Category Archives: Genome

Genome of a human B-cell in 3D
3D genome reconstruction from a Hi-C dataset. Professor Jianlin Cheng #39;s Group Bioinformatics, Data Mining and Machine Learning Lab Department of Computer Sci...

By: Tuan Trieu

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Genome of a human B-cell in 3D - Video

Map to reference and MIRA assembly of mitogenomes in Geneious (Part 5)
In this last mitochondrial genome assembly tutorial we complete our assembly. We were not able to recover the control region, due to the high genetic distance to the reference genome. Also...

By: luckylion

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Map to reference and MIRA assembly of mitogenomes in Geneious (Part 5) - Video

Jan 26, 2015, Shenzhen, China -Scientists from Jiangxi Agricultural University, BGI and University of California published their latest research on genetic mechanism of pig altitude-adaptations in Nature Genetics online. Their research underlined the importance of introgression for the first time as a potential reason for pig adaptations to cold and hot environments, which provided novel insights into the evolutionary history of pigs and the role of introgression in adaptation more generally.

Pigs, as one of the earliest domesticated animals, were domesticated largely in Near East and China approximately 10,000 years ago. Since then, under the combined effects of natural selection and human-driven artificial selection, pigs evolved phenotypic diversity in appearance, fertility, growth, palatability, and local fitness. As the genetic basis of those adaptive evolution remained largely unexplored, scientists of this article conducted whole-genome sequencing and selective sweep analysis trying to figure out the genetic basis contributed to the adaptation of domesticated Chinese pig breeds, especially related to thermostatic regulation for varying-latitude environments.

In the current study, the scientists selected 69 pig individuals represented 11 geographically diverse breeds and 3 populations of wild boar from cold and hot environments in China. This is one of the first population genomics analyses to use high-coverage whole-genome sequencing in pigs, each individual has been sequenced more than 20-fold depth with the genome coverage of 95%. Totally, 41 million variants have been identified, with 21 million variants were absent from the dbSNP database. Substantially, a nearly complete catalogue of the genetic variants has been compiled, which allowed the scientist to identify a genome-wide set of loci for local adaptation in Chinese pigs.

From the genome wide scan, a set of gene loci correspond to thermostatic regulation has been identified. Notably, an exceptionally large (14 Mb) and low-recombination region on the X chromosome appeared to have two distinct haplotypes in the high- and low-latitude populations, which may be possibly responsible for adaptations to cold and hot environments respectively. Another surprising finding of this study was that the adaptive haplotype in the high-latitude populations was likely introduced from another divergent Sus species. This is the first example of adaptive evolution triggered by interspecies introgression in domesticated animals, which gave us a clue that introgression event between divergent species may be an important resource for evolutionary adaptation and could largely facilitate this process.

Likai Mao, the project manager of BGI, said, "We found lots of loci could be related with environmental adaptation. When we noticed a big region with special pattern on the haplotype figure of chromosome X, we knew something must be there. "

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Introgression in the pig genome leads to their altitude adaptation

Genome sequencing | Nazneen Rahman
Would you want to know your genome sequence? What information might it provide? Professor Nazneen Rahman is Head of the Division of Genetics and Epidemiology at The Institute of Cancer ...

By: Wellcome Collection

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Genome sequencing | Nazneen Rahman - Video

Study is cover of Nature Medicine; included in historic first upload to Autism Speaks MSSNG portal for open-access research

TORONTO, ONT. (January 26, 2015) - The largest-ever autism genome study, funded by Autism Speaks, reveals that the disorder's genetic underpinnings are even more complex than previously thought: Most siblings who have autism spectrum disorder (ASD) have different autism-linked genes.

Led by the director of the Autism Speaks MSSNG project (pronounced "missing"), the report made the cover of today's Nature Medicine.

Simultaneous with publication, the study's data became part of the historic first upload of approximately 1,000 autism genomes to the Autism Speaks MSSNG portal in Google Cloud Platform. Autism Speaks is making the de-identified data openly available for global research in order to speed understanding of autism and the development of individualized treatments.

"This is a historic day," says study leader Stephen Scherer, "as it marks the first time whole genome sequences for autism will be available for research on the MSSNG open-science database. This is an exemplar for a future when open-access genomics will lead to personalized treatments for many developmental and medical disorders." In addition to leading Autism Speaks' MSSNG program, Dr. Scherer directs the Centre for Applied Genomics at Toronto's Hospital for Sick Children and the McLaughlin Centre at the University of Toronto.

"By using the cloud to make data like this openly accessible to researchers around the world, we're breaking down barriers in a way never done before," says Robert Ring, chief science officer of Autism Speaks and co-author on the Nature Medicine paper. "As always, our goal at Autism Speaks is to accelerate scientific discovery that will ultimately improve the lives of individuals with autism at home and around the world."

In total, the MSSNG project aims to make at least 10,000 autism genomes available for research, along with a "tool box" of state-of-the-art tools to aide analysis.

Autism's Surprising Diversity

In the new study, Dr. Scherer's team sequenced 340 whole genomes from 85 families, each with two children affected by autism. The majority of siblings (69 percent) had little to no overlap in the gene variations known to contribute to autism. They found that the sibling pairs shared the same autism-associated gene changes less than one third of the time (31 percent).

The findings challenge long-held presumptions. Because autism often runs in families, experts had assumed that siblings with the disorder were inheriting the same autism-predisposing genes from their parents. It now appears this may not be true.

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Largest-ever autism genome study finds most siblings have different autism-risk genes

Results of the largest autism study to use whole genome sequencing suggest that no two autism cases are the same, even if they come from the same family.

The study, published online Monday in the journal Nature Medicine, shows that there is a large genetic diversity in autism. It also underscores the need to do whole genome sequencing on patients, Dr. Stephen Scherer from Toronto's Hospital for Sick Children said in a statement.

"We already knew that there are many differences between autism cases, but our recent findings firmly nail that down," he said. "It shows that a full assessment of each individual's genome is needed to determine how to best use knowledge of their own genetic makeup for autism treatment."

For the study, researchers analyzed the DNA of 85 different families, each with two children with autism. Whole genome sequencing technology was used to detect any genetic mutations in the children.

Scherer said the results showed that no two autism cases are the same, even if they come from the same family.

"We believe each child with autism is like a snowflake; one is unique from another. Surprisingly, our research found that in more cases than not, even siblings can have two different 'forms' of autism," he said.

Scherer said the results will have a large impact on the field of genetics and DNA analysis.

"This means we cannot just look at parts of the DNA if we want to fully understand the underpinnings of autism and other disorders we need to analyze the entire genome," he said.

The data collected for the study is part of a larger project named MSSNG, headed by Autism Speaks and Google. The goal of the project is to sequence the genomes of 10,000 families with autism, and make the data open-source and accessible to researchers from around the world.

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Whole genome sequencing reveals, 'each child with autism is like a snowflake'

Georgia Tech researchers, working with colleagues in the National Center for Biotechnology Information (NCBI), have released a new version of a genome annotation system capable of analyzing more than 2,000 prokaryotic genomes per day, helping researchers accelerate prokaryotic genomics-based studies worldwide.

In biology, prokaryote generally describes a microorganism that lacks a distinct membrane-bound nucleus and has its genetic material contained in a single molecule of DNA. These include bacteria and archaea.

The NCBI operates the Prokaryotic Genome Annotation Pipeline, a high- performance software system designed to analyze gene sequences of these microorganisms. As more high-quality genomes become available -- and as the cost of sequencing continues to fall -- the need for high-throughput analysis and annotation pipelines cannot be overstated.

The latest advance comes as the NCBI incorporates Georgia Tech's GeneMarkS+ into the PGAP system. Developed by Mark Borodovsky's team at Georgia Tech, GeneMarkS+ is a self-training machine learning tool for novel gene identification that can combine intrinsic evidence revealed by genomic sequence patterns with extrinsic evidence derived from already annotated genomes.

"The new system enables researchers to get critically important analysis that consistently integrates information of all sources of evidence nearly in real time instead of days and weeks," said Borodovsky, a Regents' professor with a joint appointment in the School of Computational Science and Engineering and the Coulter Department of Biomedical Engineering. "Our group is excited to be a part of the whole team working on this project with high international visibility."

Before implementing GeneMark+ into the pipeline, the system could handle only 20 annotations daily.

"Dr. Borodovsky worked closely with Tatiana Tatusova's team at NCBI to incorporate and refine GeneMarkS+ in the context of the NCBI annotation pipeline," said Jim Ostell, chief of NCBI's Information Engineering Branch. "It provides a critical core infrastructure to NCBI and to users of NCBI resources."

PGAP uses GeneMarkS+ in conjunction with proteomic evidence obtained from large groups of orthologous gene clusters representing the core protein complement for well-annotated species. As new organisms are sequenced, PGAP adjusts by mining the existing protein information to build new core protein clusters, iteratively improving its annotation based on the ever-increasing wealth of available evidence from submitted bacterial genomes.

The new system offers a modular structure, permitting easy extension with new algorithms. PGAP also provides extensive tracking of execution and decision making, and thus permits an easy trace-back to understand the evidence behind key algorithmic decisions. The PGAP process is described at http://www.ncbi.nlm.nih.gov/genome/annotation_prok/process/

PGAP produces high-quality annotation designed to meet INSDC standards for sequence submission and follows UniProt naming guidelines. PGAP is available at NCBI for bacterial genomes as part of GenBank sequence submission, making it a valuable resource to researchers worldwide.

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Faster annotation system for prokaryotic genomes unveiled

Less than a third of siblings with autism shared the same DNA mutations in genes associated with the disorder, according to a new study that is the largest whole-genome sequencing for autism to date.

Canadian researchers sequenced whole genomes from 170 siblings with autism spectrum disorder and both their parents. They found that these sibling pairs shared the same autism-relevant gene variations only about 31% of the time, according to the study published online Monday in the journal Nature Medicine.

More than a third of the mutations believed to be relevant to autism arose in a seemingly random way, the study also found.

It isnt really autism; its autisms, said the studys lead investigator, Dr. Stephen W. Scherer, head of the Center for Applied Genomics, Genetics and Genome Biology at the Hospital for Sick Children in Toronto. In some cases, he added, its like lightning striking twice in the same family.

The results are part of 1,000 whole genomes that are being made available to researchers via a massive Google database that autism advocates hope will grow to 10 times that size by next year.

The effort, spearheaded by the research and advocacy group Autism Speaks, has been somewhat controversial from the start, with some questioning whether results from the relatively costly and time-consuming process will be too complicated or obscure to yield significant breakthroughs.

Indeed, researchers associated with the effort acknowledged that much of their data remain a mysterious ocean of jumbled, deleted or inserted DNA code, much of which is not located on areas of the genome that program the proteins that directly affect biological functions.

You might expect that youd see some commonalities in the mutations between kids in the same family, but thats actually not the case here, said Rob Ring, chief science officer of Autism Speaks. Were not really sure what might explain that at this time.

Said Scherer: Weve really just scratched the surface of this data.

Thats where Googles cloud-based data capabilities will come in, according to Ring and Scherer. Making these whole genomes potentially 10,000 of them available to any researcher could yield unexpected connections and order in data thatare the equivalent of more than 13 years of streaming high-definition television programming.

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Autism genomes add to disorder's mystery

Scientists are leveraging cloud services provided by Google and other companies to streamline and share massive amounts of data generated by sequencing the human genome. The hope is that the increased power and speed of cloud services will accelerate research and increase opportunities for advances in medicine and other fields.

For example, a thousand genomes of people who fall within the autism spectrum were uploaded to Googles servers Monday as part of a new projectsponsored by the nonprofit Autism Speaks.

The data dump represents the first of 10,000 genomes that will eventually be stored in the companys cloud and shared among autism specialists. The funders of the project, known as Mssng, hope researchers will use the trove of genomes to enable earlier diagnosis, develop targeted treatments or even find a cure for the disorder thought to have at least some basis in genetics.

Mssng is the latest in a series of genome-based projects that use cloud storage technology to advance science. Through these initiatives, cloud storage technology has proven to be a boon for both companies and scientists. Worldwide, cloud services make up a $45.7 billion industry,according to analystsat International Data Corp. Google has welcomed researchers by creating theGoogle Genomicsplatform to allow for easy upload, storage and sharing of genomic data and theCompute EngineandBigQuerytools for quick analysis.

Cloud storage has been used in other genomic research. One such project is called Chargeand is run by Baylor College of Medicine in conjunction with Amazon and a company called DNAnexus. The project resulted in 3,751 genomes being analyzed to study heart disease and aging. In a similar venture, IBM and the New York Genome Center recentlyentered into a partnershipto leverage Watsons smart computing software for genomic research.

This first upload by Mssng of autistic genomes to Google was also part of a study published Monday by Nature Medicine that analyzed the genomes of siblings for clues about how genetics influences the disorders development. The results showed that a brother and sister who both have autism do not necessarily share the same autism-linked genes from their parents, according to a statement provided by Autism Speaks. Researchers already knew that parents of a child with autism are more likely to have a second child who is affected, and that even identical twins do not always exhibit the same type of autism.

Mssngs developers hope this new data paired with cloud-based analytical tools will help researchers learn more about the inheritability of autism, which affects one in 68 children in the U.S., according to a blog post written by Robert Ring, chief science officer at Autism Speaks, when the project was announced.

Google may hold other interests in furthering genomic study. Two years ago it started a health care company called Calico that is partnering with drug company AbbVie to build a $1.5 billion research facility in the San Francisco Bay area to seek ways to extend longevity, according to the San Jose Mercury News. The team could look for solutions that engineer or make repairs to parts of the genome. Last year, the company joined Merck & Co. and Amgen as members of the Global Alliance for Genomics and Health, a health consortium focused on developing medicine based in genomics.

Genomic data has been highly prized since it was made possible by DNA sequencing techniques in the late 1970s. In 2003, the Human Genome Project gave geneticists a map of all the genetic variety that exists within humankind. Sequencing a genome in the early days, though, could cost as much as $100,000,according to Nature. Costs have since come down to about $5,000 per genome and set off an explosion of data within the field. In the past, server capacity and analytical tools have placed limits on how much of this data was used or shared.

"In the beginning, we shared genomic information by shipping hard drives around the world, Ring wrote in his blog post. Downloading even one individual's whole genome in a conventional manner can take hours the equivalent of downloading a hundred feature films.

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Google Cloud Hosts 1,000 Genomes Uploaded By Autism Researchers, Advancing Science Through Data Storage

Comparison: 23andMe and Prometheus Genome Analysis
This video compares the aesthetic and functional aspects of 23andMe and Promethease test reports. It focuses primarily on layout and information provided, wi...

By: Rob Flanagan

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Comparison: 23andMe and Prometheus Genome Analysis - Video