculescu et al., Science Translational Medicine 2017

In a bid to detect cancers early and in a noninvasive way, scientists at the Johns Hopkins Kimmel Cancer Center report they have developed a test that spots tiny amounts of cancer-specific DNA in blood and have used it to accurately identify more than half of 138 people with relatively early-stage colorectal, breast, lung and ovarian cancers. The test, the scientists say, is novel in that it can distinguish between DNA shed from tumors and other altered DNA that can be mistaken for cancer biomarkers.

A report on the research, performed on blood and tumor tissue samples from 200 people with all stages of cancer in the U.S., Denmark and the Netherlands, appears in the Aug. 16 issue of Science Translational Medicine.

"This study shows that identifying cancer early using DNA changes in the blood is feasible and that our high accuracy sequencing method is a promising approach to achieve this goal," says Victor Velculescu, M.D., Ph.D., professor of oncology at the Johns Hopkins Kimmel Cancer Center.

Blood tests for cancer are a growing part of clinical oncology, but they remain in the early stages of development. To find small bits of cancer-derived DNA in the blood of cancer patients, scientists have frequently relied on DNA alterations found in patients' biopsied tumor samples as guideposts for the genetic mistakes they should be looking for among the masses of DNA circulating in those patients' blood samples.

To develop a cancer screening test that could be used to screen seemingly healthy people, scientists had to find novel ways to spot DNA alterations that could be lurking in a person's blood but had not been previously identified.

"The challenge was to develop a blood test that could predict the probable presence of cancer without knowing the genetic mutations present in a person's tumor," says Velculescu.

The goal, adds Jillian Phallen, a graduate student at the Johns Hopkins Kimmel Cancer Center who was involved in the research, was to develop a screening test that is highly specific for cancer and accurate enough to detect the cancer when present, while reducing the risk of "false positive" results that often lead to unnecessary overtesting and overtreatments.

The task is notably complicated, says Phallen, by the need to sort between true cancer-derived mutations and genetic alterations that occur in blood cells and as part of normal, inherited variations in DNA.

As blood cells divide, for example, Velculescu says there is a chance these cells will acquire mistakes or mutations. In a small fraction of people, these changes will spur a blood cell to multiply faster than its neighboring cells, potentially leading to pre-leukemic conditions. However, most of the time, the blood-derived mutations are not cancer-initiating.

His team also ruled out so-called "germline" mutations. While germline mutations are indeed alterations in DNA, they occur as a result of normal variations between individuals, and are not usually linked to particular cancers.

To develop the new test, Velculescu, Phallen and their colleagues obtained blood samples from 200 patients with breast, lung, ovarian and colorectal cancer. The scientists' blood test screened the patients' blood samples for mutations within 58 genes widely linked to various cancers.

Overall, the scientists were able to detect 86 of 138 (62 percent) stage I and II cancers. More specifically, among 42 people with colorectal cancer, the test correctly predicted cancer in half of the eight patients with stage I disease, eight of nine (89 percent) with stage II disease, nine of 10 (90 percent) with stage III and 14 of 15 (93 percent) with stage IV disease. Of 71 people with lung cancer, the scientists' test identified cancer among 13 of 29 (45 percent) with stage I disease, 23 of 32 (72 percent) with stage II disease, three of four (75 percent) with stage III disease and five of six (83 percent) with stage IV cancer. For 42 patients with ovarian cancer, 16 of 24 (67 percent) with stage I disease were correctly identified, as well as three of four (75 percent) with stage II disease, six of eight (75 percent) with stage III cancer and five of six (83 percent) with stage IV disease. Among 45 breast cancer patients, the test spotted cancer-derived mutations in two of three (67 percent) patients with stage I disease, 17 of 29 (59 percent) with stage II disease and six of 13 (46 percent) with stage III cancers.

They found none of the cancer-derived mutations among blood samples of 44 healthy individuals.

Despite these initial promising results for early detection, the blood test needs to be validated in studies of much larger numbers of people, say the scientists.

Velculescu and his team also performed independent genomic sequencing on available tumors removed from 100 of the 200 patients with cancer and found that 82 (82 percent) had mutations in their tumors that correlated with the genetic alterations found in the blood.

The Johns Hopkins-developed blood test uses a type of genomic sequencing the researchers call "targeted error correction sequencing." The sequencing method is based on deep sequencing, which reads each chemical code in DNA 30,000 times. "We're trying to find the needle in the haystack, so when we do find a DNA alteration, we want to make sure it is what we think it is," says Velculescu.

Such deep sequencing, covering more than 80,000 base pairs of DNA, has the potential to be very costly, but Velculescu says sequencing technology is becoming cheaper, and his research team may eventually be able to reduce the number of DNA locations they screen while preserving the test's accuracy.

He says the populations that could benefit most from such a DNA-based blood test include those at high risk for cancer including smokersfor whom standard computed tomography scans for identifying lung cancer often lead to false positivesand women with hereditary mutations for breast and ovarian cancer within BRCA1 and BRCA2 genes.

Explore further: Blood biopsy test reads platelets to detect human lung cancer

More information: J. Phallen el al., "Direct detection of early-stage cancers using circulating tumor DNA," Science Translational Medicine (2017). stm.sciencemag.org/lookup/doi/ scitranslmed.aan2415

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Scientists develop blood test that spots tumor-derived DNA in people with early-stage cancers - Medical Xpress

In BriefA group of biohackers at the University of Washington found away to sequence gene bases to implant malware through a laboratorycomputer. Though still in its early stages, they have invented asci-fi device of biopunk ingenuity. Welcome to the World of Biohacking

Biologists pay scrupulous attention to DNA synthesis, not just out of a need for precision, but also as a precaution. Scientists dont want to create or spread a dangerous stretch of genetic code that, with a little bit of criminal ingenuity, could be used to make a toxin or an infectious disease. But recently, a group of biohackers has found a way to cross biology with the digital by resequencing DNA, not to infect humans or animals, but computers.

A group of researchers from the University of Washington has shown that, for the first time, its possible to encode malicious software into physical strands of DNA. And so, when a gene sequencer performs an analysis, the output transforms into a program which corrupts gene-sequencing software to gain control of an entire computer.

This is a far cry from a criminal implementation. Researchers agree that this new method could be integrated into real-world applications once DNA sequencing grows more powerful and ubiquitous.

We know that if an adversary has control over the data a computer is processing, it can potentially take over that computer, said Tadayoshi Kohno, Computer Science Professor at the University of Washington in an interview with WIRED, noting the similarity to traditional hacker attacks. That means when youre looking at the security of computational biology systems, youre not only thinking about the network connectivity and the USB drive and the user at the keyboard but also the information stored in the DNA theyre sequencing. Its about considering a different class of threat, he added.

While, currently, this feels more like an alternate take on Neal Stephensons Snow Crashthan an imminent cyber threat, the means for disseminating this bio-delivered code are already coming into being. University labs, for one, are employing increasingly centralized services for students and professors working with college-owned (and expensive) gene sequencing equipment. And as other, non-academic environs like corporations, medical facilities, and government-run facilities follow suit, this DNA-malware delivery trick will become feasible. Additionally, the DNA-malware delivery will come from outside sources, which could provide the perfect window for malware insertion.

Called an exploit by hackers, this specific kind of computer attack is known as a buffer overflow which fills the space in a computers memory allocated for the gene sequence and then spills out into other parts of the computers memory until it can plant its own commands.

So far, challenges to the process like squeezing the code into a few hundred DNA bases and the tendency of redundant base patterns to cause DNA to fold into itself have limited the digital translation to a mere 37% success rate. Clearly, DNA-hacking is still only a reality for readers of biopunk sci-fi, but wed be naive to dismiss it as the next generations problem (or boon). After all, Seth Shipman of a Harvard team recently encoded a video in a DNA sample. Once perfected, DNA storage could replace magnetic encoding in flash memory because DNA maintains its structure for much longer.

DNA coding and bio-exploitation might sound like fiction today, but, like the cell phones origins in Star Trek canon, its only a matter of doing.

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Researchers Hacked Into DNA and Encoded it With Malware - Futurism

Like middle-aged women dying their hair fluorescent colors and young women dying their hair iron gray, DNA testing has become fashionable even without necessarily leading to positive results.

Do we really need to know more about our ancestral heritage, as if we're characters out of "Game of Thrones" and desperate to figure out whether to pledge allegiance to wolves, dragons or the incestuous Lannisters, thereby becoming part of some larger powerful dynasty?

While finding out information about your grandparents' hometown might be fun, shrines to bloodlines aren't such a good idea, especially when neo-Nazis armed with their hand- painted homemade shields (as if arts and crafts have replaced Sturm und Drang) might just change their goal from world domination to "extreme ancestry."

In an increasingly diverse world, why are we trying to locate our individual genetic pattern anyhow? Is it because, when you go to the website for a popular DNA testing service called "23 and Me," you're greeted with the motto "Everyone Has a DNA Story"?

Maybe your family is perfect, but my first reaction was that a lot of DNA stories should be put on "do not resuscitate" orders they should not be revived but, like sleeping dogs, left to lie.

Remember, it wasn't until about 60 years ago that you could tell if your DNA matched the rest of your family's. There was a reason why Homer (not from the "The Simpsons" but the "The Odyssey") observed, "It's a wise child that knows its own father."

Illustrating "Everyone Has a DNA Story" is a cheerful white woman in athletic gear, sporting an iPod and an unfocused gaze. Next to her is the following text: "Scandinavian 34.5 percent and lactose intolerant."

So the mysteries solved by hundreds of years of science are that Blondie is partly Scandinavian and gets gassy when she eats cheese? For that she needed to know what land masses her distant relatives traversed to get her family to, say, Milwaukee?

At another popular site run by Ancestry.com, a white woman cheerfully announces "Holy crow! I'm related to George Washington." We learn that "Emily found a presidential cousin who could be hiding in your family tree?"

I think my family tree was the one cut down by the young George Washington. Not that I'm bitter.

Families have a wide assortment of pasts. Some people have excruciatingly detailed family histories and can trace their lineage back to amoebas, presumably wearing tiny distinctive crests or tartans when they separated in the primordial muck. They're very proud of being able to point to the first traces of these organisms, as if dissemination were somehow an acquired skill, like the bro-sis couple in "Game of Thrones."

Some family trees don't fork. But they do spoon.

But enough about white supremacists, neo-Nazis, the KKK and other groups giving the lunatic fringe a bad reputation; the rest of us have to start seeing the points at which our lives connect rather than disconnect.

Sniffing out ethnic or racial bloodlines and tracking individual family trace molecules won't bring us closer as a community or as a nation.

Discovering our collective human blueprints might.

You do that through education, by sharing values and understanding history. You don't do it by swabbing the inside of your cheek.

Those who believe in the superiority of an ethnic white heritage are a feeble and fearful group. Fueled by fanatical beliefs they cannot render in intelligible terms and driven by degraded ideologies the origins of which are rooted in superstition, bigotry and pathology, they want to blame their failures on somebody as long as that person doesn't look like their kin.

Threatening, lazy and impotent, metaphorically if not literally, they regard every successful woman, every successful person of color, every successful recent immigrant, every successful person who is slightly different in any way (queer, non-fundamentalist-Christian, artistic, funny or well-dressed) as repudiation.

There must be an excuse for the fact that they have nothing to strive for, except a past that might have an ancestor hiding in a branch somewhere.

They might believe that branch is currently the executive one. Let's prove them wrong. The past is done and the future doesn't belong to them. It's not about any single group's DNA, resume, IQ or ZIP code. It's about all of us.

Gina Barreca is an English professor at UConn and author of "If You Lean In, Will Men Just Look Down Your Blouse?" and eight other books. She can be reached at ginabarreca.com.

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Gina Barreca: White Supremacists Wrong, It's Not Our DNA - Hartford Courant