Category Archives: Genome

Researchers from Stanford University have a developed a method dubbed genome cloaking, which keeps a patients private genetic information protected when doctors analyze complete human genomes.

The method uses cryptography to hide almost 99 percent of genetic information, while allowing researchers to access specific gene mutations, according to the study. Now researchers can scour complete genomes -- without seeing any genetic information irrelevant to the inquiry.

The cloaking technique could alleviate privacy and potential discrimination concerns when it comes to genomic sequencing.

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We now have the tools in hand to make certain that genomic discrimination doesnt happen, Gill Bejerano associate professor of developmental biology, of pediatrics and of computer science at Stanford said in a statement.

There are ways to simultaneously share and protect this information, he added. Now we can perform powerful genetic analyses while also completely protecting our participants privacy.

The genome cloaking approach lets patients encrypt their genetic data using an algorithm on their computer or smart device. The researchers said the information is uploaded into the cloud, where researchers use a multi-party computation to analyze the data and reveal only the necessary gene variants relevant to the investigation.

This means that no one has access to the complete set of genetic data other than the patient, Bejerano explained.

The researchers hope that this method -- if routinely implemented -- could help patients overcome access concerns that may be preventing them from sharing their genomic data. Many patients are concerned about how their genomic sequence could be used against them -- like in obtaining insurance.

Often people who have diseases, or those who know that a particular genetic disease runs in their family, are the most reluctant to share their genomic information because they know it could potentially be used against them in some way, Bejerano said.

They are missing out on helping themselves and others by allowing researchers and clinicians to learn from their DNA sequences.

Twitter:@JessieFDavis Email the writer: jessica.davis@himssmedia.com

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Genome cloaking can protect patient privacy, Stanford researchers say - Healthcare IT News

A cryptographer and a geneticist walk into a seminar room. An hour later, after a talk by the cryptographer, the geneticist approaches him with a napkin covered in scrawls. The cryptographer furrows his brow, then nods. Nearly two years later, they reveal the product of their combined prowess: an algorithm that finds harmful mutations without actually seeing anyones genes.

The goal of the scientists, Stanford University cryptographer Dan Boneh and geneticist Gill Bejerano, along with their students, is to protect the privacy of patients who have shared their genetic data. Rapid and affordable genome sequencing has launched a revolution in personalized medicine, allowing doctors to zero in on the causes of a disease and propose tailor-made solutions. The challenge is that such comparisons typically rely on inspecting the genes of many different patientsincluding patients from unrelated institutions and studies. The simplest means to do this is for the caregiver or scientist to obtain patient consent, then post every letter of every gene in an anonymized database. The data is usually protected by licensing agreements and restricted registration, but ultimately the only thing keeping it from being shared, de-anonymized or misused is the good behavior of users. Ideally, it should be not just illegal but impossible for a researchersay, one who is hacked or who joins an insurance companyto leak the data.

When patients share their genomes, researchers managing the databases face a tough choice. If the whole genome is made available to the community, the patient risks future discrimination. For example, Stephen Kingsmore, CEO of Rady Children's Institute for Genomic Medicine, encounters many parents in the military who refuse to compare their genomes with those of their sick children, fearing they will be discharged if the military learns of harmful mutations. On the other hand, if the scientists share only summaries or limited segments of the genome, other researchers may struggle to discover critical patterns in a diseases genetics or to pinpoint the genetic causes of individual patients health problems.

Boneh and Bejerano promise the best of both worlds using a cryptographic concept called secure multiparty computation (SMC). This is, in effect, an approach to the millionaires problema hypothetical situation in which two individuals want to determine who is richest without revealing their net worth. SMC techniques work beautifully for such conjectural examples, but with the exception of one Danish sugar beet auction, they have almost never been put into practice. The Stanford groups work, published last week in Science, is among the first to apply this mind-bending technology to genomics. The new algorithm lets patients or hospitals keep genomic data private while still joining forces with faraway researchers and clinicians to find disease-linked mutationsor at least that is the hope. For widespread adoption, the new method will need to overcome the same pragmatic barriers that often leave cryptographic innovations gathering dust.

Intuitively, Boneh and Bejeranos plan seems preposterous. If someone can see they can leak it. And how could they infer anything from a genome they cant see? But cryptographers have been grappling with just such problems for years. Cryptography lets you do a lot of things like [SMC]keep data hidden and still operate on that data, Boneh says. When Bejerano attended Bonehs talk on recent developments in cryptography, he realized SMC was a perfect fit for genomic privacy.

The particular SMC technique that the Stanford team wedded to genomics is known as Yaos protocol. Say, for instance, that Alice and Bobthe ever-present denizens of cryptographers imaginationswant to check whether they share a mutation in gene X. Under Yaos protocol Alice (who knows only her own genome) writes down the answer for every possible combination of her and Bobs genes. She then encrypts each one twiceanalogous to locking it behind two layers of doorsand works with Bob to find the correct answer by strategically arranging a cryptographic garden of forking paths for him to navigate.

She sets up outer doors to correspond to the possibilities for her gene. Call them Alice doors: If Bob enters door 3, any answers he finds inside will assume that Alice has genetic variant 3. Behind each Alice door, Alice adds a second layer of doorsthe Bob doorscorresponding to the options for Bobs gene. Each combination of doors leads to the answer for the corresponding pair of Alice and Bobs genes. Bob then simply has to get the right pair of keys (essentially passwords) to unlock the doors. By scrambling the order of the doors and carefully choosing who gets to see which keys and labels, Alice can ensure that the only answer Bob will be able to unlock is the correct one, although still preventing herself from learning Bobs gene or vice versa.

Using a digital equivalent of this process, the Stanford team demonstrated three different kinds of privacy-preserving genomic analyses. They searched for the most common mutations in patients with four rare diseases, in all cases finding the known causal gene. They also diagnosed a babys illness by comparing his genome with those of his parents. Perhaps the researchers biggest triumph was discovering a previously unknown disease gene by having two hospitals search their genome databases for patients with identical mutations. In all cases the patients full genomes never left the hands of their care providers.

In addition to patient benefits keeping genomes under wraps would do much to soothe the minds of the custodians of those genome databases, who fear the trust implications of a breach, says Giske Ursin, director of the Cancer Registry of Norway. We [must] always be slightly more neurotic, she says. Genomic privacy likewise offers help for second- and third-degree relatives, [who] share a significant fraction of the genome, notes Bejeranos student Karthik Jagadeesh, one of the papers first authors. Bejerano further points to the conundrums genomicists face when they spot harmful mutations unrelated to their work. The ethical question of what mutations a genomicist must scan for or discuss with the patient does not arise if most genes stayed concealed.

Bejerano argues the SMC technique makes genomic privacy a practical option. Its a policy statement, in some sense. It says, If you want to both keep your genome private and use it for your own good and the good of others, you can. You should just demand that this opportunity is given to you.

Other researchers and clinicians, although agreeing the technique is technically sound, worry that it faces an uphill battle on the practical side. Yaniv Erlich, a Columbia University assistant professor of computer science and computational biology, predicts the technology could end up like PGP (pretty good privacy) encryption. Despite its technical strengths as a tool for encrypting e-mails, PGP is used by almost no onelargely because cryptography is typically so hard to use. And usability is of particular concern to medical practitioners: Several echo Erlichs sentiment that their priority is diagnosing and treating a condition as quickly as possible, making any friction in the process intolerable. Its great to have it as a tool in the toolbox, Erlich says, but my senseis that the field is not going in this direction.

Kingsmore, Erlich and others are also skeptical that the papers approach would solve some of the real-world problems that concern the research and clinical communities. For example, they feel it would be hard to apply it directly to oncology, where genomes are useful primarily in conjunction with detailed medical and symptomatic records.

Still, Kingsmore and Erlich do see some potential for replacing todays clunky data-management mechanisms with more widespread genome sharing. In any case, the takeaway for Bejerano is not that genome hiding is destined to happen, but that it is a technological possibility. You would think we have no choice: If we want to use the data, it must be revealed. Now that we know that is not true, it is up to society to decide what to do next.

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Cryptographers and Geneticists Unite to Analyze Genomes They Can't See - Scientific American

A new survey suggests that Americans are becoming more accepting of the use of genome editing in humans, andthere is strong support for morepublic involvement in discussions on the technology.

The results, published in the journal Science, come just one week after scientists successfully usedgenome editing to correct a disease-causing mutation in human embryos (see BioNews 912). The surveyaimed to gauge the American public's attitudes toward the technology, and ascertain whether they want to be included in shaping future policy around its use.

Around two-thirds of respondents felt that 'therapeutic' genome editing to treat disease in humans was generally acceptable, an increase from previous surveys (see BioNews 862). This included treatments that would correct mutations in both somatic cells and germ cells, such as eggs and sperm. However, that support dropped when it came to using genome editing to enhance healthy humans (e.g to increase IQ or change eye colour), with only one-third of respondents feeling that this was an acceptable use.

The survey, conducted by researchers from the University of Madison-Wisconsin,the Morgridge Institute for Research, Wisconsin, and Temple University in Philadelphia, Pennsylvania, also found that a respondent's religious beliefs and level of scientific knowledge influenced their level of support.

People with religious beliefs were generally less supportive for both treatment and enhancement purposes than people who classed themselves as not religious, while respondents with a higher level of scientific knowledge were more likely to be supportive of genome editing for disease treatment than those with less. Interestingly, high-knowledge respondents had strong views both for and against human genome editing for enhancement, with about 41 per cent being supportive and a similar percentage being against it, while around half of low-knowledge respondents were neither for nor against this use of genome editing.

Despite the split in opinion on acceptable uses of genome editing, almost all respondents agreed that the public should be involved in conversations between scientists and policymakers about the role genome editing will play in society. However, it is still unclear how that process of dialogue with the public will happen.

Professor Dietram Schufele at the University of Madison-Wisconsin, who led the research, said: 'The public may be split along lines of religiosity or knowledge with regard to what they think about the technology and scientific community, but they are united in the idea that this is an issue that requires public involvement Our findings show very nicely that the public is ready for these discussions and that the time to have the discussions is now, before the science is fully ready and while we have time to carefully think through different options regarding how we want to move forward.'

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Americans becoming open to human genome editing - BioNews

Research News

Understanding the connection microorganisms have with our bodies may enable the development of precision medicine and empower individuals to have greater control over their health.

Published August 21, 2017

Four studies focused on improving our understanding of the human genome and microbiome were awarded funding through the third round of research pilots supported by UBs Community of Excellence in Genome, Environment and Microbiome (GEM).

The projects, which total $150,000, will study how the relationship between the human body and the collection of microorganisms that reside on or within it affect our risk for certain diseases.

Understanding the connection these microorganisms have with our bodies may enable the development of precision medicine and empower individuals to have greater control over their health.

The pilot grants award researchers from a variety of disciplines up to $50,000 to develop innovative projects focused on the microbiome. The funds support up to one year of research.

The awards are provided through GEM, an interdisciplinary community of UB faculty and staff dedicated to advancing research on the genome and microbiome. GEM is one of UBs three Communities of Excellence, a $9 million initiative to harness the strengths of faculty and staff from fields across the university to confront the challenges facing humankind through research, education and engagement.

Changes in the genome our own or those of the microbes in, on or around us have a tremendous impact on human health and our environment, says Jennifer Surtees, GEM co-director and associate professor in the Department of Biochemistry in the Jacobs School of Medicine and Biomedical Sciences.

With these newest projects, UB scientists from across disciplines have come together to dig deeper into these changes and to help establish the infrastructure necessary for advanced precision medicine.

Along with Surtees, GEM is led by Timothy Murphy, executive director and SUNY Distinguished Professor in the Department of Medicine; and Norma Nowak, co-director, professor in the Department of Biochemistry, and executive director of UBs New York State Center of Excellence in Bioinformatics and Life Sciences.

The funded projects involve faculty teams from the Jacobs School of Medicine and Biomedical Sciences, the School of Public Health and Health Professions, and the School of Dental Medicine.

Inflammation in the central nervous system can increase susceptibility to seizures.

Given the role the intestinal microbiome plays in shaping inflammation in the body, UB researchers believe the tiny organisms may have an impact on the onset, strength and duration of seizures.

The study, led by Ira J. Blader, professor in the Department of Microbiology and Immunology, and Alexis Thompson, senior research scientist in UBs Research Institute on Addictions, will examine in mice the composition of the microbiome and which of its components affect seizures.

If correct, this may suggest the gut microbiome as a therapeutic target for the treatment of seizures and epilepsy.

To better understand how the human genome and microbiome interact to influence health, UB researchers will establish Spit For Buffalo, a project that will collect DNA samples from volunteer UBMD patients for use in future studies.

The researchers will collect saliva samples, anonymously link the samples to each patients electronic medical record, and sequence the genome and oral microbiome. By determining which genes are associated with which diseases, new connections between specific genes and diseases will be made.

Samples currently are being collected from patients in the UBMD Neurology, Internal Medicine and OBGYN clinics in the Conventus Center for Collaborative Medicine.

The project will provide an infrastructure resource for genome and microbiome investigations at UB.

The research is led by Richard M. Gronostajski, professor in the Department of Biochemistry and director of both the WNY Stem Cell Culture and Analysis Center and the Genetics, Genomics and Bioinformatics Graduate Program; Gil I. Wolfe, professor and Irvin and Rosemary Smith Chair of the Department of Neurology; Michael Buck, associate professor in the Department of Biochemistry and director of the WNY Stem Cell Sequencing/Epigenomics Center; and Nowak.

The parasite Trypanosoma brucei, the cause of Human African Trypanosomiasis commonly known as sleeping sickness radically alters its physiology and morphology as it moves between insect and mammal over the course of its life cycle.

These changes, researchers have found, are caused by various RNA binding proteins, allowing the organism to survive in environments that range from the human bloodstream to the insect gut. UB researchers will examine how these proteins regulate the parasites transformations.

The study is led by Laurie K. Read, professor in the Department of Microbiology and Immunology; and Jie Wang, research assistant professor in the Department of Biochemistry.

UB researchers will investigate the connection between oral and gut bacteria and the onset and progression of atherosclerotic cardiovascular disease (CVD), or the buildup of plaque around the artery walls that eventually blocks blood flow.

The study will seek to understand how the microbes in the body contribute to plaque formation in the arteries, providing the basis for interventions that reduce the effects of the microorganisms on CVD.

Previous studies have found microbes present in arterial plaques, but have not provided conclusive links to the parts of the body where the microbes originate. Researchers will use next-generation sequencing and advanced bioinformatics analysis methods to identify and characterize microorganisms in the artery walls and compare the bacteria with those present in oral, gut and skin microbiomes.

Environmental factors such as smoking, blood cholesterol and periodontal disease status also will be examined as potential factors that influence the bacteria-CVD relationship.

The research is led by Robert J. Genco, SUNY Distinguished Professor in the departments of Oral Biology and Microbiology and Immunology, and director of the UB Microbiome Center; and Michael J. LaMonte, research associate professor in the Department of Epidemiology and Environmental Health.

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GEM awards $150000 in third round of funding for microbiome and genomic research - University at Buffalo Reporter

SAN FRANCISCO--(BUSINESS WIRE)--Now based in the genomics center of the Silicon Valley, the consumer genomic startup, AWAKENS, Inc., hails from Tokyo, Japan. Though consumer genomics is just picking up the pace, the founders at AWAKENS envision a future in which every human owns and can easily access their whole genome data. AWAKENS was founded with the goal of empowering each individual to build a smarter and healthier lifestyle based on their genetic makeup, and to transform consumer genomics.

AWAKENS has launched their first consumer product GENOMIC EXPLORER (https://genomicexplorer.io). The service is currently free for genome data holders, such as those who have taken ancestry genetic tests. New users can order their whole genome sequence through the website (https://genomicexplorer.io). Users with whole genome data will also be able to upload their data soon.

Visualize Your Inner Universe with GENOMIC EXPLORER

Full access to whole genome data and reliable information on how to interpret the data is AWAKENS top value proposition. Most genetic testing services today read only 0.03% of the genome. GENOMIC EXPLORER reads and visualizes 100%.

AWAKENS strives to visualize what existing genetic testing services have abstracted in their genetic reports. You can browse through a comprehensive visual representation of your genome and learn about 100+ traits: this tool connects your genome data to an in-house annotation database, which tells you how specific regions of the genome can be understood. Traits include personality, intelligence, and nutrition. The only information serving the purpose of science education are released in the U.S for now. Information on medical traits, such as the risk for a certain disease, will be provided in the future as partnerships with healthcare institutions and healthcare companies are established.

Today for the genome is like the 90s for the Internet. Although technological innovations made the Internet accessible for many, applications for daily use had not been developed. Everyone was scrambling to figure out how to make the best use of the Internet, explained Tomohiro Takano, CEO and Co-Founder of AWAKENS, Inc. Through partnerships with many industries, we at AWAKENS are striving to unlock the vast potential of the whole genome. We want to develop an ecosystem where anyone can access valuable information, actionable insights, and related services based on their genetic information.

The field of genomics

15 years ago, sequencing the whole genome cost 3 billion USD. 5-10 years from now, the price will drop to a few hundred USD. Against the backdrop of these circumstances, we can expect to gain access to a wide range of consumer genomics services in our daily lives, spanning medicine, healthcare, nutrition, fitness, and education. Soon, pharmacogenomics will inform drug efficacy and risk of serious side effects at the individual level. Beyond medical applications, academic research in fitness and genomics, nutrigenomics, and educational genomics are booming. The potential for consumer applications will only grow from here.

About AWAKENS, Inc.

AWAKENS is a genomic software company transforming the landscape of consumer genomics. They empower consumers with easily accessible insights of their own genome data, and diversify consumer genomics services by providing an API toolkit for existing services to provide personalized solutions tailored to each persons genetic makeup. Founded in January 2017 in Tokyo, Japan, AWAKENS is currently located in the genomic center in Silicon Valley. The companys products include the consumer-facing GENOMIC EXPLORER and the business-facing GENOME LINK.

Awakens is funded by private corporations and angel investors (as of Aug 2017):

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AWAKENS, Inc., a Japanese Consumer Genomics Startup ... - Business Wire (press release)

LA JOLLA, Calif., Aug. 20, 2017 /PRNewswire/ -- Tom Wamberg, one of the nation's foremost experts on employee benefits and insurance, today announced the formation of Wamberg Genomic Advisors (WGA). WGA advises employers, employee benefit brokers, and life insurance companies, enabling them to create programs that provide employees and policyholders with easy access to affordable genomic tests.

Genomics is the study of the structure and function of genomes, including all of an individual's genes. In contrast, genetics focuses on the variation and function of single or limited numbers of genes within a genome. In the context of human health, genomics seeks to identify the interrelation of factors beyond genes, which can lead to a deeper understanding of the risk of disease, resulting in more effective preventive measures or treatments. Genetics looks for specific mutations or variations within genes, rather than the entire genome. While genetics provides important information in understanding a person's health status or risk for certain diseases or conditions, the information that can be learned from examining an entire genome is broader.

"Knowledge of a person's genome is enabling medical professionals to develop personalized health strategies, treatments, and care paths that can be used to better manage or prevent disease and enhance health and longevity," said Wamberg. "When patients are empowered with this knowledge, they can become more actively engaged in managing their own health and make better decisions. As more people have their genome sequenced and analyzed, the medical and health care communities are better equipped to provide deeper insights into risk and disease, and make new medical discoveries.

"Our mission is to help drive the genomic revolution by making genomic testing readily accessible and affordable for everyone," added Wamberg. "The most promising avenues for widespread delivery of genomic testing are employee benefit programs and life insurance policies."

For more than three decades, Wamberg has developed innovative benefit and financial strategies for employers of all sizes, from emerging growth companies to the Fortune 100, as well as life insurance companies. Before starting WGA, Wamberg was chairman and CEO of Clark Consulting, a leader in the executive benefits space. In addition to serving as CEO of WGA, Wamberg is chairman of Uniphy Health LLC, which he co-founded, and a member of the Board of Trustees of Cleveland Clinic.

WGA will focus initially on the following types of genomic products and services:

Whole genome sequencing and reporting. The most comprehensive method for analyzing the genome

Exome sequencing and reporting. Information on all the genes that express proteins in a genome

Cancer genomic profiling. Sequencing of a cancer tumor to learn about coding mutations that contribute to tumor progression

Cancer liquid biopsy. Blood test that today can be used in limited circumstances to detect cancer genomic material circulating in the blood, such as when sufficient tumor material is unavailable

Lifetime stem cell banking. Stem cells gathered at birth to serve as a source of cellular material for the treatment of conditions throughout a person's life

Lifetime connectivity to one's DNA. Information and updates on variations in a person's genome when compared against constantly updated genomic databases

About Wamberg Genomic Advisors

Wamberg Genomic Advisors (WGA) is your partner in the Genomic Revolution. Our mission to make genomic testing readily available at prices everyone can afford. Our focus is on delivering genomic products and services to employers and their employees via their trusted benefit brokers, and policyholders of life insurance companies. To discover more about WGA and the future of genomics, visitwamberggenomic.com.

View original content with multimedia:http://www.prnewswire.com/news-releases/wamberg-genomic-advisors-launched-to-provide-easy-access-to-affordable-genomic-testing-300506867.html

SOURCE Wamberg Genomic Advisors

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Wamberg Genomic Advisors Launched to Provide Easy Access to Affordable Genomic Testing - Markets Insider

In this picture taken on June 5, 2017 a piglet is seen at a pig farm on the outskirts of Beijing. NICOLAS ASFOURI AFP/Getty Images

Organ transplants save the lives of people whose own body parts fail, yet the supply of human donor organs will never be enough to keep every one of the 116,000 patients in the United States on the transplant waiting list alive. The need for more options has never been greater. But now, we have encouraging scientific evidence that new organ transplant sources may finally be within closer reach.

In the August 10 issue of Science , we report on one of the most promising developments in the quest for safe new organ and tissue sources. For more than 100 years, humans have considered the potential for pigs to generate donor organs because they share much of the same anatomy. However, the risk of a virus endemic to pigs has stymied xenotransplantation effortsuntil now.

The virus, known as Active Porcine Endogenous Retrovirus, or PERV, is a type of retrovirus found in pig DNA. Although not always active, the risk of cross-species disease transmission has precluded the use of pig organs for human transplant.

Now, our team at eGenesis has successfully manipulated the pig embryo genome to eradicate PERV. Those modified embryos were then implanted into sows, resulting in the first-ever pigs born free of the virus. Further study of these piglets will verify the long-term results, but so far, there is no evidence of PERV in the genetic material of the new line of piglets.

This is a remarkable achievement made possible by the enormous advances in genetic engineering and our ability to understand cells and the DNA that directs how those cells function and replicate. Other barriers remain, such as organ rejection sparked by the human immune response, but these PERV-free pigs are an important step toward addressing safety concerns about cross-species virus transmission.

Our process is based on the genome-editing tool CRISPR, which refers to Clustered Regularly Interspaced Short Palindromic Repeats occurring in the genome of certain bacteria. It can selectively delete, modify, or correct a disease-causing abnormality in a specific DNA segment. CRISPR technology uses a protein-RNA complex composed of Cas-9, which binds to a guide RNA (gRNA) molecule that has been designed to recognize a particular DNA sequence.

CRISPR and next-generation genome-editing tools may also help us address other outstanding issues of using pig organs for human transplantation. Our hope is to edit the pig genome to create immune and functional compatibly between pig organs and human recipients.

There are many questions that need to be addressed before xenotransplantation becomes a clinical reality. The risk of cross-species transmission of virus has been a good reason to proceed with caution. Our scientists at eGenesis have been working toward a safe, responsible, and near-term pathway to human clinical testing, though it is too early to speculate on timelines. We have taken lessons from previous clinical experience and combined it with the latest innovations in both research and technology to power our groundbreaking platform. The potential to deliver safe and effective transplantable cells, tissues, and organs for humans around the world represents a powerful opportunity to address a dire need.

More than 20,000 people in the United States have received donor organs so far this year, but tens of thousands wait anxiously every day. Every 10 minutes, another person joins the waiting list, and every day, 20 people die because no organ was available to them. We strive to create a world where there is no organ shortage. That is the best way to honor all life and have a major impact on public health worldwide.

Luhan Yang, Ph.D. is chief scientific officer and co-founder of eGenesis.

Continue reading here:
One Day You Might Have a Pig Organ. And It Could Save Your Life. - Fortune

August 15, 2017

Whole genome sequencing using long fragment read (LFR), a technology that can analyze the entire genomic content of small numbers of cells, detected potentially targetable mutations using only five circulating tumor cells (CTCs) in a patient with metastatic breast cancer.

The study is published in Cancer Research, a journal of the American Association for Cancer Research, by Brock Peters, PhD, senior director of research at Complete Genomics Inc. in San Jose, California, and BGI-Shenzhen in Shenzhen, China; John W. Park, MD, professor of clinical medicine, and director of Novel Therapeutics, Breast Oncology, at University of California, San Francisco (UCSF); Hope S. Rugo, MD, professor of medicine and director of breast oncology and clinical trials education at UCSF.

The Complete Genomics team and colleagues from UCSF evaluated CTCs from two liquid biopsies drawn from a 61-year-old female patient with ER-positive/HER2-negative metastatic breast cancer at two different time points during her course of treatment. First, they isolated 34 highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting (IE/FACS) technology developed by Park and Mark Magbanua, PhD, at UCSF. Then they used LFR to perform advanced whole-genome sequencing by splitting the genomic DNA from the CTCs into 3,072 individual compartments, with each compartment containing approximately 5 percent of the cancer genome. The DNA in each compartment was subsequently labeled with a unique barcode, the compartments were combined, and the genomic DNA and barcodes were sequenced.

"From 34 cells we accurately detected mutations present in as few as 12 percent of CTCs, established the tissue of origin, and identified potential personalized combination therapies for this patient's highly heterogeneous disease," said Peters.

According to Peters, this research is the first application of LFR technology to CTCs. "LFR subdivides the genome into compartments, allowing us to count the fragments with somatic mutations across all the compartments to accurately quantify the number of mutations present in a population of cells. It also serves to remove false-positive single nucleotide variants," explained Peters.

"LFR, which explores the more than 20,000 genes in the genome and all non-coding regions, is more comprehensive than gene panels, which examine about 100 genes and focus on small genomic regions typically associated with a disease," he continued.

Because prior studies indicate that five CTCs can be expected in about half of the patients with metastatic disease, and evaluating 34 CTCs is cost-prohibitive, Peters and colleagues analyzed five different batches of five CTCs and replicated their findings. The researchers estimated that the cost of their advanced whole genome sequencing technique on five CTCs would be about $3,000 within the next few years, in line with current oncology diagnostic tests.

"That our sequencing method could detect the most important somatic mutations from just five CTCs in a noninvasive liquid biopsy is important, demonstrating cost-effectiveness and utility in clinical settings," said Peters.

"Our work highlights the importance and utility of using accurate and quantitative whole genome analysis in a clinical setting," said Peters. "We identified targetable mutations that would have been missed by current clinical sequencing strategies. In the near precision medicine future, this type of information will be critical for selecting effective personalized multi-drug treatments."

Study co-author John W. Park, MD, professor of clinical medicine, and director of Novel Therapeutics, Breast Oncology, at University of California, San Francisco (UCSF), said, "We observed that it is possible to develop a robust strategy for liquid biopsy using whole genome sequencing of circulating tumor cells. This approach allows detailed molecular profiling across the patient's entire cancer genome."

Study co-author, Hope S. Rugo, MD, professor of medicine and director of breast oncology and clinical trials education at UCSF, said, "The IE/FACS allows for exquisite and full-scale isolation of highly pure CTCs with little or no contamination of normal blood cells, thus providing the robustness needed for accurate whole genome sequencing of a few cells. Taken together, the liquid biopsy platform we described in this study suggests a viable approach for minimally invasive yet comprehensive and real-time testing of metastatic cancer in the clinic."

According to Peters, the main limitations to the study are that only a single patient was studied and none of the suggested possible therapies could actually be tested, emphasizing the need for larger studies.

Explore further: Researchers working on blood test to detect brain metastases while still treatable

As the field of liquid biopsies for tracking disease progression and therapeutic response heats up, many doctors are looking for ways to apply this approach to their patients. Currently, assays for circulating tumor cells ...

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Genome sequencing method can detect clinically relevant mutations using five CTCs - Medical Xpress

In a first, researchers from the Oregon Health and Science University along with colleagues in California, China and South Korea repaired a mutation in human embryos by using a gene-editing tool called CRISPR-Cas9.

The mutation seen in the MYBPC3 gene causes a common heart condition called hypertrophic cardiomyopathy, which is marked by thickening of the heart muscle.

The mutation is seen in about one in 500 people and can lead to sudden death later in life. It is an inherited cardiac disease and the presence of even one copy of the gene can cause symptoms, which usually manifest as heart failure. Correcting the mutation in the embryo ensures that the child is born healthy and the defective gene is not passed on to future generations. There is currently no cure for the condition.

CRISPR-Cas9 is a system used by bacterial cells to recognise and destroy viral DNA as a form of adaptive immunity. Using components of the CRISPR system, researchers can remove, add or alter specific DNA sequences in the genome of higher organisms.

The gene editing tool has two components a single-guide RNA (sgRNA) that contains a sequence that can bind to DNA, and the Cas9 enzyme which acts as a molecular scissor that can cleave DNA. The genetic sequence of the sgRNA matches the target sequence of the DNA that has to be edited. In order to selectively edit a desired sequence in DNA, the sgRNA is designed to find and bind to the target.

Upon finding its target, the Cas9 enzyme swings into an active form that cuts both strands of the target DNA. One of the two main DNA-repair pathways in the cell then gets activated to repair the double-stranded breaks. While one of the repair mechanisms result in changes to the DNA sequence, the other is more suitable for introducing specific sequences to enable tailored repair. In theory, the guide RNA will only bind to the target sequence and no other regions of the genome.

But the CRISPR-Cas9 system can also recognise and cleave different regions of the genome than the one that was intended to be edited. These off-target changes are very likely to take place when the gene-editing tool binds to DNA sequences that are very similar to the target one. Though many studies have found few unwanted changes suggesting that the tool is probably safe, researchers are working on safer alternatives.

Along with sperm from a man with hypertrophic cardiomyopathy, the gene-editing tool was also introduced into eggs from 12 healthy women before fertilisation. In normal conditions, a piece of DNA with the correct sequence serves as a template for the repair to work, although the efficiency can be significantly low. Instead of the repair template that was provided by the researchers, the cells used the healthy copy of the DNA from the egg as a template. This came as a big surprise.

Normally, if sperm from a father with one mutant copy of the gene is fertilized in vitro with normal eggs, 50% of the embryos would inherit the condition. When the gene-editing tool was used, 42 out of the 58 embryos did not carry the mutation. The remaining 16 embryos had unwanted additions or deletions of DNA.

Thus the probability of inheriting the healthy gene increased from 50 to 72.4%. There was no off-target snipping of the DNA. According to Nature, the edited embryos developed similarly to the control embryos, with 50% reaching an early stage of development (blastocyst). This indicates that editing does not block development.

Clinical trials are under way in China and in the U.S. to use this tool for treating cancer. In May this year, it was shown in mice that it is possible to shut down HIV-1 replication and even eliminate the virus from infected cells. In agriculture, a new breed of crops that are gene-edited will become commercially available in a few years. In February this year, the National Academy of Sciences (NAS) and the National Academy of Medicine said scientific advances make gene editing in human reproductive cells a realistic possibility that deserves serious consideration.

R. Prasad

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The lowdown on genome editing - NATIONAL - The Hindu - The Hindu

The use of genome-editing techniques in medical therapies has proved to be a promising development in the treatment of certain diseases, such as cancer, HIV and rare diseases, by genetically altering specific types of cells. Compared to other techniques used to insert, delete or replace DNA in the genome of an organism, CRISPR/Cas9 is much quicker, easier to use and less costly, may be more precise in its application, and can also be used to edit multiple genes simultaneously. The technique therefore has the potential to be a true game-changer in medicine with profound beneficial effects on human health. However, the enthusiasm for the opportunities of this promising technology should be accompanied by adequate regulatory oversight to guarantee the safety of products and applications that use this technology.

The first clinical trial using CRISPR-edited immune cells began in patients with lung cancer in China in 2016. Earlier this year, FDAs Recombinant DNA Advisory Committee did not find any objections to the first clinical protocol to use CRISPR/Cas9-mediated gene editing, and the first US clinical trial is expected to start shortly. Several more clinical trials have since been approved and started in China, including one which proposes to perform gene editing in vivo i.e. directly within the body of live patients (as opposed to ex vivo, e.g. using cells extracted from donors).

Most recently, in August 2017, a team of US-based scientists at Oregon Health and Science University published a paper describing the successful use of CRISPR/Cas9 to fix a disease-causing DNA error in dozens of early-stage human embryos, which, according to biologist Shoukrat Mitalipov, brings us much closer to clinical applications. Clinical use of this work would mean actually implanting some of these embryos with the goal of children being born that possess genes which have been artificially edited using CRISPR technology and would be capable of passing those edited genes to their offspring. These developments are exciting for patients and their loved ones, but in equal measure represent a challenge to existing regulatory structures and society at large. At any rate, with the pace of development in the CRISPR field around the world, clinical trials involving CRISPR in the EU may not be far away.

Regulators in the EU and abroad will need to stay abreast of this new (r)evolution in genome-editing technologies. In this respect, different groups established within the European Commission, including the European Group on Ethics in Science and New Technologies, have emphasised the great potential [of the CRISPR/Cas9 genome-editing technology] due to its many advantages to previous methods and acknowledged that the CRISPR/Cas9 system challenges the international regulatory landscape for the modification of human cells in the near to medium term.

While no specific regulatory guidance has been issued to date, the European Medicines Agency (EMA) has started to lay the groundwork for the regulatory implications to come, by launching a public consultation on the revision of its Guideline on medicinal products containing genetically modified cells on 20 July 2017. The EMA specifically recognises that the current 2012 guideline focuses on genetic modifications by traditional methods (based on the use of vectors carrying recombinant nucleic acids), but that the introduction of the CRISPR/Cas9 system has rapidly increased the use of genome-editing technologies to genetically modify cells ex vivo for clinical applications, and aims to take these aspects into consideration in its revised draft guideline, which is expected by March 2018.

Regulation of gene-edited products in the EU

1.EU-wide classification and authorisation of Advanced Therapy Medicinal Products

Currently, in the EU, new medicinal products based on genes (gene therapy), cells (cell therapy) and tissues (tissue engineering) also known as advanced therapy medicinal products or ATMP are regulated by the ATMP Regulation (Regulation (EC) No. 1394/2007 on advanced therapy medicinal products). The ATMP Regulation is a lex specialis supplementing the provisions of Directive 2001/83/EC and Regulation (EC) No 726/2004. It regulates ATMPs which are intended to be placed on the market in [EU] Member States and either prepared industrially or manufactured by a method involving an industrial process.

Like all other modern biotechnology medicinal products, ATMPs are regulated at EU level and are subject to the centralised marketing authorisation procedure. In addition to the general regulatory requirements that apply to all medicinal products, given their complexity, ATMPs are subject to specific technical requirements, including the type and amount of quality pre-clinical and clinical data necessary to demonstrate the quality, safety and efficacy of the product and obtain a marketing authorisation. To facilitate the development of these products and help pharmaceutical companies prepare for marketing authorisation applications, the EMA has adopted a raft of scientific guidelines. Whether the existing regulatory framework and guidelines will be fit for purpose for genome-editing applications remains to be seen. Some clarifications and modifications seem unavoidable as is reflected by the EMAs on-going revision of its overarching guideline on medicinal products containing genetically modified cells in light of the CRISPR/Cas9 advances.

The ATMP Regulation distinguishes three types of ATMPs, two of which are of interest when considering CRISPR products and applications: (i) gene therapy medicinal products (GTMPs) and (ii) somatic cell therapy medicinal products (sCTMPs).

Pursuant to Directive 2001/83/EC (Annex I, Part IV, Section 2.1), a GTMP corresponds to a biological medicinal product with the following characteristics:

a)it contains an active substance which contains or consists of a recombinant nucleic acid used in or administered to human beings with a view to regulating, repairing, replacing, adding or deleting a genetic sequence; and

b)its therapeutic, prophylactic or diagnostic effect relates directly to the recombinant nucleic acid sequence it contains, or to the product of genetic expression of this sequence.

In contrast, the Directive (Annex I, Part IV, Section 2.2) defines an sCTMP as a biological medicinal product that:

a)contains or consists of cells or tissues that have been subject to substantial manipulation so that biological characteristics, physiological functions or structural properties relevant for the intended clinical use have been altered, or of cells or tissues that are not intended to be used for the same essential function(s) in the recipient and the donor; and

b)is presented as having properties for, or is used in or administered to human beings with a view to treating, preventing or diagnosing a disease through the pharmacological, immunological or metabolic action of its cells or tissues.

Depending on the primary mode of action of a therapy, CRISPR-modified cells that are used in therapy could likely be categorised as either GTMPs or sCTMPs (though given the early stages of CRISPR-related clinical trials, this has not yet been confirmed by regulatory authorities to date). For example, where the primary use of genome-edited haematopoietic stem cells (HSCs) is immune reconstitution and the genetic modification is for the secondary purpose of limiting risk of graft versus host disease, the therapy is likely to be classified as an sCTMP. This is because HSCs themselves can reconstitute a patients immune system without any genetic modification. In contrast, where the primary mode of action is a direct result of the genetic modification, it is likely to be classified as a GTMP. For example, where a gene is inserted into T-cells, resulting in a receptor being expressed on the cell surface designed to recognise and attack target cells (such as cancer cells), this is likely to be considered a GTMP because the T-cells alone, without this genetic modification, would not provide any therapeutic effect. Notwithstanding the above, the ATMP Regulation requires that a product meeting the definition of both GTMP and sCTMP be classified as a GTMP.

If an applicant is unsure whether a product is an ATMP, it can request a recommendation from the EMAs specialised Committee for Advanced Therapies (CAT), which must respond within 60 days (after consultation with the European Commission). Non-confidential summaries of these recommendations are publicly available. The CAT provides advice on whether a product falls within the definition of an ATMP, formulates draft opinions on the quality, safety and efficacy of ATMPs for final approval by the Committee for Medicinal Products for Human Use (CHMP), and advises the latter on any data generated in the development of ATMPs. The CAT has previously evaluated cell therapies involving genetically modified cells and the evaluation of CRISPR-modified medicinal products is likely to be analogous (see for example Autologous anti-BCMA CAR T-cells which were classified as a gene therapy medicinal product). Companies interested in the development and marketing of CRISPR edited medicinal products should consider monitoring CAT recommendations, reports and publications in order to better understand how CRISPR products will be classified and regulated in the context of the ATMP Regulation.

2.National approvals by competent authorities and ethics committees of clinical trials with ATMPs

ATMPs must go through clinical trials in the same way as any other medicine. Clinical trials are approved on a national basis, by the national competent regulatory authorities after the provision of the opinion of an ethics committee, in accordance with the harmonised procedures and principles established by the Clinical Trials Directive (Directive 2001/20/EC). However, the application procedure will be streamlined significantly as applications will be submitted through a single EU portal and undergo a (partly) harmonised assessment (by all Member States involved) once the Clinical Trials Regulation (EU) No 536/2014 will become applicable (at the earliest, October 2018 according to the timeframe drawn up by the EMA but most likely later).

Given the complexity of ATMPs (and the corresponding clinical trial dossiers), specific written authorisation is required, and the timelines for approval of clinical trials with these products are often longer than for regular medicinal products. Currently, the time period for the national competent authority to consider a request for authorisation of a clinical trial which in principle may not exceed 60 days may be extended by 30 days in the case of GTMPs and sCTMPs. This maximum period of 90 days may be extended by a further 90 days in the event of consultation of a group or a committee in accordance with the regulations and procedures of the Member States concerned. Under the new Clinical Trials Regulation, review timelines will remain lengthier in the case of clinical trials involving an ATMP.

Ethical aspects remain the responsibility of individual EU Member States and (even under the new Clinical Trial Regulation) local ethics committees need to give their opinion before a clinical trial can be authorised. It is clear that the debate around trials involving products created by CRISPR techniques (or therapies involving the direct in vivo use of CRISPR in patients) is likely to be complex given the numerous ethical issues (such as the fear of designer babies and other eugenic applications) raised by this technology. Currently, for ATMPs, ethics committees can extend the time period to give their reasoned opinion on a clinical trial with these products from 60 to 90 days (which may be further extended by 90 days in the event of consultation of a specific committee), and despite the intention of the Clinical Trials Regulation to shorten the timelines for clinical trial approvals in the EU these extended timelines are likely to be indispensible for CRISPR related trials.

However, importantly, to date, it is clearly established in EU law that gene therapy trials resulting in modifications to the subjects germ line genetic identity are prohibited (and this prohibition is maintained under the EU Clinical Trials Regulation). Therefore, one of the most controversial applications of CRISPR (which was the subject of the August 2017 Mitalipov paper) the editing of genes at a germ-line level (in egg cells, sperm cells and embryos) so that the edited gene is inheritable by future generations is unlikely to be permitted in the EU for the foreseeable future.

3.Other regulations to consider

Additional legislation supporting the ATMP regulation will have to be considered as well. For example, where tissues and cells are used as starting materials, the donation, procurement and testing of the cells are covered by the Tissues and Cells Directive (Directive 2004/23/EC). Other relevant legislation includes Directive 2005/28/EC that lays down detailed guidelines for good clinical practice (GCP) and the requirements for authorisation of the manufacturing or importation of ATMPs.

This is an exciting time for research and development wherein the use of CRISPR in medicine may lead to rapid and significant progress for human health. The regulation of the developments triggered by this new technology is important to ensure that, on the one hand, appropriate quality and safety standards are adhered to, by way of evaluating and mitigating potential risks and, on the other, a clear and certain regulatory environment is created to encourage researchers to explore fully the potential of this technology within the ethical bounds society deems appropriate. It appears that the regulation of gene and cell therapies under the EU ATMP Regulation possibly with some regulatory modifications and the adoption of adequate scientific guidelines - could also govern revolutionary gene-editing techniques such as CRISPR/Cas9, and is therefore the legal instrument to watch as CRISPR continues to conquer the world of medicine.

Read more here:
August 2017 Regulating CRISPR genome editing in humans: where do we go from here? - JD Supra (press release)