Category Archives: Genome

CRISPR technology for genome editing - Mandarin
CRISPR, a pioneering genome-editing technique, technology will allow AstraZeneca to identify and validate new drug targets in preclinical models that closely...

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Britains parliament allows human genome manipulation for first time
Mother #39;s day may be about to get more complicated in the UK after parliamentMother #39;s day may be about to get more complicated in the UK after parliamentCom...

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Nature lovers are fascinated by the increasing number of singing birds when spring is approaching. Scientists also take advantage of this seasonal phenomenon because they are able to investigate the underlying mechanism; however the evolutionary and molecularbiological background is largely unknown. A team of researchers from the Max Planck Institute for Ornithology in Seewiesen and from the Max Planck Institute for Molecular Genetics in Berlin have now identified the genome of the canary. With these data they were able to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

Canaries have been domesticated since the 15th century and are the descendants of the wild canary that lives on the Azores, Madeira and Canary Islands in the North Atlantic Ocean. Like their wild ancestors, domesticated canaries sing stereotyped songs under long-day (breeding) conditions and more variable songs under short-day (non-breeding) photoperiods. The canary has become a preferred model to investigate the neurological changes affecting hormone-dependent song. This is because it has a pronounced reproductive season, with seasonal changes in song and steroid hormone concentrations, and a varying degree of brain plasticity between the breeding and the non-breeding season.

A team of researchers from the department of Behavioural Neurobiology around Manfred Gahr at the Max Planck Institute for Ornithology in Seewiesen and from the Sequencing Core Facility under guidance of Bernd Timmermann from the Max Planck Institute for Molecular Genetics in Berlin together with colleagues from Brazil and the UK now have studied how hormone-sensitive gene regulation has evolved in songbirds. The work resulted in the first high quality assembly and annotation of a female canary genome. In birds, females are the 'heterogametic' sex (ZW) and therefore the analysed genome sequence contained both types of sex chromosomes, says Heiner Kuhl from the Max Planck Institute for Molecular Genetics.

Whole genome alignments between the canary and already identified genomes throughout the bird taxa showed that on a global scale bird genomes are quite similar. However, differences appeared when comparisons were conducted on a finer scale. For example, at the level of the nucleotide there are considerable species differences, which can impact small genetic sequences, such as steroid hormone receptor binding sites. Such differences in these regions might lead to major differences in gene regulation, even between closely related species, says Carolina Frankl-Vilches from the Max Planck Institute for Ornithology.

Following this global analysis the scientists focused on gene networks that had three characteristics -- were showing enrichment or under- representation in the expression profiles of the song control regions HVC and RA, showed seasonality, and were testosterone-sensitive. To verify whether the hormone-sensitive elements among these genes are specific for the canary, they also looked at the genes of the zebra finch because this species did not evolve hormone-sensitive song expression. Among all HVC expressed genes, including the seasonal and testosterone-induced gene pools, many were strictly canary-specific. These analyses reveal specific evolutionary changes in different parts of the song system that control seasonal singing behaviour. Thus, in the canary, those genes that are sensitive for testosterone and estrogen, and are also involved in the rewiring of neurons, might be crucial for re-differentiation of the underlying neuronal substrate, such as HVC, leading to seasonal song patterning. The present study demonstrates the need for high-quality genome assembly to detect the evolution of genes in comparative studies, says the coordinator of the study, Manfred Gahr from the Max Planck Institute for Ornithology.

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The above story is based on materials provided by Max-Planck-Gesellschaft. Note: Materials may be edited for content and length.

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Mapping of the canary genome

New software developed at Nationwide Children's Hospital in Ohio can take raw sequence data on a person's genome and search it for disease-causing variations in a matter of hours, which its creators claim puts it ahead of the pack as the fastest genome analysis software around. They believe that this makes it now feasible to do large-scale analysis across entire populations.

Whereas it took 13 years and cost US$3 billion to sequence a human genome for the first time, senior author Peter White notes that now "even the smallest research groups can complete genomic sequencing in a matter of days." The chokepoint lies in the next step: calibrating and analyzing the billions of generated data points for genetic variants that could lead to diseases.

White and his team tackled the problem by automating the analytical process in a computational pipeline they called Churchill. Churchill spreads each analysis step across multiple computing instances a process its creators call balanced regional parallelization with special care taken to preserve data integrity so that results are "100 per cent reproducible."

Tests showed that Churchill can analyze a whole genome sequence in as little as 90 minutes from a raw FASTQ text-based format through to identifying variant cells at high confidence. An exome, which contains the bulk of disease-causing variants despite being a mere one per cent of the whole genome, can be analyzed in less than an hour. Churchill's performance was validated against the National Institute of Standards and Technology's benchmarks, with scores of 99.7 per cent on sensitivity, 99.99 per cent on accuracy, and 99.66 per cent on diagnostic effectiveness.

While the goal of the research was to create an ultra-fast analysis pipeline, White and his team found an unexpected benefit. Churchill scales efficiently across many servers, which makes it possible to perform population-scale analysis.

They took the first phase of the raw data generated by the 1000 Genomes Project an international research collaboration started in 2008 to establish an extensive public catalog of human genetic variation across the globe and put Churchill to task on all 1,088 whole genome samples across a cluster of computers in Amazon Web Services' Elastic Compute Cloud. Churchill averaged a mere nine minutes per genome in its week-long analysis, which the researchers note compares favorably to a similar analysis performed in 2013 on a Cray XE6 supercomputer.

The Cray supercomputer test analyzed 61 whole genomes in two days, at an average of 50 minutes per genome around five times longer than Churchill required in its cloud test.

"Given that several population-scale genomic studies are underway, we believe that Churchill may be an optimal approach to tackle the data analysis challenges these studies are presenting," White says.

The Churchill algorithm has been licensed to a company called GenomeNext, which adapted the technology for use in a commercial setting. People can get their genome sequenced in a local lab or clinic and then upload the raw data to the GenomeNext system for analysis.

A paper describing the Churchill algorithms and research was published in the journal Genome Biology. The Churchill software is also available, for research purposes only, via its project page.

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Software analyzes human genome in as little as 90 minutes

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One of the most exciting scientific advances made in recent years is CRISPRthe ability to precisely edit the genome of cells. However, although this method has incredible potential, the process is extremely inefficient. Fortunately, scientists at the Gladstone Institutes have discovered a way to enhance the efficiency of CRISPR with the introduction of a few key chemical compounds.

"Currently, there is a trade-off with CRISPR: the technology is very precise, but it is also quite inefficient," says first author Chen Yu, a postdoctoral fellow at the Gladstone Institutes. "We improved this by introducing small molecules that are able to maintain the precision of the technology while boosting its efficiency."

In CRISPR, a protein is delivered into the cell that cuts the genome at an exact specified location. The cell's DNA can then either fuse back together after the faulty gene is removed, or scientists can insert a new gene in the old one's place, substituting bad DNA for good.

Published in the journal Cell Stem Cell, the researchers, in collaboration with co-senior author Lei Stanley Qi, PhD, at Stanford University, successfully identified two small molecules that significantly improve the insertion of new genetic information into a cell's DNA. During their search, the scientists also discovered two compounds that inhibit insertion but enhance deletion of DNA, suggesting the two processes are competitive actions in the cell.

Notably, the researchers were able to accomplish this genome manipulation in several different cell lines, including induced pluripotent stem cells and tissue-specific cells. This is particularly important as it indicates the method can be used in a variety of cell types to create disease models and contribute to the discovery of new disease-specific therapeutics.

Senior author Sheng Ding, PhD, a senior investigator at Gladstone, says that the potential of this discovery extends beyond improving the efficiency of CRISPR. "This study is the first to show that we can successfully manipulate genome engineering using small molecules. This gives us greater capability, enabling us to tune the machinery and also turn it on or off with chemicals, which has important implications for regulating the genome editing process."

Explore further: Bioengineers develop tool for reprogramming genetic code

Biology relies upon the precise activation of specific genes to work properly. If that sequence gets out of whack, or one gene turns on only partially, the outcome can often lead to a disease.

A powerful "genome editing" technology known as CRISPR has been used by researchers since 2012 to trim, disrupt, replace or add to sequences of an organism's DNA. Now, scientists at Johns Hopkins Medicine have shown that ...

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Improving genome editing with drugs

Genome defined

By: Gina Crisci

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Genome defined - Video

Consumer genetics firm 23AndMe has issued the first ever genome-wide association study of motion sickness. After the rocky legal back-and-forth between 23AndMe and the FDA that prevents the genetics company from extensively analyzing customer genetics, this studys results are a solid win, and vindicate 23AndMes goals of using its vast bank of genetics data benevolently.

The study, published in Oxford Journals Human Molecular Genetics, is the first to reveal the genetic variants of motion sickness and involved 80,000 consenting customers who had submitted material to 23AndMe to be genetically analyzed.

The study found 35 genetic factors associated with motion sickness that statistically stand out at genome-wide scalein other words, significant when compared among the whole human genome instead of just looking at particular genes. Many of these factors are in or near genes involved in balance and eye, ear, and cranial developmentmeaning motion sickness likely triggers effects in these areas. They even found that several of these factors had the potential to hit women harder, potentially tripling motion sickness' effect on those systems.

Given that roughly one in three people are affected by motion sickness, the study is obviously valuableand given the highly hereditary nature of motion sickness effects, mapping genetic effects of motion sickness is a perfect fit for 23AndMe. Results from a 2006 study have estimated that up to 70% of variation in risk for motion sickness is due to genetics.

The study also confirmed what wed already knownthat people suffering motion sickness are more prone to migraines, vertigo, and morning sickness. Overall, the results pointed toward the importance of the nervous system in motion sickness and a possible role for glucose levels in motion-induced nausea and vomiting.

While the FDA is preventing 23AndMe from giving U.S. customers analyses of their genetic data, 23AndMe is still selling genetics-gathering kits (sending the customers back ancestry reports instead of a report analyzing their genetic predisposition to disease) and then selling that data to pharmaceutical giants and academic labs. That sounds like just the data profiteering that Facebook has come under fire for, but the results of the motion sickness study back up 23AndMes claims that it can participate in illuminating research and make money doing it. To date, 23AndMe and its partners have published or contributed to 22 peer-reviewed papers about breast cancer, asthma, hyperthyroidism, and other genetically affected conditions.

23AndMe customers willingness to share data has sped up research speed by magnitudesa true crowdsourcing of genetic data.

"Researchers came to 23andMe to learn whether or not a certain gene was more prevalent in cancer patients," VP of Communications at 23AndMe Angela Calman-Wonson tells Fast Company. "23andMe sent surveys to individuals in our database with that particular gene, asking several cancer-related questions. We received more than 10,000 responses in 12 hours, and were able to determine that the gene was not prevalent among cancer patients. This type of research typically takes months and thousands of dollars, and in this case it took about 48 hours."

[via EurekaAlert ]

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Feeling Woozy? 23AndMe Releases First-Ever Genome-Wide Study Of Motion Sickness

Personalized medicine has taken a great leap forward with the advent of affordable whole genome sequencing and new ways to characterize other molecules in the body. Rather than looking for a handful of known bits of genetic code associated with disease, the genome reveals all three billion characters in the code.

A new generation of medical tests could soon provide a molecular snapshot of the body, the health of most every major organ and the presence of disease even in its earliest stages, according to Pieter Cullis, a professor of biochemistry and molecular biology at the University of B.C.

Cullis is among the featured speakers at a public forum on the power and potential of personalized health care at the Vancouver Public Library Wednesday) from 6 p.m. to 8 p.m. (Visit lsi.ubc.ca/talks for details and to RSVP.)

What can the genome tell us now?

Your genome is the blueprint for your entire body and it can reveal the risk of getting disorders such as heart disease by identifying disease-related gene variants in the patients genetic sequence. In the case of purely genetic disorders, such as Huntingtons Disease, it reveals the presence of disease before symptoms arise with absolute certainty. By comparing the genomes of healthy people and those of people with illnesses, scientists are detecting many previously unknown genetic variants related to disease, expanding the predictive power of genomics.

How are doctors using this technology?

By identifying who is at greater risk of disease, doctors can intervene sooner and patients can take steps in their personal conduct to manage or even prevent the onset of disease. By analyzing the genetic code of cancer cells doctors can target therapies precisely to the mutations present in a tumour and determine in advance if a patient is likely to have a life-threatening reaction to a drug before it is administered. Without the benefit of genomic analysis, nearly 75 per cent of the drugs administered to treat cancers fail to treat the patients specific illness.

Whats around the corner?

Analysis of the proteome the entire set of proteins that can be created by our genetic instruction set will potentially reveal the health of all of our organs in a single blood test. Our blood contains over 10,000 proteins many of which leach from our organs into the blood and can be used to assess the health of the organ and detect disease. Cancers shed proteins into the blood as well, which suggests such tools will have powerful early diagnostic value.

How is the practice of medicine going to change?

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Technology leads to bold new directions in personalized medicine

Released: 3-Feb-2015 9:00 AM EST Source Newsroom: 23andMe Contact Information

Available for logged-in reporters only

Newswise Mountain View, California February 3, 2015 23andMe, Inc., the leading personal genetics company, today announced the publication of the first ever genome-wide association study of motion sickness.

Published in Oxford Journals Human Molecular Genetics, this study is the first to identify genetic variants associated with motion sickness, a condition that affects roughly one in three people. Motion sickness has been shown to have high heritability, meaning genetics accounts for a large part of why some are more prone to motion sickness than others. Estimates indicate that up to 70 percent of variation in risk for motion sickness is due to genetics (1).

Until now theres been a poor understanding of the genetics of motion sickness, despite it being a fairly common condition, said 23andMe Scientist Bethann Hromatka, lead author of the study. With the help of 23andMe customers weve been able to uncover some of the underlying genetics of this condition. These findings could help provide clues about the causes of motion sickness and other related conditions, and how to treat them, which is very exciting.

The study, which involved the consented participation of more than 80,000 23andMe customers*, found 35 genetic factors associated with motion sickness at a genome-wide significant level. Many of these factors, referred to as single-nucleotide polymorphisms (SNPs), are in or near genes involved in balance, and eye, ear, and cranial development (e.g., PVRL3, TSHZ1, MUTED, HOXB3, HOXD3). Other SNPs may affect motion sickness through nearby genes with roles in the nervous system, glucose homeostasis, or hypoxia. The study shows that several of these SNPs display sex-specific effects, with up to three times stronger effects in women.

The work also confirmed previously known links with other conditions, finding that people with motion sickness are more likely to have experienced migraines, vertigo, and morning sickness as well as postoperative nausea and vomiting (PONV). The study also found new phenotypic associations between motion sickness and altitude sickness as well as many gastrointestinal conditions. Two of these related conditions (PONV and migraines) were found to share underlying genetic factors with motion sickness.

The results point to the importance of the nervous system in motion sickness and suggest a role for glucose levels in motion-induced nausea and vomiting a finding that may provide insight into other nausea-related conditions like PONV. Because the study also identified associations between motion sickness and lifestyle for instance, there is an association between being a poor sleeper and having a propensity for motion sickness the findings could also help researchers identify risk factors for the condition and future treatments.

23andMe has published numerous genome-wide association studies, but this is the first 23andMe study to include association results across a broad set of phenotypes (i.e. the relationship between specific traits).

Full paper citation and availability: Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis. Bethann S. Hromatka; Joyce Y. Tung; Amy K. Kiefer; Chuong B. Do; David A. Hinds; Nicholas Eriksson Human Molecular Genetics 2015; doi: 10.1093/hmg/ddv028 http://hmg.oxfordjournals.org/content/early/2015/01/26/hmg.ddv028.full.pdf?keytype=ref&ijkey=2ntxck5YUKc8QSA.

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23andMe Study Uncovers the Genetics of Motion Sickness

Short Film: Bael Genome - Part I
Please Subscribe if you enjoy the film! This is part one of our indie sci-fi horror film revolving around a viral outbreak at a remote Greenland research facility, operated by the "Paragon...

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