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Category Archives: Genetic Medicine

Dispute Over British Baby’s Fate Draws In Pope and US President – New York Times

Three courts in Britain agreed with the hospital, as did the European Court of Human Rights, which last week rejected a last-ditch appeal by Charlies parents.

But Pope Francis and Mr. Trump have also weighed in, adding another dimension to an extraordinarily thorny bioethical and legal dispute that pits Britains medical and judicial establishment against the wishes of the childs parents.

Judges in the case have acknowledged that the case highlights differences in law and medicine and an American willingness to try anything, however unlikely the possibility of success but have held that prolonging the infants life would be inhumane and unreasonable. The case echoes the one of Terri Schiavo, a Florida woman who was left in a persistent vegetative state after a cardiac arrest and was also the subject of a court battle.

A Vatican spokesman, Greg Burke, told Vatican Radio on Sunday that the pope had been following the parents case with affection and sadness, praying that their desire to accompany and care for their own child to the end is not ignored.

Italys top pediatric hospital, which is run by the Vatican, told the Italian news agency ANSA on Monday that it would be willing to take Charlie.

We understand that the situation is desperate, said Mariella Enoc, director of the Bambino Ges hospital in Rome, noting that she had been in touch with British officials to signal a willingness to take the patient, the agency reported. We are close to the parents in prayer and, if this is their desire, we are open to receiving their child at our structure for the time it will take for him to live.

Mr. Trump, who was not known to have previously expressed a view on the matter, wrote on Twitter on Monday that if the United States could help, we would be delighted to do so.

Both the pope and the president stopped short of criticizing the court rulings or the hospital. Helen Aguirre Ferr, the director of the White House office of media affairs, said Mr. Trump had decided to speak out after he learned about this heartbreaking situation. Mr. Trump has not spoken with the family, she said, and does not want to pressure them in any way.

The president is just trying to be helpful if at all possible, she added.

Charlie was born on Aug. 4 with encephalomyopathic mitochondrial DNA depletion syndrome. He is thought to be one of only 16 children globally with the condition, the result of a genetic mutation.

Brendan Lee, the chairman of the department of molecular and human genetics at Baylor College of Medicine, who is not involved in the case, said in a phone interview that mitochondrial depletion syndrome has no cure. Treatments involve different types of vitamin supplementation, but none have been shown to definitively work through studies, he said.

Charlies parents, Connie Yates and Chris Gard, both in their 30s, have been waging a long and wrenching legal battle to keep him alive. They have raised more than 1.3 million pounds, or about $1.7 million, to help finance experimental treatment in the United States. There is also an international campaign, with an online petition, and there have been street protests in front of Buckingham Palace.

Charlie has been treated since October at Great Ormond Street Hospital, where doctors eventually decided that withdrawing life support was the only justifiable option. Although Charlies parents have parental responsibility, overriding control is by law vested in the court exercising its independent and objective judgment in the childs best interests, the hospital said in a statement laying out its position.

Siding with the hospital were the High Court, on April 11; the Court of Appeal, on May 25; and the Supreme Court of the United Kingdom, on June 8.

The High Court ruled that Charlie would face significant harm if his suffering were to be prolonged without any realistic prospect of improvement. Moreover, it said the experimental treatment, known as nucleoside therapy, would not be effective.

Money is not at issue; an academic medical center in the United States has offered to provide the experimental treatment. But a neurologist at the hospital, who has offered to oversee the treatment, told the court by telephone: I can understand the opinion that he is so severely affected by encephalopathy that any attempt at therapy would be futile. I agree that it is very unlikely that he will improve with that therapy.

Neither the hospital nor the neurologist was identified in court documents, and the White House has declined to identify either.

The Court of Human Rights ruled last week that the British courts had acted appropriately in concluding that it was most likely Charlie was being exposed to continued pain, suffering and distress, and that undergoing experimental treatment with no prospects of success would offer no benefit, and continue to cause him significant harm.

The case has drawn attention to important differences in legal systems.

Claire Fenton-Glynn, a legal scholar at the University of Cambridge who studies childrens rights, said that under British law, the courts were the final arbiter in medical disputes about the treatment of children.

She noted a 2001 case of conjoined twins, Jodie and Mary, who were born sharing an aorta. Separating the twins would lead to the death of the weaker twin; if they were not separated, both would die. A court ruled that the twins should be separated against the wishes of their parents; as expected, one died.

Courts in the United States are less inclined to get involved when there are disputes between parents and doctors, said Professor Moreno of the University of Pennsylvania, stressing that it was usually left to doctors, in consultation with parents, to decide on a childs treatment.

He noted the case of Baby Jane Doe, who was born in 1983 with spina bifida and whose parents declined to approve surgery to prolong her life. That case led to a law, signed by President Ronald Reagan, that defined instances in which withholding medical treatment from infants could be considered child abuse, but also provided that in certain cases doctors and parents might choose to withhold treatment from seriously handicapped babies when such action would merely prolong dying.

G. Kevin Donovan, the director of the Pellegrino Center for Clinical Bioethics at Georgetown University Medical Center and a professor of pediatrics, said that in the United States, if parents insisted on continuing life-prolonging treatment against a doctors advice, the child would simply be transferred to another institution willing to comply with the parents wishes.

It doesnt seem to be a supportable position morally or ethically, he said of the stance taken by the hospital in London, adding that what is legal and what is ethical are not always the same.

In the Schiavo case, her husband, who was her legal guardian, wanted to have her feeding tube removed, but her parents disagreed, setting off a seven-year fight that ended in 2005, after courts ruled in the husbands favor. Life support was removed from Ms. Schiavo, who died at 41.

In that case, too, the pope, then John Paul II, and the president, George W. Bush, weighed in. Mr. Bush signed an act of Congress allowing federal courts to intercede in the case. But their interventions did not ultimately affect the outcome.

There was no immediate response to Mr. Trumps statement from Charlies parents, who last week appeared to accept the finality of the courts rulings. Photographs of the couple sleeping with their sick child have circulated on social media recently.

We are really grateful for all the support from the public at this extremely difficult time, Ms. Yates said on Friday. Were making precious memories that we can treasure forever with very heavy hearts. Please respect our privacy while we prepare to say the final goodbye to our son Charlie.

There was also no immediate reaction from the hospital.

In Charlies case we have been discussing for many months how the withdrawal of treatment may work, the hospital said. There would be no rush for any action to be taken immediately. It added that it would consult the family and that discussions and planning in these situations usually take some days.

Follow Dan Bilefsky @DanBilefsky and Sewell Chan @sewellchan on Twitter.

Reporting was contributed by Aneri Pattani and Roni Caryn Rabin from New York, Michael D. Shear from Washington, and Elisabetta Povoledo from Rome.

A version of this article appears in print on July 4, 2017, on Page A1 of the New York edition with the headline: Dispute Over British Babys Fate Draws In President and Pope.

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Dispute Over British Baby's Fate Draws In Pope and US President - New York Times

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The future of medicine: Personal, ubiquitous, and mobile – Computerworld

Appleholic, (noun), pl-hlk: An imaginative person who thinks about what Apple is doing, why and where it is going. Delivering popular Apple-related news, advice and entertainment since 1999.

Weve discussed before how Apples devices can be good for your health, but we should see the potential of its mobile health solutions take a quantum leap in the next few years, as genetic information is used to deliver utterly personalized, precision medical care.

The UKs chief medical officer this week recommended routine DNA testing for cancer patients to help develop personalized treatment.

"This technology has the potential to change medicine forever - but we need all NHS staff, patients and the public to recognise and embrace its huge potential, said Professor Dame Sally Davies. The age of precision medicine is now.

Think about the implications of this:

While such information isnt necessarily going to help develop treatments for every patient and every illness, there are some problems that can be better addressed once a persons genetic make-up is understood.

The idea must be that by understanding a persons individual genetic construction, it becomes easier to identify external factors that may impact that person.

While there are clear potential benefits, there are also concerns.

The World Health Organization warns that: Knowledge of genetic risks can lead to potential social and psychological consequences for the individual.

However, Dame Davies statement suggests such testing will become part of future healthcare it will be up to each of us to ensure such data doesnt become the thin end of a drive to genetic discrimination. There aredystopian ways to abuse such technologies.

How does this relate to Apple? Apple Watch can already help you to follow a healthy exercise routine. Its built-in heart rate monitor is already saving lives.

Apple is already working to extend the capabilities of its connected devices to monitor different types of health data, with Apple CEO Tim Cook reportedly wearing an iPhone-connected diabetes blood sugar monitor.

From software for medical research to development of new sensor technologies, there can be little doubt that Apple wants to build a connected ecosystem of products and services that may provide tangible benefits to public health.

There have been claims Apple is also expanding its reach into electronic health record technologies, citing a range of hires and acquisitions that appear to support this idea.

Apple also made numerous significant enhancements to its CareKit and ResearchKit frameworks at WWDC 2017, including the addition of more tracking options for diabetes treatment and better integration with healthcare provider platforms, such as Medables Synapse.

The idea might be that by securely combining a patient health data with ambient sensor-based insight, a person will be empowered to manage and improve their health, and healthcare professionals will be able to access deep collections of related data to help improve treatment and diagnosis.

There are also clear implications for artificial intelligence in this.

So now we have a situation in which an augmented human is better equipped to maintain their own health while also being empowered to monitor any existing conditions. (Though we still need effective ways to ensure health-focused solutions are actually good for your health).

Now imagine how much more effective such personalized solutions may become if informed about your own unique genomic code.

This combination should enable remote diagnostic systems to match a persons personalized status with current activity in order to determine potential future health challenges.

Apple has been exploring the potential of genetics in digital health since at least May 2015. Working with 23andMe, Apple in 2016 added a new ResearchKit module tht allows study participants to easily contribute their genetic data to medical research.

Collecting this type of information will help researchers determine genomic indicators for specific diseases and conditions, said Eric Schadt, PhD, the Jean C. and James W. Crystal Professor of Genomics at the Icahn School of Medicine at Mount Sinai, and Founding Director of the Icahn Institute for Genomics and Multiscale Biology.

The momentum behind use of genomic data in medical care and research in conjunction with the statement from the UKs chief medical officer suggests this will indeed become part of the future of healthcare.

Apple appears to be building itself a strong position to be part of that future.

Google+?If you use social media and happen to be a Google+ user, why not joinAppleHolic's Kool Aid Corner communityand join the conversation as we pursue the spirit of the New Model Apple?

Got a story?Drop me a line via Twitterand let me know. I'd like it if you chose to follow me on Twitter so I can let you know when fresh items are published here first on Computerworld.

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Greater access to genetic testing needed for cancer diagnosis and treatment – Cancer Research UK

Cancer patients should have routine access to genetic testing to improve diagnosis and treatment, according to Englands chief medical officer.

Despite the UK being a world leader in genomic medicine its full potential is still not being realised, Professor Dame Sally Davies said in a new report.

This timely report from the chief medical officer showcases just how much is now possible in genomics research and care within the NHS. - Sir Harpal Kumar, Cancer Research UK

Davies urged clinicians and the Government to work together and make wider use of new genetic techniques in an attempt to improve cancer survival rates.

Genetic testing can pinpoint the faults in DNA that have led to a cancer forming. Different cancers have different faults, and these determine which treatments may or may not work.

Such testing could lead to patients being diagnosed faster and receiving more targeted or precise treatments.

Davies said that the age of precision medicine is now and that the NHS must act quickly to remain world class.

This technology has the potential to change medicine forever but we need all NHS staff, patients and the public to recognise and embrace its huge potential. said Davies.

Sir Harpal Kumar, Cancer Research UKs chief executive, agreed, saying that it would be a disservice to patients if the UK were slow to respond to innovations in this area.

The report recommends that within 5 years training should be available to current and future clinicians and that all patients should be being offered genomic tests just as readily as theyre given MRI scans today.

Davies also called for research and international collaboration to be prioritised, along with investment in research and services so that patients across the country have equal access.

However the report recognises potential challenges such as data protection issues and attitudes of clinicians and the public.

This timely report from the chief medical officer showcases just how much is now possible in genomics research and care within the NHS, added Sir Kumar.

Cancer Research UK is determined to streamline research, to find the right clinical trial for cancer patients and to ensure laboratory discoveries benefit patients.

And the design of clinical trials are starting to change. A number of trials are underway, like Cancer Research UKs National Lung Matrix Trial with AstraZeneca and Pfizer, where patients with a certain type of lung cancer are assigned a specific treatment based on the genetic makeup of their cancer.

However, Sir Harpal Kumar stressed that to bring the reports vision to life the Government, the NHS, regulators and research funders need to act together.

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Patients Who Tested Positive For Genetic Mutations Fear Bias … – NPR – NPR

Patients who underwent genetic screenings now fear that documentation of the results in their medical records could lead to problems if a new health law is enacted. Sam Edwards/Caiaimage/Getty Images hide caption

Patients who underwent genetic screenings now fear that documentation of the results in their medical records could lead to problems if a new health law is enacted.

Two years ago, Cheasanee Huette, a 20-year-old college student in Northern California, decided to find out if she was a carrier of the genetic mutation that gave rise to a disease that killed her mother. She took comfort in knowing that whatever the result, she'd be protected by the Affordable Care Act's guarantees of insurance coverage for pre-existing conditions.

Her results came back positive. Like her mother, she's a carrier of one of the mutations known as Lynch syndrome. The term refers to a cluster of mutations that can boost the risk of a wide range of cancers, particularly colon and rectal.

As Republican lawmakers advance proposals to overhaul the ACA's consumer protections, Huette frets that her future health coverage and employment options will be defined by that test.

She even wonders if documentation of the mutation in her medical records and related screenings could rule out individual insurance plans. She's currently covered under her father's policy. "Once I move to my own health care plan, I'm concerned about who is going to be willing to cover me, and how much will that cost," she says.

In recent years, doctors have urged patients to be screened for a variety of diseases and predisposition to illness, confident it would not affect their future insurability. Being predisposed to an illness such as carrying the BRCA gene mutations associated with breast and ovarian cancer does not mean a patient will come down with the illness. But knowing they could be at risk may allow patients to take steps to prevent its development.

Under the current health law, many screening tests for widespread conditions such as prediabetes are covered in full by insurance. The Centers for Disease Control and Prevention and the American Medical Association have urged primary care doctors to test patients at risk for prediabetes. But doctors, genetic counselors and patient advocacy groups now worry that people will shy away from testing as the ACA's future becomes more uncertain.

Dr. Kenneth Lin, a family physician at Georgetown University School of Medicine in Washington, D.C., says if the changes proposed by the GOP become law, "you can bet that I'll be even more reluctant to test patients or record the diagnosis of prediabetes in their charts." He thinks such a notation could mean hundreds of dollars a month more in premiums for individuals in some states under the new bill.

Huette says she's sharing her story publicly since her genetic mutation is already on her medical record.

But elsewhere, there have been "panicked expressions of concern," says Lisa Schlager of the patient advocacy group Facing Our Risk of Cancer Empowered (FORCE). "Somebody who had cancer even saying, 'I don't want my daughter to test now.' Or 'I'm going to be dropped from my insurance because I have the BRCA mutation.' There's a lot of fear."

Those fears, which come in an era of accelerating genetics-driven medicine, rest upon whether a gap that was closed by the ACA will be reopened. That remains unclear.

A law passed in 2008, the Genetic Information Nondiscrimination Act, bans health insurance discrimination if someone tests positive for a mutation. But that protection stops once the mutation causes "manifest disease" essentially, a diagnosable health condition.

That means "when you become symptomatic," although it's not clear how severe the symptoms must be to constitute having the disease, says Mark Rothstein, an attorney and bioethicist at the University of Louisville School of Medicine in Kentucky, who has written extensively about GINA.

The ACA, passed two years after GINA, closed that gap by barring health insurance discrimination based on pre-existing conditions, Rothstein says.

On paper, the legislation unveiled by Senate Majority Leader Mitch McConnell last week wouldn't let insurers set higher rates for people with pre-existing conditions, but it could effectively exclude such patients from coverage by allowing states to offer insurance plans that don't cover certain maladies, health analysts say. Meanwhile, the bill that passed the House last month does have a provision that allows states to waive protections for people with pre-existing conditions, if they have a gap in coverage of 63 days or longer in the prior year.

When members of a Lynch Syndrome social media group were asked for their views on genetic testing amid the current health care debate, about two dozen men and women responded. Nearly all said they were delaying action for themselves or suggesting that family members, particularly children, hold off.

Huette was the only one who agreed to speak for attribution. She says before the ACA was enacted, she witnessed the impact that fears about insurance coverage had on patients. Her mother, a veterinarian, had wanted to run her own practice but instead took a federal government job for the guarantee of health insurance. She died at the age of 57 of pancreatic cancer, one of six malignancies she had been diagnosed with over the years.

Huette says she doesn't regret getting tested. Without the result, Huette points out, how would she have persuaded a doctor to give her a colonoscopy in her 20s?

"Ultimately, my health is more important than my bank account," she says.

Kaiser Health News, a nonprofit health newsroom whose stories appear in news outlets nationwide, is an editorially independent part of the Kaiser Family Foundation.

Patients Who Tested Positive For Genetic Mutations Fear Bias ... - NPR - NPR

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Genetic Testing for the Healthy – Harvard Medical School (registration)

Whole genome sequencing involves the analysis of all three billion pairs of letters in an individuals DNA and has been hailed as a technology that will usher in a new era of predicting and preventing disease.

However, the use of genome sequencing in healthy individuals is controversial because no one fully understands how many patients carry variants that put them at risk for rare genetic conditions and how theyand their doctorswill respond to learning about these risks.

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In a new paper published June 26 in the Annals of Internal Medicine by investigators at Harvard Medical School and Brigham and Womens Hospital, along with collaborators at Baylor College of Medicine, report the results of the four-year, NIH-funded MedSeq Project, the first-ever randomized trial conducted to examine the impact of whole genome sequencing in healthy primary care patients.

In the MedSeq Project, 100 healthy individuals and their primary care physicians were enrolled and randomized so that half of the patients received whole genome sequencing and half did not.

Nearly 5,000 genes associated with rare genetic conditions were expertly analyzed in each sequenced patient, and co-investigators from many different disciplines, including clinical genetics, molecular genetics, primary care, ethicsand law, were involved in analyzing the results.

Researchers found that among the 50 healthy primary care patients who were randomized to receive genome sequencing, 11 (22 percent) carried genetic variants predicted to cause previously undiagnosed rare disease.

Two of these patients were then noted to have signs or symptoms of the underlying conditions, including one patient who had variants causing an eye disease called fundus albipunctatus, which impairs night vision.

This patient knew he had difficulty seeing in low-light conditions but had not considered the possibility that his visual problems had a genetic cause.

Another patient was found to have a genetic variant associated with variegate porphyria, which finally explained the patients and family members mysterious rashes and sun sensitivity.

The other nine participants had no evidence of the genetic diseases for which they were predicted to be at risk. For example, two patients had variants that have been associated with heart rhythm abnormalities, but their cardiology workups were normal. It is possible, but not at all certain, that they could develop heart problems in the future.

Sequencing healthy individuals will inevitably reveal new findings for that individual, only some of which will have actual health implications, said lead author Jason Vassy,an HMS assistant professor of medicine at Brigham and Womens and primary care physician at the VA Boston Healthcare System.

This study provides some reassuring evidence that primary care providers can be trained to manage their patients sequencing results appropriately, and that patients who receive their results are not likely to experience anxiety connected to those results. Continued research on the outcomes of sequencing will be needed before the routine use of genome sequencing in the primary care of generally healthy adults can be medically justified, Vassy said.

Primary care physicians received six hours of training at the beginning of the study regarding how to interpret a specially designed, one-page genome testing report summarizing the laboratory analysis.

Consultation with genetic specialists was available, but not required. Primary care physicians then used their own judgment about what to do with the information, and researchers monitored the interactions for safety and tracked medical, behavioral and economic outcomes.

The researchers noted that they analyzed variants from nearly 5,000 genes associated with rare genetic diseases. These included single genes causing a significantly higher risk for rare disorders than the low-risk variants for common disorders reported by direct-to-consumer genetic testing companies. No prior study has ever examined healthy individuals for pathogenic (high-risk) variants in so many rare disease genes.

We were surprised to see how many ostensibly healthy individuals are carrying a risk variant for a rare genetic disease, said Heidi Rehm, HMS associate professor of pathology at Brigham and Women's anddirector of the Laboratory for Molecular Medicine at Brigham and Women's.

We found that about one-fifth of this sample population carried pathogenic variants, and this suggests that the potential burden of rare disease risk throughout our general population could be far higher than previously suspected,said Rehm, a co-investigator on the study who directed the genome analysis.However, the penetrance, or likelihood that persons carrying one of these variants will eventually develop the disease, is not fully known.

Additionally, investigators compared the two arms of the studyand found that patients who received genome sequencing results did not show higher levels of anxiety. They did, however, undergo a greater number of medical tests and incurred an average of $350 more in health care expenses in the six months following disclosure of their results. The economic differences were not statistically significant with the small sample size in this study.

Because participants in the MedSeq Project were randomized, we could carefully examine levels of anxiety or distress in those who received genetic risk information and compare it to those who did not, said Amy McGuire,director of the Center for Medical Ethics and Health Policy at Baylor College of Medicine.

While many patients chose not to participate in the study out of concerns about what they might learn, or with fears of future insurance discrimination, those who did participate evinced no increase in distress, even when they learned they were carrying risk variants for untreatable conditions, saidMcGuire, who supervised the ethical and legal components of the MedSeq Project.

There has also been great concern in the medical community about whether primary care physicians can appropriately manage these complicated findings. But when a panel of expert geneticists reviewed how well the primary care physicians managed the patients with possible genetic risk variants, the experts determined that only two of the 11 cases were managed inappropriately and that no harm had come to these patients.

MedSeq Project investigators note that the studys findings should be interpreted with caution because of the small sample size and because the study was conducted at an academic medical center where neither the patients nor the primary care physicians are representative of the general population. They also stressed that carrying a genetic risk marker does not mean that patients have or will definitely get the disease in question. Critical questions remain about whether discovering such risk markers in healthy individuals will actually provide health benefits, or will generate unnecessary testing and subsequent procedures that could do more harm than good.

Integrating genome sequencing and other -omics technologies into the day-to-day practice of medicine is an extraordinarily exciting prospect with the potential to anticipate and prevent diseases throughout an individuals lifetime, said senior author Robert C. Green, HMSprofessor of medicineat Brigham and Womens Hospital,associate member of the Broad Institute of Harvard and MITandleader ofthe MedSeq Project. But we will need additionalrigorously designed and well-controlled outcomes studies like the MedSeq Project with larger sample sizes and with outcomes collected over longer periods of time to demonstrate the full potential of genomic medicine.

The MedSeq Project is one of the sites in the Clinical Sequencing Exploratory Research Consortium and was funded by the National Human Genome Research Institute, part of the National Institutes of Health.

The Genomes2People Research Program at Brigham and Womens Hospital, the Broad Institute and Harvard Medical School conducts empirical research in translational genomics and health outcomes. NIH-funded research within G2P seeks to understand the medical, behavioral and economic impact of using genetic risk information to inform future standards. The REVEAL Study has conducted several randomized clinical trials examining the impact of disclosing genetic risk for a frightening disease. The Impact of Personal Genomics (PGen) Study examined the impact of direct-to-consumer genetic testing on over 1,000 consumers of two different companies. The MedSeq Project has conducted the first randomized clinical trial to measure the impact of whole genome sequencing on the practice of medicine. The BabySeq Project is recruiting families of both healthy and sick newborns into a randomized clinical trial where half will have their babys genome sequenced. Green directs the Program.

Adapted from a Brigham and Women's news release.

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Researchers build SEQSpark to analyze massive genetic data sets – Medical Xpress

June 30, 2017

Uncovering rare susceptibility variants that contribute to the causes of complex diseases requires large sample sizes and massively parallel sequencing technologies. These sample sizes, often made up of exome and genome data from tens to hundreds of thousands of individuals, are often too large for current analytical tools to process. A team at Baylor College of Medicine, led by Dr. Suzanne Leal, professor of molecular and human genetics, has developed new software called SEQSpark to overcome this processing obstacle. A study on the new technology appears in The American Journal of Human Genetics.

"To handle these large data sets, we built the SEQSpark tool based on the commonly used Spark program, which allows SEQSpark to utilize multiple processing platforms to increase the speed and efficiency of performing data quality control, annotation and rare variant association analysis," Leal said.

To test and validate the versatility and speed of SEQSpark, Leal and her team analyzed benchmarks from the whole genome sequence data from the UK10K, testing specifically for waist-to-hip ratios.

"The analysis and related tasks took about one and a half hours to complete, in total. This includes loading the data, annotation, principal components analysis and single and rare variant aggregate association analysis for the more than 9 million variants present in this sample set," explained Di Zhang, a postdoctoral associate in the Leal lab at Baylor and first author on the paper.

To evaluate SEQSpark's performance in a larger data set, Leal and the research team generated 50,000 simulated exomes. The SEQSprak program ran the analysis for a quantitative trait using several variant aggregate association methods in an hour and forty-five minutes.

When compared to other variant association tools, SEQSpark was consistently faster, reducing computation to a hundredth of the time in some cases.

"What is unique about SEQSpark is that it is scalable, and smaller labs can run it without super specific hardware, and it can also be run in a multi-server environment to increase its speed and capacity for large genetic data sets," Zhang said. "It is ideal for large-scale genetic epidemiological studies and is highly efficient from a computational standpoint."

"We see this software as being very useful as the demand for the analysis of massively parallel sequence data grows. SEQSpark is highly versatile, and as we analyze increasingly large sets of rare variant data, it has the potential to play a key role in furthering personalized medicine," Leal said.

In the future, Leal and her team will continue to test and increase SEQSpark's capabilities and will be analyzing soon data sets that have 500,000 samples or more.

Explore further: Genetic test for familial data improves detection genes causing complex diseases such as Alzheimer's

More information: Di Zhang et al. SEQSpark: A Complete Analysis Tool for Large-Scale Rare Variant Association Studies using Whole-Genome and Exome Sequence Data, The American Journal of Human Genetics (2017). DOI: 10.1016/j.ajhg.2017.05.017

A team of researchers at Baylor College of Medicine has developed a family-based association test that improves the detection in families of rare disease-causing variants of genes involved in complex conditions such as Alzheimer's. ...

Precision medicine, which utilizes genetic and molecular techniques to individually tailor treatments and preventative measures for chronic diseases, has become a major national project, with President Obama launching the ...

A multi-institutional team of researchers has sequenced the DNA of 6,700 exomes, the portion of the genome that contains protein-coding genes, as part of the National Heart, Lung and Blood Institute (NHLBI)-funded Exome Sequencing ...

(Medical Xpress)Via genetic analysis, a large international team of researchers has found rare, damaging gene variants that they believe contribute to the risk of a person developing schizophrenia. In their paper published ...

Human genome sequencing costs have dropped precipitously over the last few years, however the analytical ability to meet the growing demand for making sense of large data sets remains as a bottleneck. With the introduction ...

Researchers at EMBL-EBI have developed a new approach to studying the effect of multiple genetic variations on different traits. The new algorithm, published in Nature Methods, makes it possible to perform genetic analysis ...

Following up on findings from a an earlier genome-wide association study (GWAS) of type 2 diabetes (T2D) in Latinos, researchers from the Broad Institute of MIT and Harvard and Massachusetts General Hospital (MGH) traced ...

Although the basic outlines of human hearing have been known for years - sensory cells in the inner ear turn sound waves into the electrical signals that the brain understands as sound - the molecular details have remained ...

Using a new skin cell model, researchers have overcome a barrier that previously prevented the study of living tissue from people at risk for early heart disease and stroke. This research could lead to a new understanding ...

The first results from a functional genetic catalogue of the laboratory mouse has been shared with the biomedical research community, revealing new insights into a range of rare diseases and the possibility of accelerating ...

Whole genome sequencing involves the analysis of all three billion pairs of letters in an individual's DNA and has been hailed as a technology that will usher in a new era of predicting and preventing disease. However, the ...

Researchers have found that genes for coronary heart disease (CAD) also influence reproduction, so in order to reproduce successfully, the genes for heart disease will also be inherited.

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Researchers build SEQSpark to analyze massive genetic data sets - Medical Xpress

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