Category Archives: Genome

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Using this very high quality genome, scientists from INRA-France were able to conduct epigenetic studies focused on the transmission of information independently of the apple DNA sequence.

Apples are one of the most widely consumed fruits in the world, and 84.6 million tonnes of the fruit are produced each year. In order to enable the more efficient selection of new apple varieties, it is essential to gain access to a high quality genome. This will permit the genetic and epigenetic studies that are essential to identifying the key genes involved, for example, in fruit size and colour or disease resistance.

Based on a genetic map with a high density of markers, it was possible to assemble the genome in 17 pseudo-molecules representing the 17 chromosomes of the apple. With a total size of 649.3 Mb assembled in 280 fragments, this genome comprises 42,140 genes.

This new genome has, for example, enabled scientists to identify important rearrangements that occurred in the apple genome about 21 million years ago. These changes may have been due to the emergence of the Tian Shan mountain range in Kazakhstan, the region where the fruit originated. These geological and environmental events may have contributed to the contrasted evolution of the common ancestor of the apple and pear.

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Using this very high quality genome, the scientists were able to conduct epigenetic studies focused on the transmission of information independently of the DNA sequence. This allowed them to demonstrate that epigenetic markers can influence fruit development through the differential expression of genes.

This genome is an essential tool for the entire community working on apple breeding, and more generally in order to acquire knowledge on genome evolution and regulation. It will also facilitate an acceleration of the creation of new and more resistant varieties that will reduce the use of pesticides, improve apple quality or adapt these varieties to environmental constraints and climate change.

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Discovery of very high quality apple genome obtained - New Food

Updated June 08, 2017 20:47:39

Australian scientists now have access to revolutionary tools which could give them a cutting edge in the fight against diseases like cancer.

The new genome sequencing platform, known as the NovaSeq Series, has been called a game changer and will give researchers a clearer and fuller picture of a patient's genetic make-up.

And that means the ability to decode the DNA of things like tumours.

Professor Sean Grimmond, from the University of Melbourne Centre for Cancer Research, said the implications could be wide-reaching.

"This is the biggest chance we've got in the next five to ten years of advancing, certainly on our intractable and rare cancers," he said.

The new technology means that scientists will be able to give patients a better diagnosis.

"What we're doing here now is drilling right down to the DNA," Professor Grimmond said.

"We know that different cancer types have different patterns of damage to the DNA.

"So we can use that information now to get a much higher resolution and understanding of what your tumour is and what's actually driving it.

"So as a cancer researcher, if I can decode the DNA from your tumour, I have a way of understanding what exactly went wrong in your disease.

"Then maybe I can find a way to tackle your cancer in a personalised fashion.

"I guess the onus on us now with this fantastic new tool is really to work out where that clinical utility is, and how it will actually improve different aspects of treating cancer.

"And then working out how quickly we can get that into the standard of care."

A genome is the sum of a person's genetic information like their genetic blueprint.

The new technology means genomes can be decoded in a couple of days and for just a few hundred dollars.

Dr Irene Kourtis from the Australian Genome Research Facility said the first human genome took about 13 years to sequence, costing around $2.7 billion.

"What we can do now with the NovaSeq is to be able to analyse 50 human genomes in less than two days," she said.

Professor Grimmond said the DNA a person is born with plays an important role in a range of diseases.

"The DNA effectively in your cells is like the hard drive on your computer," he said.

"And [the technology] allows us to decode and understand every piece of information that is on your DNA."

And he said until now scientists had been relying on centuries-old equipment.

"Traditionally the way we would diagnose cancers is by using a microscope, which is effectively a 300-year-old instrument," Professor Grimmond said.

"We look at cells, we can see that they're abnormal and maybe we'd look at one or two proteins to see if they're present or absent, to give us comfort that we think it's a particular cancer type."

Topics: science-and-technology, genetics, cloning-and-dna, dna, diseases-and-disorders, cancer, medical-research, australia

First posted June 08, 2017 20:16:55

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Scientists get new genome platform to decode DNA in fight against complex diseases - ABC Online

A taxpayer-funded professor at the University of Washington is now predictingthat Donald Trumps presidency will create trauma on such a massive scale that it will permanently change the human genome.

The professor, Peter Ward, offered his dire prediction at Gizmodo on Monday as one of seven evolutionary biologists answering the burning question: Can Superhuman Mutants Be Living Among Us?

Ward, who works in the University of Washingtons earth and space sciences department, first explains his view that the U.S. military will use genetics to create mutant freak super-soldiers who dont need to drink as much water, dont need to eat for five or six days and dont need to sleep.

Then the professor who is fairly well knownfor a bizarre hypothesis that multi-cell organisms collectively seek to commit suicide gets to the heart of the matter.

Were finding more and more that, for instance, people who have gone through combat, or women who have been abused when you have these horrendous episodes in life, it causes permanent change, which is then passed on to your kids, Ward writes. These are actual genetic shifts that are taking place within people.

These individual genetic changes add up to trigger huge evolutionary change.

On a larger scale, the amount of stress that Americans are going through now, because of Trump there is going to be an evolutionary consequence, Ward explains.

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Biology Professor: Trauma Of Trump Presidency Will Mutate Human Genome For All Eternity - The Daily Caller

June 7, 2017 by Claudia Lutz Professor of Cell and Developmental Biology Lisa Stubbs leads the Gene Networks in Neural & Developmental Plasticity research theme at the Carl R. Woese Institute for Genomic Biology at the University of Illinois. Credit: Don Hamerman

Mice have a reputation for timidity. Yet when confronted with an unfamiliar peer, a mouse may respond by rearing, chasing, grappling, and bitingand come away with altered sensitivity toward future potential threats.

What changes in the brain of an animal when its behavior is altered by experience? Research at the University of Illinois led by Professor of Cell and Developmental Biology Lisa Stubbs is working toward an answer to this question by focusing on the collective actions of genes. In a recent Genome Research publication, Stubbs and her colleagues identified and documented the activity of networks of genes involved in the response to social stress.

"The goal of this study was to understand the downstream events in mice, and how they are conveyed across interacting brain regions . . . how they might set the stage for emotional learning in response to social threat," said Stubbs. Answers to these questions could help scientists understand how the brains of other animals, including humans, generate social behavior, as well as what goes wrong in disorders of social behavior.

The new results are part of a large-scale research project funded by the Simons Foundation that is headed by Stubbs and includes many of her coauthors, including first authors Michael Saul and Christopher Seward. Stubbs, Saul, Seward, and other coauthors are members of the Carl R. Woese Institute for Genomic Biology (IGB); Saul is an IGB Fellow and Seward is a graduate student.

An aggressive encounter between two mice is just one strand of the web of interactions that connects a population of social animals. Like individuals in a community, the genes in a genome cannot be completely understood until their relationships to one another are examined in context, including how those relationships may change across different tissues and over time.

Stubbs' team wanted to gather information that would allow them to construct this type of comprehensive gene network to reflect how the brain of a social animal responds to an aggressive encounter. They staged a controlled encounter between pairs of mice; one mouse in its home cage, and a second, unfamiliar mouse introduced behind a screen. The presence of the intruder mouse created a social challenge for the resident mouse, while the screen prevented a physical encounter.

The researchers then quantified the activity of genes in several different regions of the brain associated with social behaviorsthe frontal cortex, hypothalamus, and amygdalaand at several time points in the two hours following the encounter. In analyses of the resulting data, they looked for groups of genes acting together. In particular, they sought to identify transcription factors, genes whose protein products help control other genes, that might be orchestrating the brain's molecular response.

Stubbs was excited to discover that the results mirrored and expanded upon previous work in other species by collaborators at the IGB, including work by the laboratory of Director Gene Robinson in honey bees.

"As we examined the regulatory networks active in the mouse brain over time, we could see that some of the same pathways already explicated in honey bees... were also dysregulated similarly by social challenge in mice," she said. "That cross-species concordance is extremely exciting, and opens new doors to experimentation that is not being pursued actively by other research groups."

Among the genes responding to social challenge were many related to metabolism and neurochemical signaling. In general terms, it appeared that cells in the brains of challenged mice may alter the way they consume energy and communicate with one another, changes that could adjust the neural response to future social experiences.

The researchers looked for associations between genes' responses to social experience and their epigenetic state. How different regions of DNA are packaged into the cell (sometimes referred to as chromatin structure) can influence the activity of genes, and so-called epigenetic modifications, changes to this structure, help to modify that activity in different situations.

"We found that the chromatin landscape is profoundly remodeled over a very short time in the brain regions responding to social challenge," said Stubbs. "This is surprising because chromatin profiles are thought to be relatively stable in adult tissues over time." Because such changes are stable, they are sometimes hypothesized to reinforce long-term behavioral responses to experience.

Stubbs and her colleagues hope that by identifying genomic mechanisms of social behavior that are basic enough to be shared even between distantly related animal species, they can discover which biological mechanisms are most central.

"The most exciting thing in my view is using [comparisons between species] to drill through the complex response in a particular species to the 'core' conserved functions," she said, "thereby providing mechanistic hypotheses that we can follow by exploiting the power of genetic models like the mouse."

Explore further: Different species share a 'genetic toolkit' for behavioral traits, study finds

More information: Michael C. Saul et al, Transcriptional regulatory dynamics drive coordinated metabolic and neural response to social challenge in mice, Genome Research (2017). DOI: 10.1101/gr.214221.116

The house mouse, stickleback fish and honey bee appear to have little in common, but at the genetic level these creatures respond in strikingly similar ways to danger, researchers report. When any of these animals confronts ...

In the nucleus of eukaryotic cells, DNA is packaged with histone proteins into complexes known as chromatin, which are further compacted into chromosomes during cell division. Abnormalities in the structure of chromosomes ...

Scientists studying the role of a protein complex in the normal development of the mouse brain unexpectedly created a mouse model that replicates clinical symptoms of patients with complex neurological disorders such as hyperactivity, ...

It is almost axiomatic in medicine that the study of rare disorders informs the understanding of more common, widespread ailments. Researchers from the Perelman School of Medicine at the University of Pennsylvania who study ...

Heart disease kills more than 600,000 Americans every year, which translates to more than one in every four deaths. Although lifestyle choices contribute to the disease, genetics play a major role. This genetic facet has ...

Our DNA influences our ability to read a person's thoughts and emotions from looking at their eyes, suggests a new study published in the journal Molecular Psychiatry.

Mice have a reputation for timidity. Yet when confronted with an unfamiliar peer, a mouse may respond by rearing, chasing, grappling, and bitingand come away with altered sensitivity toward future potential threats.

Researchers at Queen's University have published new findings, providing a proof-of-concept use of genetic editing tools to treat genetic diseases. The study, published in Nature Scientific Reports, offers an important first ...

Yale scientists have discovered the cause of a disfiguring skin disorder and determined that a commonly used medication can help treat the condition.

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Social experience tweaks genome function to modify future behavior - Medical Xpress

The Federal Court has finished hearing an appeal against a patent granted to two US companies for identifying genetic traits in cattle.

Research and marketing bodies Meat and Livestock Australia (MLA) and Dairy Australia launched legal action against the patent holders, Cargill USA and Branhaven LLC, after losing an earlier appeal before the Australian Patent Office.

Cargill is a major global commodities giant, but did not defend the appeal, while little is known about Branhaven except that it acquired the patent after it bought many of the assets of a biotechnology company called Metamorphix when it liquidated in 2011.

A hearing into the matter started last month and ended on Wednesday afternoon, lasting six and a half days in total.

MLA, beef and dairy farmers, and livestock researchers allege the patent could restrict access to genomic testing and research into cattle genetics because it could give Cargill and Branhaven the right to license service providers or charge licensing fees for genomic testing.

These concerns were similar to those raised before the High Court in the landmark breast cancer gene case.

University of Queensland intellectual property expert Professor Matthew Rimmer told the ABC the case was a "test of the limits and boundaries" of what is patentable in Australia.

On both sides, some of Australia's top intellectual property lawyers argued before Justice Jonathan Beach, with Christian Dimitriadis SC appearing for Branhaven, and Katrina Howard SC appearing for MLA.

MLA argued before the court the broadest claim in the patent potentially extends to nearly two thirds of the cattle genome.

The patent, first written in 2003 and filed in Australia in 2010, describes a method for identifying genetic traits in cattle through the use of genetic markers called SNPs (single nucleotide polymorphisms and pronounced 'snips').

Genomic testing is increasingly used in the livestock sector to select animals with superior genetic traits (tender meat, better milk production).

(ABC News: Roxanne Taylor)

Genomic testing is increasingly used in the livestock sector to select animals with superior genetic traits (tender meat, better milk production).

It identifies 2,510 specific SNPs (there are billions through the genome), but it also lays claims to a large region (500,000 base pairs of DNA) either side of each of the 2,510 identified SNPs.

Much of the concern about the patent comes from the secondary claim because, although the field of genetics has advanced rapidly since 2003, and many millions more SNPs have been located since then, researchers believe their current work could still infringe on the patent.

This is because it includes the 500,000 base pairs of DNA either side of the SNPs actually identified in the patent.

"If this patent was concerned with human genes, there would be a public outcry," MLA's senior council Katrina Howard SC told the court.

"There's no good reason it should apply to cattle."

While MLA attacked the patent on almost every legal ground, a central pillar of its argument was that the method described for identifying the genetic markers was common knowledge before the patent was written in 2003.

They argued that work being done on the human genome, as well as scientific papers published before 2003, meant methods described in the patent was obvious to skilled geneticist.

But Branhaven said that work to map the bovine genome had just started, and was not finished until 2009 so therefore, the patent describes a significant and noteworthy achievement and invention.

No date has been set for a judgement in the matter.

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Federal Court finishes hearing legal argument in controversial cattle genome case - ABC Online

In a study of 124 patients with advanced breast, lung, and prostate cancers, a new, high-intensity genomic sequencing approach detected circulating tumor DNA at a high rate. In 89% of patients, at least one genetic change detected in the tumor was also detected in the blood. Overall, 627 (73%) genetic changes found in tumor samples were also found in blood samples with this approach.

The study was featured in a press briefing on June 3rd and presented at the 2017 American Society of Clinical Oncology (ASCO) Annual Meeting.

This innovative approach using high-intensity sequencing to detect cancer from circulating tumor DNA in the bloodstream heralds the development of future tests for early cancer detection.

The high-intensity sequencing approach used in this study has a unique combination of breadth and depth. It scans a very broad area of the genome (508 genes and more than two million base pairs or letters of the genome, i.e. A, T, C, and G) with high accuracy (each region of the genome is sequenced or read 60,000 times), yielding about 100 times more data than other sequencing approaches. This enormous amount of data will be instrumental in developing a blood test to detect cancer early.

This approach, however, differs from liquid biopsies, including commercial tests, which only profile a relatively small portion of the genome in patients already diagnosed with cancer for the purpose of helping monitor the disease or detect actionable alterations that can be matched to available drugs or clinical trials.

Our findings show that high-intensity circulating tumor DNA sequencing is possible and may provide invaluable information for clinical decision-making, potentially without any need for tumor tissue samples, said lead study author Pedram Razavi, MD, PhD, a medical oncologist and instructor in medicine at Memorial Sloan Kettering Cancer Center (MSK) in New York, NY. This study is also an important step in the process of developing blood tests for early detection of cancer.

Circulating tumor DNA is a term used to describe the tiny pieces of genetic material that dying cancer cells shed into the blood circulation. To create a picture of the entire genomic landscape of the tumor from circulating tumor DNA, scientists read each tiny fragment and then piece them together as a puzzle. In the bloodstream, circulating tumor DNA is only a small subset of the total cell-free DNA, as most circulating fragments of genetic material come from normal cells.

About the Study

The researchers prospectively collected blood and tissue samples from 161 patients with metastatic breast cancer, non-small-cell lung cancer (NSCLC), or castration-resistant prostate cancer. Thirty-seven patients were excluded due to unavailability of the results of the genetic analysis of the tumor or cell-free DNA samples. For 124 evaluable patients for concordance analysis, researchers compared genetic changes in the tumors to those in circulating tumor DNA from the blood samples.

Tumor tissues were analyzed using MSK-IMPACT, a 410-gene diagnostic test that provides detailed genetic information about a patients cancer. In each blood sample, the researchers separated the plasma, the liquid part of the blood, from the blood cells. The cell-free DNA extracted from the plasma and, separately, the genome of white blood cells were then sequenced using the high-intensity, 508-gene sequencing assay.

Finding tumor DNA in the blood is like looking for a needle in a haystack. For every 100 DNA fragments, only one may come from the tumor, and the rest may come from normal cells, mainly bone marrow cells, said Dr. Razavi. Our combined analysis of cell-free DNA and white blood cell DNA allows for identification of tumor DNA with much higher sensitivity, and deep sequencing also helps us find those rare tumor DNA fragments.

Patients tumors may have various genetic changes; there can be different changes in different parts of the same tumor, as well as in different sites where the tumor spreads in the body. For these reasons, sequencing over very broad regions of the genome is critically important to identify the multitude and diversity of genetic changes in the tumor.

Key Findings

In 89% of patients, at least one genetic change detected in the tumor was also detected in the blood (97% in metastatic breast cancer patients, 85% in those with NSCLC, and 84% in those with metastatic prostate cancer). Overall, including all genomic variations present in most if not all tumor cells (clonal) as well as those present only in subsets of the cancer cells (subclonal) from tumor tissue, the researchers detected a total of 864 genetic changes in tissue samples across the three tumor types, and 627 (73%) of those were also found in the blood.

Importantly, without any prior knowledge from the analysis of tumor tissue, 76% of actionable mutations (genetic changes that can be matched to an approved targeted therapy or one being tested in clinical trials) detected in tissue were also detected in blood.

Prior research in the field has primarily focused on using knowledge from tumor tissue sequencing to identify specific changes to look for in circulating tumor DNA. This approach allows us to detect, with high confidence, changes in circulating tumor DNA across a large part of the genome without information from tumor tissue, said Dr. Razavi. While circulating tumor DNA tests targeting a smaller set of cancer genes are already available for use in routine practice to guide care, by covering a much larger number of cancer genes, this high-intensity sequencing approach may enable development of future tests for early detection of cancer.

Next Steps

The high-intensity sequencing approach used in this study is a research platform and is not intended to be commercially available to patients. To understand the current performance and potential of this assay, the researchers first tested it in advanced cancer, an area where circulating tumor DNA has been previously characterized.

This study will inform development of technology for a future test that could eventually be used as a blood test for early cancer detection. In patients undergoing cancer screening, tumor tissue is not available, and we will need to detect changes in circulating tumor DNA without prior knowledge of tissue analysis results, said Dr. Razavi.

Advantages of Liquid Biopsy Genomic changes can differ between various areas within a tumor, as well as among the different organs where the cancer has spread. A circulating tumor DNA test provides a summary report of all the genomic changes in the primary tumor and metastases. In contrast, a tissue biopsy, which typically takes only a small piece of the tumor, sometimes misses key genetic changes that fuel cancer growth.

Another advantage of liquid biopsy is its ability to capture genomic changes in real time, helping guide treatment planning without the need of additional conventional tissue biopsies. Genomic changes evolve as the cancer grows and spreads. New changes may lead to cancer recurrence or resistance to treatment. A liquid biopsy test requires only a simple blood draw. It is generally safe and convenient to repeat, allowing doctors to keep easier track of new mutations.

This study was funded in part by GRAIL, Inc.

This article has been republished frommaterialsprovided byASCO. Note: material may have been edited for length and content. For further information, please contact the cited source.

The full abstract be be viewed here.

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New Technology Dives Deep Into the Cancer Genome - Technology Networks

February 6, 2013 A paper describing the unified Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and MSU Rice Genome Annotation Project Release 7 has been published.

February 7, 2012 The GFF3 and brief info files were updated on the FTP site. The update corrects issues with the UTR feature type and several cases where the mRNA coordinates were incorrect. The sequence files and other features in the GFF3 files were not changed.

October 31, 2011 Release 7 of the MSU Rice Genome Annotation Project is available. This release is based on a new pseudomolecule assembly (Os-Nipponbare-Reference-IRGSP-1.0) made in collaboration with the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan. This set of pseudomolecules unifies the previous MSU with the IRGSP/RAP effort. Genome browser has been updated with 81 tracks of data. Orthologous group analysis has been updated to include Zea mays release 5b filtered gene models.

We have planned server maintenance on the first Wednesday of every month. The Rice Genome Annotation Project web pages may be unavailable or only partially functional during server maintenance.

Feb 6, 2013 - A paper describing the unified Os-Nipponbare-Reference-IRGSP-1.0 pseudomolecules and MSU Rice Genome Annotation Project Release 7 has been published in the journal Rice.

The MSU Rice Genome Annotation Project Database and Resource is a National Science Foundation project and provides sequence and annotation data for the rice genome.

This website provides genome sequence from the Nipponbare subspecies of rice and annotation of the 12 rice chromosomes. These data are available through search pages and our Genome Browser that provides an integrated display of annotation data.

In cooperation with researchers at the Agrogenomics Research Center at the National Institute of Agrobiological Sciences, Tsukuba, Japan, we have prepared a final assembly of the rice pseudomolecules. These pseudomolecule sequences are now common to both the MSU Rice Genome Annotation Project and the Rice Annotation Project Database (RAP-DB)/International Rice Genome Sequencing Project. This effort was undertaken in order to allow researchers to easily compare annotations from both the MSU and RAP-DB projects. Gene loci, gene models and associated annotations created by MSU-RAP and RAP-DB were independently derived, but the pseudomolecules used by the two rice annotation projects to generated those annotations are now identical and can be easily compared. A manuscript describing the generation of the final rice pseudomolecule assembly is in preparation.

While many researchers utilize the MSU loci, gene models and transcripts in their own databases and genome browsers, these sites may have outdated annotation and may have modified or further annotated our official gene set. All MSU rice gene names are of the form LOC_Os##g##### as explained on our nomenclature page. MSU rice genes are created using de novo gene predictions from Fgenesh followed by improvements and/or modifications by the PASA program which uses other de novo gene prediction software and rice full length cDNA and EST alignments. Our gene set is constructed entirely "in house" and is not equivalent to annotation from RefSeq, RAP, SwissProt or UniProt. Because we can not guarantee that data that is labeled as MSU/TIGR genes at other websites are really our data, we suggest that users always refer back to the MSU Rice Genome Annotation Project for our genuine and current MSU rice gene data. Please note that while we can not prevent users from downloading our entire Genome Browser, we do not sponsor or approve of public re-display of our rice genome browser.

Researchers who wish to cite the Rice Genome Annotation Project website are encouraged to refer to our recent publication:

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Rice Genome Annotation Project

In case you havent already heard of CRISPR-Cas9, it is the revolutionary gene-editing technology, discovered just a few years ago, that allows scientists to edit the DNA of any species with an unprecedented precision and efficiency. Today, thousands of researchers around the world are doing experiments with CRISPR, in the hope to cure us from genetic diseases and even deliver us designer babies. The first clinical trial to employ CRISPR-Cas9 is now underway in China, hoping to fight targeted cancers with modified immune cells.

The gene-editing method is based on the protective mechanism of bacteria against viruses. An RNA molecule carries segments of DNA from a previously encountered virus together with an enzyme (Cas9). Once the molecule encounters that same sequence of DNA, the enzyme gets activated and cuts it out. Researchers discovered that they can use this system to cut any DNA sequence at a precisely chosen location.

While the tool is touted for its precision, it is far from error free. Mutations do occur around the areas where the DNA has been cut and needs to be repaired. And sometimes CRISPR may hit unintended parts of the genome. Computer algorithms identify the most likely areas for these off-target mutations, which are later examined by researchers for deletions and insertions. However, whole-genome sequencing (WGS) - examining the entire DNA of living animals that had undergone gene editing - hadn't been done.

In a recently published study in the journal Nature Methods, titled Unexpected mutations after CRISPRCas9 editing in vivo scientists used whole-genome sequencing to study the mutations that had occurred in the DNA of mice that had undergone CRISPR gene editing.

Genetic Engineering and Biotechnology News reports that the investigators were able to determine that CRISPR had successfully corrected a gene that causes blindness, but found that the genomes of two independent gene therapy recipients had sustained more than 1500 single-nucleotide mutations and more than 100 larger deletions and insertions. None of these DNA mutations were predicted by computer algorithms that are widely used by researchers to look for off-target effects.

Co-author of the study Vinit Mahajan, M.D., Ph.D. said:

"We're still upbeat about CRISPR, we're physicians, and we know that every new therapy has some potential side effectsbut we need to be aware of what they are."

The authors are encouraging scientists to use the WGS method to determine all off-target effects of their CRISPR experiments.

In the last few days, however, some scientists have raised concerns about the validity of the study, questioning its methodology. Dr Gaetan Burgio, Group leader and head of the transgenesis facility at the Australian National University said in a Journal club review of the paper:

The claims over this paper are unsurprising as Cas9 enzyme could remain in the cells for days and create random indels in the genome. However, the main issues for me resides in the overestimation of the number of off target effects due to the lack of rigor in the experimental design to detect these unexpected mutations. In short my main point is these unintended mutation are likely to have preexisted prior to the injection of CRISPR system.

One thing is sure there is a lot more work to be done to ensure the safety of the CRISPR/Cas9 technology.

Photo Credit:Pixabay

See more here:
CRISPR May Cause Hundreds of Unintended Mutations Into the ... - Big Think

The last podcast in this series looks at current opportunities presented by advancements in Precision Medicine. How are healthcare organizations and patients learning to leverage the knowledge locked in our genes? And how can this knowledge become a real opportunity today?

Join Jennifer Girka, healthcare strategist within Dell EMCs Healthcare & Life Sciences division, as she provides an introduction to precision medicine. Girka is responsible for providing strategic insight to help Dell EMC advance its support of healthcare organizations, medical professionals and patients as they transform healthcare into the digital era. With more than 20 years helping to advance the healthcare industry with new opportunities and emerging technology, she works closely with healthcare customers and practitioners to bring them the right mix of technology innovation and solutions that will help them navigate through the ever-changing and increasingly complex world of healthcare.

Sources: To Adopt Precision Medicine, Redesign Clinical Care." NEJM Catalyst. February 5, 2017.http://catalyst.nejm.org/adopt-precision-medicine-personalized-health/ "Partners Data Lake Offers Healthcare Analytics as a Service." Health IT Analytics. March 17, 2016.http://healthitanalytics.com/news/partners-data-lake-offers-healthcare-analytics-as-a-service "Personalized Health Planning in Primary Care Settings." Fed Pract. 2016 January;33(1):27-34.http://www.mdedge.com/fedprac/article/105690/personalized-health-planning-primary-care-settings/page/0/1 Alice Park. "A Powerful New Tool for Editing the Human Genome." Time Magazine. April 4, 2016.http://time.com/4207612/a-scientist-gets-the-green-light-to-edit-the-human-genome/ City of Hope and Translational Genomics Research Institute combine to advance precision medicine and speed translational research.https://www.tgen.org/home/news/2016-media-releases/tgen-forges-alliance-with-city-of-hope.aspx#.WP9Y0dLyvIU

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The genome is out of the bottle: Embrace the possibilities - Healthcare IT News

When the 2015/2016 Zika virus epidemic swept through the Americas and several islands in the Pacific and Southeast Asia, researchers were urged to focus their efforts on developing treatments and vaccines to combat the virus effects.

A team of researchers from the Center for Genome Architecture at Baylor College of Medicine coincidentally had crucial but fragmented pieces of relevant data from previous research that could greatly impact this effort. Using a 3-D genome assembly approach referred to as HI-C, the team was able to quickly assemble the 1.2 billion letter genome of Aedes aegypti, the Zika-carrying mosquito, producing the first end-to-end assembly of each of its three chromosomes.

When the Aedes mosquito came into the spotlight in relation to the Zika epidemic, we found ourselves sitting on a bunch of relevant data and proof-of-principle work, said Olga Dudchenko, a postdoctoral fellow at The Center for Genome Architecture. The situation prompted us to polish our methods and share the data we had.

The development provides a much-needed boost to research and treatment options for the Zika virus by identifying vulnerabilities in the mosquito that the virus uses to spread.

With the success of assembling the Aedes genome, the Baylor team has also shown that the 3-D assembly technique can be an important tool for similar outbreaks in the future, and could also aid in personalized care for human patients suffering from a variety of diseases.

Timeline Erez Lieberman Aiden, Director of the Center for Genome Architecture, originally proposed the general idea of 3-D assembly in 2009. Lieberman Aiden and colleagues first tested their technique in 2013 by sequencing a human genome, and comparing the data to that made available by the Human Genome Project.

The team found their assembly correlated with the reference data from the Human Genome Project with 99 percent accuracy, validating the method. However, the 3-D assembly method produced similar results in a fraction of the time, and at significantly less cost.

They then switched their focus toward the Aedes aegypti mosquito, which is responsible for the spread of not only Zika virus, but dengue, chikungunya and yellow fever. When the Zika outbreak began to become a global health threat, the team knew they could piece together information they acquired from previous research to create a clear, cohesive picture of the mosquitos genome.

3-D assembly allowed the team to create the 1.2 billion-letter genome of the mosquito for about $10,000a price comparable to that of an MRI scan. The third phase of their research included assembling the genome of the Culex quinquefasciatus mosquito, a carrier of West Nile virus.

Culex is another important genome to have since it is responsible for transmitting so many diseases, said Lieberman Aiden. Still, trying to guess what genome is going to be critical ahead of time is not a good plan. Instead, we need to be able to respond quickly to unexpected events. Whether it is a patient with a medical emergency or the outbreak of an epidemic, these methods will allow us to assemble de novo genomes in days, instead of years.

For the Culex sequence, the researchers carried out their work with IBMs VOLTRONa high performance computing (HPC) system. VOLTRON is based on the companys Power Systems platform, which provides scalable HPC capabilities necessary to accommodate a broad spectrum of data-enabled research activities. The Power Systems platform has also been selected for use by the Department of Energys Oak Ridge and Lawrence Livermore National Laboratories, and the UK governments Science and Technology Facilities Councils Hartree Centre.

3-D assembly and IBM technology are a terrific combination: one requires extraordinary computational firepower, which the other provides, said Lieberman Aiden. Incorporated into the design of VOLTRON is a POWER and Tesla technology combination that allowed Baylor researchers to handle extreme amounts of data with incredible speed. VOLTRON comprises a cluster of four systems, each featuring a set of eight NVIDIA Tesla GPUs tuned by NVIDIA engineers to help Baylors researchers achieve optimum performance on their data-intensive genomic research computations.

The team also made a new discovery about these mosquito families during sequencing. They found that chromosome content did not mix much across the species, which could prove helpful in any future outbreak with a mosquito as a carrier, regardless of whether its genome is sequenced or not.

If youre looking at various mammals, chromosome content will mix a lot from one species to another. But what turned out to happen in mosquitoes was a very different story. What we saw is that although things mix a lot locally, (within chromosome arms) very little content jumped from one arm to another, or from one chromosome to another chromosome, explained Dudchenko.

This fundamental fact of mosquito evolution offers immediate benefit for researchers. If another epidemic hit through a completely different mosquito carrier that researchers and health officials know nothing about, they can at least infer where to look for particular genes or targets within the new carrier because of this unique property. In the event of a new outbreak, this technology could answer questions much faster and lead to the rapid development of a treatment or vaccine, saving lives and money.

Advancing capabilities As Dudchenko explained to Laboratory Equipment, the field of genome assembly is a very actively developing field, providing researchers with genetic information that was previously unobtainable.

But for certain applications, assembly methods can be suboptimal.

Prior to the 3-D genome assembly method, it was challenging and extremely expensive to sequence a genome by starting at the beginning of a chromosome and reading all the way through to the end. Instead, researchers would use methods that read small snippets of chromosomes many times over, find overlaps in those snippets and piece them together to create longer, continuous sequences.

The problem arises, however, when repetitive fragments appear, or theres a large amount of variation across a species.

Its like reading a book in which the pages arent bound or numbered in any meaningful way, Dudchenko said. In some sense, the information is all there and if youre lucky enough that the information you want to read off is in the paragraph on the same page, you can make sense of it. But if you have longer stretches of text, or are unlucky and hit the end of the page, you dont know where to go from there, and theres not a lot you can do with this information.

Another problem with short-reads or jumping methods is when DNA is being extracted, the chromosomes rarely remain unbroken.

But HI-C provides the needed information at the scale of whole chromosomes.

The technique traces the genome as it folds inside the nucleus, and shows how frequently different stretches of the genome come into contact with each other. This enabled the team to stitch together hundreds of millions of short DNA reads into the sequences of entire chromosomes.

People can view HI-C as a type of jumping library that spans all scales, said Dudchenko.

Clinical relevance The short-read format also greatly reduces the cost of assembly, making it an option for doctors to conduct a personalized genome project on individual patients as needed.

This is the technology that will get you there, said Dudchenko.

Prior to HI-C, a clinician may sequence a persons DNA, but instead of fully assembling it, they align it with a reference and look for typos to see where the patient differs from the genome reference. The disadvantage with this approach is that the clinician is looking at someones genome through the lens of an existing reference, creating a biased view. It relies heavily on prior work, and if theres something unexpectedly different, the clinician may not notice, according to Dudchenko.

The next step for the Baylor team is to build more of a stable infrastructure for other research groups to utilize the HI-C technology in their respective fields, and to make it more straight-forward for people who may not necessarily come from a 3-D space with relevant expertise.

Were very excited to see how this technology will play out with different genes and assemblies, and how far we will be able to go with this technology, added Dudchenko. Right now, were pretty optimistic.

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Assembling Genomes from Scratch, at a Fraction of the Cost - Laboratory Equipment