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ASCO 2017: Genomic Sequencing Approach Step Toward Early Cancer Detection – R & D Magazine
Posted: June 6, 2017 at 5:46 am
A study of 124 advanced breast, lung and prostate cancer patients demonstrated that a new, high-intensity genomic sequencing approach can detect circulating tumor DNA at a high rate.
In the study, which was presented at the 2017 American Society of Clinical Oncology (ASCO) Annual Meeting, 89 percent of the patients had at least one genetic change detected in the tumor that was also detected in the blood.
Also, 627 genetic changes found in tumor samples were also found in blood samples using this new approach.
Our findings show that high-intensity circulating tumor DNA sequencing is possible and may provide invaluable information for clinical decision-making, potentially without any need for tumor tissue samples, lead study author Dr. Pedram Razavi, Ph.D., a medical oncologist and instructor in medicine at Memorial Sloan Kettering Cancer Center, said in a statement. This study is also an important step in the process of developing blood tests for early detection of cancer.
Razavi said the approach is not intended to be commercially available to patients and the researchers will now use the technology to potentially develop a blood test for early cancer detection.
The researchers used a combination of breadth and depth by scanning a very broad area of the genome508 genes and more than two million base pairs or letters of the genomewith high accuracy, yielding about 100 times more data than other sequencing approaches.
In liquid biopsies, including commercial tests, only a relatively small portion of the genome are profiled. Those tests are also only used on patients already diagnosed with cancer in order to help monitor the disease or detect actionable alterations that can be matched to available drugs or clinical trials.
The researchers analyzed tumor tissues using MSK-IMPACTa 410-gene diagnostic test that provides detailed genetic information about a patients cancer. They also separated the plasma in blood cells and extracted cell-free DNA from the plasmas and separately sequenced the genome of white blood cells using the high-intensity, 508-gene sequencing assay.
Finding tumor DNA in the blood is like looking for a needle in a haystack. For every 100 DNA fragments, only one may come from the tumor and the rest may come from normal cells, mainly bone marrow cells, Razavi said. Our combined analysis of cell-free DNA and white blood cell DNA allows for identification of tumor DNA with much higher sensitivity, and deep sequencing also helps us find those rare tumor DNA fragments.
The test detected at least one genetic change in the tumor and the blood in 97 percent of the breast cancer patients, 85 percent of the lung cancer patients and 84 percent of the prostate cancer patients.
Prior research in the field has primarily focused on using knowledge from tumor tissue sequencing to identify specific changes to look for in circulating tumor DNA, Razavi said. This approach allows us to detect, with high confidence, changes in circulating tumor DNA across a large part of the genome without information from tumor tissue.
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Assembling Genomes from Scratch, at a Fraction of the Cost – Laboratory Equipment
Posted: at 5:46 am
When the 2015/2016 Zika virus epidemic swept through the Americas and several islands in the Pacific and Southeast Asia, researchers were urged to focus their efforts on developing treatments and vaccines to combat the virus effects.
A team of researchers from the Center for Genome Architecture at Baylor College of Medicine coincidentally had crucial but fragmented pieces of relevant data from previous research that could greatly impact this effort. Using a 3-D genome assembly approach referred to as HI-C, the team was able to quickly assemble the 1.2 billion letter genome of Aedes aegypti, the Zika-carrying mosquito, producing the first end-to-end assembly of each of its three chromosomes.
When the Aedes mosquito came into the spotlight in relation to the Zika epidemic, we found ourselves sitting on a bunch of relevant data and proof-of-principle work, said Olga Dudchenko, a postdoctoral fellow at The Center for Genome Architecture. The situation prompted us to polish our methods and share the data we had.
The development provides a much-needed boost to research and treatment options for the Zika virus by identifying vulnerabilities in the mosquito that the virus uses to spread.
With the success of assembling the Aedes genome, the Baylor team has also shown that the 3-D assembly technique can be an important tool for similar outbreaks in the future, and could also aid in personalized care for human patients suffering from a variety of diseases.
Timeline Erez Lieberman Aiden, Director of the Center for Genome Architecture, originally proposed the general idea of 3-D assembly in 2009. Lieberman Aiden and colleagues first tested their technique in 2013 by sequencing a human genome, and comparing the data to that made available by the Human Genome Project.
The team found their assembly correlated with the reference data from the Human Genome Project with 99 percent accuracy, validating the method. However, the 3-D assembly method produced similar results in a fraction of the time, and at significantly less cost.
They then switched their focus toward the Aedes aegypti mosquito, which is responsible for the spread of not only Zika virus, but dengue, chikungunya and yellow fever. When the Zika outbreak began to become a global health threat, the team knew they could piece together information they acquired from previous research to create a clear, cohesive picture of the mosquitos genome.
3-D assembly allowed the team to create the 1.2 billion-letter genome of the mosquito for about $10,000a price comparable to that of an MRI scan. The third phase of their research included assembling the genome of the Culex quinquefasciatus mosquito, a carrier of West Nile virus.
Culex is another important genome to have since it is responsible for transmitting so many diseases, said Lieberman Aiden. Still, trying to guess what genome is going to be critical ahead of time is not a good plan. Instead, we need to be able to respond quickly to unexpected events. Whether it is a patient with a medical emergency or the outbreak of an epidemic, these methods will allow us to assemble de novo genomes in days, instead of years.
For the Culex sequence, the researchers carried out their work with IBMs VOLTRONa high performance computing (HPC) system. VOLTRON is based on the companys Power Systems platform, which provides scalable HPC capabilities necessary to accommodate a broad spectrum of data-enabled research activities. The Power Systems platform has also been selected for use by the Department of Energys Oak Ridge and Lawrence Livermore National Laboratories, and the UK governments Science and Technology Facilities Councils Hartree Centre.
3-D assembly and IBM technology are a terrific combination: one requires extraordinary computational firepower, which the other provides, said Lieberman Aiden. Incorporated into the design of VOLTRON is a POWER and Tesla technology combination that allowed Baylor researchers to handle extreme amounts of data with incredible speed. VOLTRON comprises a cluster of four systems, each featuring a set of eight NVIDIA Tesla GPUs tuned by NVIDIA engineers to help Baylors researchers achieve optimum performance on their data-intensive genomic research computations.
The team also made a new discovery about these mosquito families during sequencing. They found that chromosome content did not mix much across the species, which could prove helpful in any future outbreak with a mosquito as a carrier, regardless of whether its genome is sequenced or not.
If youre looking at various mammals, chromosome content will mix a lot from one species to another. But what turned out to happen in mosquitoes was a very different story. What we saw is that although things mix a lot locally, (within chromosome arms) very little content jumped from one arm to another, or from one chromosome to another chromosome, explained Dudchenko.
This fundamental fact of mosquito evolution offers immediate benefit for researchers. If another epidemic hit through a completely different mosquito carrier that researchers and health officials know nothing about, they can at least infer where to look for particular genes or targets within the new carrier because of this unique property. In the event of a new outbreak, this technology could answer questions much faster and lead to the rapid development of a treatment or vaccine, saving lives and money.
Advancing capabilities As Dudchenko explained to Laboratory Equipment, the field of genome assembly is a very actively developing field, providing researchers with genetic information that was previously unobtainable.
But for certain applications, assembly methods can be suboptimal.
Prior to the 3-D genome assembly method, it was challenging and extremely expensive to sequence a genome by starting at the beginning of a chromosome and reading all the way through to the end. Instead, researchers would use methods that read small snippets of chromosomes many times over, find overlaps in those snippets and piece them together to create longer, continuous sequences.
The problem arises, however, when repetitive fragments appear, or theres a large amount of variation across a species.
Its like reading a book in which the pages arent bound or numbered in any meaningful way, Dudchenko said. In some sense, the information is all there and if youre lucky enough that the information you want to read off is in the paragraph on the same page, you can make sense of it. But if you have longer stretches of text, or are unlucky and hit the end of the page, you dont know where to go from there, and theres not a lot you can do with this information.
Another problem with short-reads or jumping methods is when DNA is being extracted, the chromosomes rarely remain unbroken.
But HI-C provides the needed information at the scale of whole chromosomes.
The technique traces the genome as it folds inside the nucleus, and shows how frequently different stretches of the genome come into contact with each other. This enabled the team to stitch together hundreds of millions of short DNA reads into the sequences of entire chromosomes.
People can view HI-C as a type of jumping library that spans all scales, said Dudchenko.
Clinical relevance The short-read format also greatly reduces the cost of assembly, making it an option for doctors to conduct a personalized genome project on individual patients as needed.
This is the technology that will get you there, said Dudchenko.
Prior to HI-C, a clinician may sequence a persons DNA, but instead of fully assembling it, they align it with a reference and look for typos to see where the patient differs from the genome reference. The disadvantage with this approach is that the clinician is looking at someones genome through the lens of an existing reference, creating a biased view. It relies heavily on prior work, and if theres something unexpectedly different, the clinician may not notice, according to Dudchenko.
The next step for the Baylor team is to build more of a stable infrastructure for other research groups to utilize the HI-C technology in their respective fields, and to make it more straight-forward for people who may not necessarily come from a 3-D space with relevant expertise.
Were very excited to see how this technology will play out with different genes and assemblies, and how far we will be able to go with this technology, added Dudchenko. Right now, were pretty optimistic.
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Researchers Sequence Genome of Mojave Desert Tortoise – Sci-News.com
Posted: at 5:46 am
An Arizona State University-led team of scientists has sequenced the genome of the Mojave desert tortoise (Gopherus agassizii), a long-lived species native to the Mojave Desert. The results could help the animal survive an increasing number of threats.
The Mojave desert tortoise (Gopherus agassizii). Image credit: Sandra Leander, Arizona State University.
The Mojave desert tortoise, one of six species of desert tortoises estimated to have arisen in North America about 35 million years ago, can be found in California, Nevada, Utah and Arizona.
Also known as the Agassizs desert tortoise, this species has been heavily impacted by habitat loss, a respiratory tract disease, and other anthropogenic factors. For instance, in one area of the species range density declined from about 225 individuals/km2 in 1979 to about 75 individuals/km2 in 1992.
The Mojave desert tortoise is listed as threatened under the U.S. Endangered Species Act and is considered vulnerable by the International Union for Conservation of Nature (IUCN).
To aid conservation efforts for preserving the genetic diversity of this species, Arizona State University Professor Kenro Kusumi and co-authors generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood.
The Mojave desert tortoise genome is an important resource for the conservation of this species, particularly because this population is suffering from a serious disease, said co-author Dr. Marc Tollis, also from Arizona State University.
Researchers dont yet fully understand its cause or what makes tortoises susceptible to it.
Decoding this genome will help us catalog which tortoise genes are evolving quickly enough to help them overcome this threat.
The researchers obtained the genetic data for a particular tortoise specimen, assembled and annotated the genome and learned about the evolutionary history of tortoises.
Decoding a genome has gotten technically a lot easier, Prof. Kusumi said.
Whats challenging now is decoding the information in the tortoise genome. We can use clues from similarities with the mouse and human genomes.
Finding the proverbial needle in the haystack would be to identify the genes that direct the immune response to infectious disease, as well as the ability to survive the harsh conditions of the Mojave Desert.
Its important for us to learn where tortoise diversity is located across its geographic range, he added.
Identifying hotspots of genetic diversity helps manage the species from a conservation standpoint and preserve tortoise populations that could respond better to unknown challenges in the years ahead.
The team is also analyzing the genetic differences between the Mojave desert tortoise and its sister species, the Sonoran desert tortoise (Gopherus morafkai).
My hope is that this study will enable other agencies to ask new questions, questions they would not have been able to ask without this research, said co-author Dr. Greer Dolby, also from Arizona State University.
For instance, What immune genes do tortoises have to fight pathogens? How does their immune system function in an environment with lots of threats? And, how might a changing environment impact this? These are important questions to answer in managing the species. Now, we can begin investigating.
The findings were published online May 31, 2017 in the journal PLoS ONE.
_____
M. Tollis et al. 2017. The Agassizs desert tortoise genome provides a resource for the conservation of a threatened species. PLoS ONE 12 (5): e0177708; doi: 10.1371/journal.pone.0177708
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India’s Tea Genome Mapping Not Linked with Chinese Study – NorthEast Today
Posted: at 5:46 am
India, which recently launched its tea genome sequencing project, is not going to replicate the work done by the Chinese but instead aims to develop climate-smart tea plantations with the genomic boost, an official said in Kolkata.
We launched the project in the first week of April and a Chinese group published a paper on their work a month later. Many are of the opinion that India has, perhaps, missed the bus. We are not replicating the work that China has done. Our target cultivar is Assam type (Camellia assamica) and that is Indian-origin tea, Biswajit Bera, Director (Research) at Tea Board of India, Union Ministry of Commerce and Industry said on Monday.
Once the project is completed, we are going to have a climate smart tea plantation wherein we will target development of tea cultivars according to our own need, he said. In a study that offers clues why tea is so popular worldwide, Chinese researchers announced on May 1 they have successfully sequenced the genome of the evergreen shrub Camellia sinensis, known as tea tree, for the first time, Xinhua reported.
The genus Camellia contains over 100 species, but the most popular varieties of tea, including black tea, green tea, Oolong tea, white tea, and chai, all come from the leaves of the evergreen shrub Camellia sinensis.
Indias tea genome mapping project involves six institutes three Tea Research Institutes, National Tea Research Foundation (NTRF), ICAR, CSIR. This exercise will help in the development of superior tea cultivars using genome sequence information, Bera said.
This will be a two-phased programme. We will generate huge genetic resource information which will be co-related with field data specifying different traits or characters. Like, for Darjeeling, we are targetting the disease blister blight. For different areas of tea plantation in India, we are targetting different traits which will be co-related with this genome sequencing. In addition, the genetic data will also aid in developing package and practices to overcome adverse climatic stress, Bera said.
Genome is the complete set of genes or genetic material present in a cell or organism. Genome mapping helps to decode the genetic controls linked to different characters of tea that govern its yield, quality and other attributes.
Bera, a botanist, said there are three main tea varieties: India tea (Assam), China tea and hybrid tea. Bera was speaking at a workshop on Sustainable Development of Tea-Gardens and Issues of Urban Wetland organised here by IIT Kharagpur and Indiana University of Pennsylvania.
Around 40 students and faculty from both institutions, who are jointly researching the tea gardens in North Bengal, participated in the event.
-IANS
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Philips, MSK Partner on Genome Analytics for Pancreatic Cancer Precision Medicine – Genetic Engineering & Biotechnology News
Posted: at 5:46 am
The Memorial Sloan Kettering Cancer Center (MSK) and Philips will exploit the latters IntelliSpace Genomics platform through their research collaboration to develop new genome analysis methods and informatics approaches for diagnosing pancreatic cancer and aiding personalized therapeutics. The collaboration will employ large-scale next-generation sequencing to generate new insights into the drivers of pancreatic cancer at the single-cell level, with the goal of enabling more precise diagnosis so that patients can be prescribed optimum treatments that target the cause of their disease.
Philips' IntelliSpace Genomics platform has been developed to support the implementation and scaling of informatics-heavy precision medicine research. "Collaborating with MSK and its experts will allow us to take a unique approach to diagnosing and treating this devastating disease, commented Henk van Houten, Ph.D., CTO at Philips. Leveraging the advanced capabilities of the Philips IntelliSpace Genomics solution we can gain new insights into the origin, development, and optimal treatment of pancreatic cancer and share these insights broadly with care providers to help improve outcomes for patients. Our ultimate goal is to translate these findings into more precise diagnostics and therapeutics to battle this devastating disease."
Philips and MSK have previously established a research collaboration in the field of radiation oncology. Just yesterday, MSK and Mabvax Therapeutics signed a research agreement to develop chimeric antigen receptor (CAR) T-cellimmunotherapies for pancreatic and small-cell lung cancer.
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Human longevity slows in UK – Financial Express Bangladesh
Posted: at 5:45 am
Recent studies suggest that the rapid pace of improvement in British longevity is now slowing, according to a global media report Monday. The Continuous Mortality Investigations group, which produces longevity projections based on the experience of insured and pensioned lives, found that longevity for men at age 65 fell by six months to 22.2 years while that of women fell by eight months to 24.1 years.
While longevity is still expected to be higher than it is today, it is by a smaller margin than earlier forecasts. PwC, the professional services firm, recently produced a study concluding that as much as 310 billion could be wiped from the liabilities of UK defined benefit schemes. Although a respected group of actuaries hit back, describing the assumption as extreme, the entire debate has escalated to the political arena.
A backdrop to the discussion is the fact that increases in the age at which state pensions are payable is open for debate. In thinking about the rate at which state pension ages rise, the UK Government Actuarys Department assumes as does the Office for National Statistics that, in future, longevity will rise at the same pace it has for the past century; that is, 1.2 per cent each year. That could change with new data to be released in the autumn.
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Gene-Targeted Drugs Fight Advanced Lung Cancers – Sioux City Journal
Posted: at 5:43 am
MONDAY, June 5, 2017 (HealthDay News) -- Two drugs that target genetic flaws are giving people with specific types of advanced lung cancer a chance to live longer and better, a pair of new clinical trials finds.
A newly approved drug called alectinib (Alecensa) works twice as long as the current standard medication in halting cancer growth in patients with ALK-positive non-small cell lung cancer, results from a new global clinical trial show.
ALK is a gene that produces a protein that helps cancer cells grow and spread, according to the American Cancer Society (ACS).
In another study, an experimental drug called dacomitinib delayed cancer growth by about half in non-small cell lung cancer patients who had a mutation of the epidermal growth factor receptor (EGFR) that caused cancer cells to grow faster, a second trial reported. Non-small cell lung cancers comprise most lung cancer cases.
EGFR is a substance normally found on cells that helps them grow and divide, the ACS says.
The drugs, alectinib in particular, will let people live months or years longer just by taking a daily pill, said Dr. Bruce Johnson, chief clinical research officer at Dana-Farber Cancer Institute in Boston. Johnson is also incoming president of the American Society of Clinical Oncology (ASCO).
Alectinib works more than a year longer than crizotinib (Xalkori), which itself supplanted chemotherapy a few years back because it proved more effective with fewer side effects, Johnson said.
"This is kind of a game changer, because the drug itself works at least for two years, plus there are other treatments" that can be substituted when it ultimately becomes ineffective, Johnson said of alectinib. "We used to have to tell these patients 10 or 15 years ago that you've got eight months to a year. Now they most likely have years."
Both of these genetically driven forms of lung cancer are more common in nonsmokers, the ACS says.
The studies were both funded by the drug manufacturers. Hoffmann-La Roche funded the alectinib study. Pfizer and SFJ Pharmaceuticals Group funded the dacomitinib study.
The first clinical trial revealed that alectinib halts lung cancer growth for about 26 months on average. That compared to about 10 months on average for crizotinib, the drug now used as front-line treatment for ALK-positive patients.
Alectinib also works 84 percent better than crizotinib at preventing spread of advanced lung cancer to the brain, because it is better able to penetrate into the brain and kill cancer cells there, said lead researcher Dr. Alice Shaw, director of thoracic oncology at Massachusetts General Hospital Cancer Center in Boston.
About 5 percent of non-small cell lung cancer cases are ALK-positive. That means they have a genetically abnormal protein that fuels cancer growth. In the United States, about 12,500 people are diagnosed with ALK-positive non-small cell lung cancer each year, researchers said in background information.
Alectinib already is approved in the United States as a treatment for ALK-positive patients who no longer respond to crizotinib, Shaw said.
The results should "establish alectinib as the new standard of care" for ALK-positive lung cancer patients, rather than crizotinib, Shaw said.
ASCO expert Dr. John Heymach agreed, calling the clinical trial a "watershed moment."
Not only did the drug work better and longer, but it also produced fewer side effects in patients, noted Heymach, chair of thoracic/head and neck oncology for the University of Texas MD Anderson Cancer Center in Houston.
The most common side effects for alectinib were fatigue, constipation, muscle aches and swelling, while crizotinib patients most often suffered from gastrointestinal problems and liver enzyme abnormalities, according to the researchers.
The second clinical trial compared a new drug, dacomitinib, to the current standard targeted drug gefitinib (Iressa) in treating EGFR-positive lung cancer.
Each year about 15,000 people in the United States are diagnosed with EGFR-positive lung cancer, which involve mutations that increase the growth of cancer cells, researchers said in background notes.
Dacomitinib blocked EGFR mutations more effectively than first-generation drug gefitinib, providing a 41 percent lower chance of cancer progression or death, researchers found. On average, dacomitinib halted cancer growth for 14.7 months in patients, compared with 9.2 months with gefitinib.
"From the perspective of doctors who treat lung cancer daily, this is really a substantial advance," Heymach said, noting that the results put the drug "at the front of the pack in terms of efficacy."
However, dacomitinib also created more side effects, including acne in about 14 percent of patients and diarrhea in 8 percent of patients. Doctors wound up reducing the dosage in about 66 percent of patients as a result of side effects, said lead researcher Dr. Tony Mok, chair of clinical oncology at the Chinese University of Hong Kong.
Heymach said the side effects are "not life-threatening toxicities."
"These are toxicities that doctors who treat this for a living become accustomed to managing," Heymach said.
"At the end of the day, I think we now have one additional choice" in treating EGRF-positive non-small cell lung cancer, Mok concluded, adding that dacomitinib should be considered as a new first-line alternative treatment. The drug has not received FDA approval.
Neither of the tested drugs will be cheap. "Almost all these targeted drugs are thousands of dollars per month," Johnson said.
The results of both trials were scheduled to be presented Monday at ASCO's annual meeting, in Chicago. The findings were also being published June 6 in the New England Journal of Medicine.
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Experimental Gene-Targeted Drug Hits Cancer Where It Lives – Montana Standard
Posted: at 5:43 am
SATURDAY, June 3, 2017 (HealthDay News) -- An experimental drug that targets a specific gene mutation can battle a range of advanced cancers in adults and children, researchers are reporting.
The genetic abnormality is known as a TRK fusion, and it's found in only a small percentage of all cancers. So the drug, called larotrectinib, is no panacea.
But researchers found that among 50 patients with TRK fusions, 76 percent saw their cancer regress after starting larotrectinib -- regardless of their age or type of cancer.
For most of those patients -- 79 percent -- the response has lasted at least one year, according to lead researcher Dr. David Hyman.
"There are few therapies that have had that kind of success for patients like these," said Hyman, an oncologist at Memorial Sloan Kettering Cancer Center in New York City.
Dr. William Oh, an oncologist who was not involved in the study, agreed.
"A 76 percent response rate for a new drug is extremely exciting," said Oh, chief of hematology and medical oncology at the Icahn School of Medicine at Mount Sinai in New York City.
"More importantly," he added, "the responses have been durable, lasting over a year -- which for some of these aggressive cancers is very promising."
This is the latest drug to target flaws in genes that occur anywhere in the body instead of just going after an organ-specific tumor. The first drug to work this way -- Keytruda (pembrolizumab) -- was approved for targeted use by the U.S. Food and Drug Administration on May 24. (Keytruda had previously received traditional FDA-approval for some organ-specific cancers.)
Targeted therapies are designed to zero in on specific abnormalities found on tumor cells -- with the aim of killing off the cancer while sparing healthy cells.
The patients in Hyman's study had a range of cancers, including colon, lung, pancreatic and gastrointestinal tumors -- as well as melanoma skin cancer and sarcoma, which arise in the bones or soft tissue like muscle or body fat.
But they also had some things in common: Their cancer had spread beyond its original tissue, sometimes to distant sites in the body. And they all had tumors marked by TRK fusions.
The abnormality is a "rare event," Hyman said.
TRK fusions occur in only about 0.5 percent to 1 percent of common cancers, such as colon, breast and lung cancers. But Hyman said they are very common in certain rare cancers such as salivary gland cancer, a form of breast cancer that affects children, and a type of sarcoma in babies.
The abnormality arises when a TRK gene in a cancer cell joins with one of many potential "partner" genes. (Scientists have found more than 50 so far). That, Hyman explained, results in TRK fusion proteins that are constantly "turned on," signaling the cancer cells to keep growing and dividing.
Larotrectinib, an oral medication, is designed to block that TRK activity wherever it occurs.
The new study involved 55 patients, including 12 children. So far, 50 have been on the drug long enough to track their progress.
Overall, Hyman said, about three-quarters have responded to treatment -- meaning their cancer regressed by at least 30 percent. Of those patients, eight in 10 were still on the drug and responding at the one-year mark.
At this point, Hyman said, the longest treatment response has been 25 months and counting.
The most common side effects are fatigue and dizziness. "Patients do very well on it," Hyman said. "You can have a good quality of life while you're taking it."
Last year, the FDA granted larotrectinib "breakthrough therapy" status. That helps speed the development and review process of promising new treatments for serious diseases.
Hyman said he couldn't estimate how long an FDA approval could take.
If the drug is approved, then the question will be: Who should get tested for TRK fusions?
According to Hyman, patients with advanced-stage cancer would have the "greatest need." And even though TRK fusions are uncommon, he thinks testing would be appropriate regardless of the cancer type.
Oh agreed. "TRK fusions are very rare, but in those patients who have them, the consequences with this drug appear to be very significant."
Plus, Oh said, cancer patients are already being tested for other molecular abnormalities to see if they can benefit from targeted drugs. That testing is becoming technically easier and cheaper, he noted.
Dr. Sumanta Kumar Pal is a medical oncologist at City of Hope in Duarte, Calif., and chair of ASCO's Cancer Communications Committee.
He said larotrectinib has the chance to be a "bit of game-changer. There are two important points: This drug may be active irrespective of the cancer site, and irrespective of age."
And while the safety results were encouraging, "it's difficult to draw conclusions based on such a small group of patients," he added.
If the drug is approved by the FDA, Pal said it would make sense to "test early" for TRK fusions in patients with the rare cancers. But with many common cancers, "we'd probably stick with standard care, and then (test) only if that fails," he said.
The study was funded by Loxo Oncology, Inc., which is developing larotrectinib. Hyman and some of his colleagues have received funding from or served as consultants to the company.
Hyman was scheduled to present the findings Saturday at the American Society of Clinical Oncology's annual meeting, in Chicago. Study results presented at meetings are usually considered preliminary until they're published in a peer-reviewed medical journal.
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Experimental Gene-Targeted Drug Hits Cancer Where It Lives - Montana Standard
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What’s In Your Genes? – Pacific Northwest Inlander
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Picture a time in the not-too-distant future when whole genome sequencing is routine. A time when, before babies even learn to talk, their parents will have the ability to learn what the future may have in store for their offspring: Is their little girl predisposed to getting breast cancer? Will their happy-go-lucky son one day develop Alzheimer's?
"There is no doubt in my mind that, in addition to going in and having blood chemistry done, you're gonna have DNA sequencing done, too. It will be there at some point," says Nicholas Schork, a quantitative geneticist at the J. Craig Venter Institute in La Jolla, California, who has studied genomic medicine for more than three decades. "We can debate about the timeline, but it'll become routine."
The hope is that genetic testing will make health care more effective by allowing doctors and patients to focus on areas that need attention the patient's genetic "vulnerabilities." At the same time, patients may learn of areas where they won't need to be quite as vigilant. And treatments could, in turn, be perfectly tailored to a patient's specific needs.
But as with any significant and broadly applicable medical advance, there are questions. For example, should patients learn that they carry markers for currently incurable genetic diseases, or that they are at high risk for developing a condition like Alzheimer's, which has no effective treatment? And just who owns all that genetic data? Who will have access to it?
Even with important questions left unanswered, health educators are moving forward to take advantage of the promises genetic testing offers. Washington State University's new Elson S. Floyd College of Medicine has announced it is partnering with Arivale, a Seattle-based company that conducts whole genome sequencing, to help complete a portrait of a person a "portrait" that can be used to promote wellness over that individual's entire lifespan. Every member of the school's inaugural class will have the opportunity to undergo testing, which will also include blood tests and a lifestyle evaluation. Then, over the next year, Arivale's team of nurses and dietitians will provide individually tailored follow-up, based on each individual's risks and goals. It's a unique partnership, made possible in large part because the medical school is new, with its first class of students starting in 2017.
Allowing the medical students to experience genetic testing firsthand is just part of the goal. "We need physicians that understand it well enough that they can make it better going forward," says John Tomkowiak, founding dean of WSU's College of Medicine. "That's where our students are going to be uniquely positioned."
WHAT GENES TELL US
Genetic testing already provides important information about a person's health or their heritage. Hospitals screen newborn babies for certain genetic disorders, and in some cases, tests can detect disorders before birth. And diagnostic testing can confirm, or rule out, many disorders in adults.
Testing doesn't have to be ordered by a physician. For $200, you can provide a saliva sample, mail it back to 23andMe.com and find out not only your ancestry, but also your risks for a number of diseases, including Alzheimer's and Parkinson's. Ancestry.com offers a glimpse into your heritage for $99. Color.com claims to reveal your risk for the most common hereditary cancers, and even offers "complimentary genetic counseling" for a $249 fee.
But if genetic testing is to revolutionize the health care industry, as many have promised, there's still a ways to go. "The technology is at the beginning stages," says Thomas May, a faculty researcher for the HudsonAlpha Institute for Biotechnology.
Companies like 23andMe offer genetic tests that may provide information about some genetic disorders from currently known genetic variants. But whole genome sequencing is different; it will reveal all your individual genetic variants.
How valuable is that information? There are a relatively small number of conditions that researchers are confident result from a specific genetic variant, May says. For example, there is one variant that researchers have found is associated with an increased risk of developing breast or ovarian cancer. A genetic test that shows an increased risk for breast cancer is considered an "actionable" outcome, meaning there are things you can do to prevent the outcome, like beginning mammograms earlier. Though there are more than 50 actionable outcomes like that, it's still a relatively small number.
Adding to the confusion is the fact that not everyone who develops breast cancer actually has the genetic variant in fact, May says only about 10 percent do. So even if testing shows that you don't have the "breast cancer gene," that doesn't mean it's OK to stop getting mammograms.
"Most variants and correlations are of that type: We can't say for certain if you're gonna get a disease," May says.
Doctors are mixed about whether genetic testing is currently having a real impact on patients. In a May survey conducted by the Medscape Physician Oncology Report on Genomics Testing, 71 percent of oncologists surveyed felt that genetic testing was either "very" or "extremely" important to the oncology field. At the same time, 61 percent said that, currently, fewer than a quarter of their patients would actually benefit from genetic testing.
The number of diseases with "actionable" outcomes will inevitably grow, as more people are tested and more data becomes available. But this leaves deeper questions, says Schork, the quantitative geneticist. A company or health care provider would likely give patients information about diseases that can be prevented or cured. If someone is predisposed to obesity, for instance, then he or she can elect to receive targeted care to reduce that risk.
But what about diseases that, right now, are incurable?
Take Huntington's disease, a genetic disorder that breaks down nerve cells in the brain. It's rare, but it's a "hideous way to die," Schork says. A person can be screened at the age of 25 and be found to carry the Huntington's gene, but there's debate about whether or not that information should be shared with a client or not. The same goes for genetic variants related to Alzheimer's disease.
"If there's nothing they can do about it, then there's a concern about whether or not that information should be imparted," Schork says.
When the Food and Drug Administration ordered 23andMe to stop telling customers their odds of contracting diseases in 2013, Harvard Medical School genetics professor Robert Green and Laura Beskow, a professor at Duke University's Institute for Genome Sciences and Policy, argued against the FDA. They cited a number of studies showing that direct-to-consumer genetic testing does not cause a large percentage of customers despair. In an interview with the New York Times in April, Green said the potential for distress based on results of a genetic test for Alzheimer's was "much smaller than anticipated."
Another question: Who really owns the DNA data that is being collected from willing users of genetic testing? Consider Myriad, a company that offers genetic testing both to help determine cancer risk and design better treatment plans for patients who already have cancer. The company has something that "others do not," Schork says: insight into which genetic variants predispose women to breast cancer.
What Myriad is really selling, then, is not the genetic test itself, but access to insights it has gained through mining its database, insights that can be leveraged into whatever level of payment the company decides to charge.
It's potentially critical information that could help save a life, and some argue that the data should be in the public domain not held by a private company.
"There have been huge debates about whether the community should challenge the monopoly that Myriad has," Schork says. "There are many groups out there that would like to counteract the monopoly Myriad has, by building public domain data sets."
JUST ONE TOOL
"Genetic testing is not a blueprint. It's really not," says Jennifer Lovejoy, chief translational science officer for Arivale. "Genes are really just one factor the environment, diet, exercise, pollutants and even emotional state have a big impact on genes."
That's why Arivale not only collects genetic information on each client, but also evaluates various blood tests and lifestyle factors to create a "dense data cloud" of information about a patient.
"That is the grand vision: that everybody would have these dense, dynamic data clouds, and understand the choices that will be optimal to optimize wellness and avoid disease," says Lovejoy.
Arivale touts the success stories among its nearly 2,000 clients. One client found out he had a gene associated with high sensitivity to saturated fat, giving him a better indication of an appropriate diet that helped him lose weight. Another client discovered that his genes may have an impact on his cholesterol. Another learned he was at risk of developing diabetes.
Ideally, this type of preventive care will soon be covered by insurance, Lovejoy says. The thinking is that preventing disease will bring down the cost of health care overall, making insurers likely to cover more preventive care, "but we have to prove it," Lovejoy says. Researchers are conducting studies and trials to do just that, and if they can prove it, then genetic testing could soon be routine in health care.
"If you think about what health care should mean, it should mean, one, the ability to deal with disease and that's what everyone does today," Arivale co-founder Leroy Hood said at a press conference in April announcing the company's partnership with WSU. "But two, it should mean the ability to optimize wellness for each individual. That is, improving their health and/or letting them avoid disease." That's a concept Hood calls "scientific wellness, and he thinks it could lead to "a whole new health care industry in the future."
Tomkowiak, of WSU's College of Medicine, agrees: "The concept of scientific wellness has the potential to disrupt the entire industry by shifting the cost curve, by keeping people healthier and reducing the cost of health care overall."
Regardless of whether or not Arivale becomes an industry leader, Tomkowiak believes that the practice of medicine will be fundamentally altered in the near future.
"We absolutely believe that seven years from now, the practice of scientific medicine and scientific wellness will be common," he says. "Instead of being behind the curve, we want... to be leading this effort."
For about $3,500, clients can sign up for Arivale's program. The fee includes whole genome sequencing, which is also available from other sources. So how do Arivale clients achieve "scientific wellness"? Here are the elements of their program:
Welcome package: Clients get a welcome package with a Fitbit to track sleep, activity and heart rate. The package asks for information to help understand a client's bacteria in their gut, and asks for a sample of saliva to measure a person's stress level.
Online test: Clients take a series of online assessments about their goals, health history, lifestyle, stress, personality and happiness.
Call from coach: You'll talk to a coach who will get to know what you want to accomplish and give you a personalized action plan.
Labs: You'll take blood tests so your coach can understand your current health. While you're there, they'll take your vital signs.
A picture emerges: The various test create a picture of you, which an Arivale coach will use to provide a step-by-step plan to "optimize your wellness," according to the company.
Follow-up: You're not done yet. You'll be contacted by your coach regularly to review your action plan, and Arivale will provide reports on how you're progressing. Every six months, you'll complete another set of clinical labs.
Source: arivale.com/your-journey
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Gene-Based Therapy May Thwart a Tough Blood Cancer – Montana Standard
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MONDAY, June 5, 2017 (HealthDay News) -- Genetically tuning a person's own immune cells to target cancer appears to provide long-lasting protection against a blood cancer called multiple myeloma, an early trial from China shows.
The treatment, called CAR T-cell therapy, caused 33 out of 35 patients with recurring multiple myeloma to either enter full remission or experience a significant reduction in their cancer.
The results are "impressive," said Dr. Len Lichtenfeld, deputy chief medical officer for the American Cancer Society.
"These are patients who have had prior treatment and had their disease return, and 100 percent of the patients are reported to have had some form of meaningful response to these cells that were administered," Lichtenfeld said.
The new therapy is custom-made for each patient. Doctors collect the patient's own T-cells -- one of the immune system's main cell types -- and genetically reprogram them to target and attack abnormal multiple myeloma cells.
Lead researcher Dr. Wanhong Zhao likened the process to fitting immune cells with a GPS that steers them to cancer cells -- making them into professional killers that never miss their target.
Zhao is associate director of hematology at the Second Affiliated Hospital of Xi'an Jiaotong University in Xi'an, China.
CAR T-cell therapy is promising because the genetically altered T-cells are expected to roost in a person's body, multiplying and providing long-term protection, Lichtenfeld said.
"The theory is they should attack the tumor and continue to grow to become a long-term monitoring and treatment system," Lichtenfeld said. "It's not a one-shot deal."
The technology represents the next step forward in immunotherapy for cancer, said Dr. Michael Sabel, chief of surgical oncology at the University of Michigan.
"Immunotherapy is now really providing hope to a lot of patients with cancers that were not really responding to our standard chemotherapies," Sabel said.
CAR T-cell therapy previously has been used to treat lymphoma and lymphocytic leukemia, Lichtenfeld said.
Zhao and his colleagues decided to try the therapy to treat multiple myeloma. They re-engineered the patients' T-cells and then reintroduced them to the body in three infusions performed within one week.
Multiple myeloma is a cancer that occurs in plasma cells, which are mainly found in bone marrow and produce antibodies to fight infections. About 30,300 people will likely be diagnosed with multiple myeloma this year in the United States, researchers said in background notes.
"Multiple myeloma is a disease that historically was fatal in the course of a couple of years," Lichtenfeld said. During the past two decades, new breakthroughs have extended survival out 10 to 15 years in some patients, he noted.
To date, 19 of the first 35 Chinese patients have been followed for more than four months, researchers report.
Fourteen of those 19 patients have reached the highest level of remission, researchers report. There hasn't been a relapse among any of these patients, including five followed for more than a year.
"That's as far as you can go in terms of driving down the amount of tumor that's in the body," Lichtenfeld said.
Out of the remaining five patients, one experienced a partial response and four a very good response, researchers said.
However, about 85 percent of the patients experienced cytokine release syndrome (CRS), a potentially dangerous side effect of CAR T-cell therapy.
Symptoms of cytokine release syndrome can include fever, low blood pressure, difficulty breathing, and impaired organ function, the researchers said. However, most of the patients experienced only transient symptoms, and "now we have drugs to treat it," Lichtenfeld said.
History suggests the therapy will cost a lot if it receives approval, Lichtenfeld said. However, prior to approval, much more research will be needed, he added.
The Chinese research team plans to enroll a total of 100 patients in this clinical trial at four hospitals in China. They also plan a similar clinical trial in the United States by 2018, Zhao said.
The study was funded by Nanjing Legend Biotech Co., the Chinese firm developing the technology.
The findings were presented Monday at the American Society of Clinical Oncology annual meeting, in Chicago. Data and conclusions presented at meetings are usually considered preliminary until published in a peer-reviewed medical journal.
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Gene-Based Therapy May Thwart a Tough Blood Cancer - Montana Standard
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