Category Archives: Genome

HGP10 Symposium: The $1,000 Genome, the $1,000,000 Interpretation - Kevin Davies
April 25, 2013 - The Genomics Landscape a Decade after the Human Genome Project More: http://www.genome.gov/27552257.

By: GenomeTV

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HGP10 Symposium: The $1,000 Genome, the $1,000,000 Interpretation - Kevin Davies - Video

May 2, 2013 Researchers at the Epigenetics and Cancer Biology Program at IDIBELL led by Manel Esteller, ICREA researcher and professor of genetics at the University of Barcelona, have described alterations in noncoding long chain RNA sequences (lncRNA) in Rett syndrome.

These molecules act as supervisor agents responsible of 'switch on' or 'switch off' other genes in our genome that regulate the activity of neurons. The work has been published in the last issue of the journal RNA Biology.

Dark genome

Only 5% of our genetic material are genes that encode proteins. The remaining 95% is known as dark genome or non-coding DNA and its function is still unknown. Part of this DNA produces RNA molecules called noncoding long chain RNA (lncRNAs).

Rett Syndrome

Rett syndrome is a neurodevelopmental disease and it is the second most common cause of mental retardation in females after Down syndrome. Clinical symptoms occur between 6 and 18 months after birth and consist of a loss of cognitive, social and motor capacities accompanied by autistic behaviors, eg, stereotypic hand movements.

Today there is no effective treatment of the disease but the control of their symptoms. The syndrome is usually due to the presence of a mutation in MeCP2 epigenetic gene that, as a magnet, regulates the expression of many other genes of the cell.

Esteller's team works with a mouse model that faithfully reproduces the characteristics of the human Rett syndrome. In this study, researchers compared the expression of long chains of RNA in healthy and diseased animals and found that the presence of mutations in the Mecp2 gene causes alterations in the activity of lncRNA.

One such altered lncARN regulates the function of a key neurotransmitter in the nervous system in all vertebrates brain (GABA receptor). "Its alteration," says Esteller, "could explain the defects of communication between neurons in girls affected by Rett Syndrome."

According to Manel Esteller "this finding, in addition to increasing knowledge about the causes of the disease, could open the door to new therapeutic strategies that target lncRNA molecules or GABA receptor."

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'Dark genome' is involved in Rett Syndrome

An analysis of the most common uterine cancer suggests the disease should be reclassified into four categories that may help lead to more targeted treatments.

About a quarter of a group of women who would be thought to have a favorable outcome under traditional diagnosis, or 10 percent of all patients, actually have genetic changes suggesting they have a more serious disease and may be in need of more aggressive treatment, according to the research in the journal Nature. A second DNA study of cancer in the New England Journal of Medicine describes almost all the major mutations in acute myeloid leukemia.

The two papers released yesterday are part of the Cancer Genome Atlas project, a U.S. National Institutes of Health effort to discover what changes make a normal cell cancerous and pinpoint more effective treatments. The work may mark the beginning of a shift from organ-based cancer research to gene- based research, said Michael Melner, scientific program director at the American Cancer Society, who wasnt involved in the research.

Whats becoming more and more evident is the potential that we can segment patients not based on the organ system where they have cancer, but the genetic defects the cancer has, he said. There might be lung cancers that are more genetically similar to brain cancers than to other lung cancers, and so they may be more appropriately treated with brain cancer drugs.

The Cancer Genome Atlas is looking at 20 types of cancer to understand the key mutations for the disease, said Richard K. Wilson, the director of the Genome Institute at Washington University in St. Louis. Right now, doctors consider the organ system, take a sample of the cancerous cells, and look at them under the microscope to determine the type.

Previous results from sequencing breast cancer, lung cancer and colon cancer were released last year. The approaches may lead to new therapies and help provide better care for current patients with existing treatments, doctors said.

The most common form of uterine cancer is found in the cells lining the womb, called the endometrium. The National Cancer Institute estimates that almost 50,000 new cases of endometrial cancer will be diagnosed this year in the U.S., and about 8,000 women will die of the disease.

In the endometrial cancer study, researchers analyzed tumors from 373 women to look for changes. Two current categories are used for endometrial cancer: endometrioid and serous. The former type is typically associated with obesity and has a favorable prognosis, while serous cancers usually have poorer outcome.

Serous and endometrioid cancers are diagnosed by pathologists looking under a microscope. However, by looking at the genomic level, yesterdays report found the endometrioid tumors that were most likely to grow and spread shared genetic features with the serous type, including alterations in the number of copies of a gene.

The finding suggests that women whose cancer has abnormal copies of a gene may be better treated by chemotherapy, which is more aggressive, rather than by radiation, after surgery. That hypothesis should be tested in clinical trials before practice is changed, the authors wrote.

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Genome Scan of Uterine Cancer Suggests New Tumor Classes

Privacy experts have identified participants in the Personal Genome Project using de-identified data.

One of the biggest questions in biology is the nature versus nurture debate, the relative roles that genetic and environmental factors play in determining human traits.

In 2006, George Church at Harvard University and a few others started the Personal Genome Project (PGP) to help answer this question. The goal is to collect genomic information from 100,000 informed members of the public along with their health records and other relevant phenotypic data. The idea is to use this information to help tease apart the relative contributions of genetic and environmental factors.

The project does not guarantee privacy for those who sign up. Indeed, the participants can reveal as much information as they like, including their ZIP code, birth date and sex.

However, the data is de-identified in the sense that the owners names and addresses are not included in their profiles on the PGP website and this generates a veneer of privacy.

Today, Latanya Sweeney and colleagues at Harvard show that even this is practically useless in keeping owners identities private. They say a relatively simple comparison of the list of PGP participants with other databases such as voter lists reveals the identity of a significant number of them with remarkable accuracy.

Thede-anonymisation procedure is simple.Voter lists contain information including name, address, but also zip code, birth date and sex. So it is straightforward to compare this list with PGP participants who have also included their zip code, birth date and sex.

When there is a match, the question is whether the zip, birth date and sex uniquely identify an individual. Sweeney has argued in the past that it does with an accuracy of up to 87 per cent, depending on factors such as the density of people living in the zip code in question.

These results seem to prove her right. Sweeney and co-submitted the results to the PGP organisation and asked them to check how accurate the de-anonymisation process had been. It turns out they accurately identified people with a success rate of up to 97 per cent.

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Participants in Personal Genome Project Identified by Privacy Experts

Privacy experts have identified participants in the Personal Genome Project using de-identified data.

One of the biggest questions in biology is the nature versus nurture debate, the relative roles that genetic and environmental factors play in determining human traits.

In 2006, George Church at Harvard University and a few others started the Personal Genome Project (PGP) to help answer this question. The goal is to collect genomic information from 100,000 informed members of the public along with their health records and other relevant phenotypic data. The idea is to use this information to help tease apart the relative contributions of genetic and environmental factors.

The project does not guarantee privacy for those who sign up. Indeed, the participants can reveal as much information as they like, including their ZIP code, birth date and sex.

However, the data is de-identified in the sense that the owners names and addresses are not included in their profiles on the PGP website and this generates a veneer of privacy.

Today, Latanya Sweeney and colleagues at Harvard show that even this is practically useless in keeping owners identities private. They say a relatively simple comparison of the list of PGP participants with other databases such as voter lists reveals the identity of a significant number of them with remarkable accuracy.

Thede-anonymisation procedure is simple.Voter lists contain information including name, address, but also zip code, birth date and sex. So it is straightforward to compare this list with PGP participants who have also included their zip code, birth date and sex.

When there is a match, the question is whether the zip, birth date and sex uniquely identify an individual. Sweeney has argued in the past that it does with an accuracy of up to 87 per cent, depending on factors such as the density of people living in the zip code in question.

These results seem to prove her right. Sweeney and co-submitted the results to the PGP organisation and asked them to check how accurate the de-anonymisation process had been. It turns out they accurately identified people with a success rate of up to 97 per cent.

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Anonymity of Personal Genome Project Broken by Privacy Experts

April 29, 2013

Brett Smith for redOrbit.com Your Universe Online

With their unique outer shell and sharp beak, turtles and their evolutionary history have long been a mystery to biologists.

A Nature Genetics report on the newly sequenced genomes of the soft-shell turtle and green sea turtle shows that the iconic reptiles have a common ancestor with crocodilians and birds diverging from these groups between 270 and 240 million years ago.

The genome-wide phylogenetic analysis of two turtles in our project, along with two crocodile genomic data additionally, makes clear the evolutionary history of turtles in diverging from other species and settles the disputes about the phylogenetic position of reptiles, said Zhuo Wang, the project manager from the Beijing Genomics Institute (BGI) in Shenzen, China who co-authored the report.

The genomic analyses and embryonic gene expression profiles have been combined to reveal the fundamental (evolutionary developmental) questions on turtle evolution and development, he said in a statement. Besides the interesting story, the genomic data we released here will provide a platform for more scientists to initialize their genome-wide studies on turtles.

For the study, the research team sequenced and analyzed the genomes of the two very different turtle species. They also researched various genes that may be associated with specific characteristics that are unique to turtles.

Their research uncovered olfactory receptor gene families that have allowed both turtles to develop superior olfaction ability. They also discovered that several genes involved in taste perception and certain metabolic functions are uniquely absent in turtles. In their report, the researchers suggested that the loss of these genes may be related to the reptiles slow metabolism.

The researchers also looked into the genes responsible for the embryonic development of turtles and compared them to those in chickens. They were able to use RNA sequencing, comparative genomics, and mathematical statistical approaches to see where the two species diverged genetically.

To understand the embryonic development of the turtles shell, researchers investigated miRNA expression and identified 20 key protein signaling genes. These genes allow for the formation of the carapacial ridge, an embryonic outgrowth that is responsible for shell development.

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Genome Study Of Turtle Species Sheds Light On Evolution Of The Shell

NEW YORK, April 30, 2013 /PRNewswire/ -- Analytic Partners, a leading global marketing consultancy, announced today the latest release of their proprietary analytics and forecasting software, GPS (Guiding Performance and Strategy). Based on the insights from Analytic Partners' ROI Genome Project, the firm has enhanced GPS' web-based, customizable interface and functionality, which includes marketing simulation, predictive planning, optimization and tracking.

GPS is currently leveraged by CIOs, CMOs and other marketers across various industries to manage and monitor global businesses, align budgets, set and monitor business objectives, assess the risks and opportunities of marketplace and spending changes, and develop and track forecasts. GPS provides a transparent and accurate view of performance and integrates data including paid, owned and earned online and offline media, promotions, and other marketing initiatives, as well as economic information.

"Over the course of our 13 year history, Analytic Partners has established and compiled an internal insights database, now coined the ROI Genome Project, to help us identify and quantify the drivers of successful business performance," said Nancy Smith, CEO of Analytic Partners. "We've applied those insights to every service we offer, including the technology we build. Those principles of success, integrated with the power we provide through GPS, have become an invaluable way for our clients to make well-informed business decisions."

Features of GPS include:

Analytic Partners is the first firm to provide both the analytics technology and consultative services to companies in a range of sectors including financial services, electronic, hospitality, retail, and CPG. Based on the individual needs of their clients, and with the assistance of Analytic Partners' team of data scientists, data is audited and compiled into GPS, ultimately producing customized reporting and insights. Organizations leveraging these dual services experience a direct impact on marketing and sales programs. Onaverage, Analytic Partners witnesses an average ROI improvement of 30% for our clients.

"In order to understand where you want to spend your marketing dollars, you first need to understand what has worked and what has not," added Nancy Smith. "Taking a granular view of the facts and reasoning behind sales fluctuations is the first step to achieving a greater ROI. Our clients partner with us in long-term relationships to continually build deep knowledge about their brands, customers and competitors."

For more information about Analytic Partners' GPS and ROI Genome Project visit: http://www.analyticpartners.com/

About Analytic Partners:

Analytic Partners is a leading global marketing consultancy, founded in 2000 to deliver customized analytics that improve sales performance and marketing ROI. Analytic Partners provides both the technology and consultants to help marketers achieve a deeper understanding of their business through insights from marketing mix modeling, cross-media attribution, digital and social media analysis, customer loyalty analysis, predictive modeling and marketing optimization. With multiple locations in the Americas, Europe and Asia-Pacific, Analytic Partners serves multinational businesses and local brands across the globe.

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Analytic Partners Taps Power of ROI Genome Project to Launch GPS for Marketers

Apr. 28, 2013 From which ancestors have turtles evolved? How did they get their shell? New data provided by the Joint International Turtle Genome Consortium, led by researchers from RIKEN in Japan, BGI in China, and the Wellcome Trust Sanger Institute in the UK provides evidence that turtles are not primitive reptiles but belong to a sister group of birds and crocodiles. The work also sheds light on the evolution of the turtle's intriguing morphology and reveals that the turtle's shell evolved by recruiting genetic information encoding for the limbs.

Turtles are often described as evolutionary monsters, with a unique body plan and a shell that is considered to be one of the most intriguing structures in the animal kingdom.

"Turtles are interesting because they offer an exceptional case to understand the big evolutionary changes that occurred in vertebrate history," explains Dr. Naoki Irie, from the RIKEN Center for Developmental Biology, who led the study.

Using next-generation DNA sequencers, the researchers from 9 international institutions have decoded the genome of the green sea turtle and Chinese soft-shell turtle and studied the expression of genetic information in the developing turtle.

Their results published in Nature Genetics show that turtles are not primitive reptiles as previously thought, but are related to the group comprising birds and crocodilians, which also includes extinct dinosaurs. Based on genomic information, the researchers predict that turtles must have split from this group around 250 million years ago, during one of the largest extinction events ever to take place on this planet.

"We expect that this research will motivate further work to elucidate the possible causal connection between these events," says Dr. Irie.

The study also reveals that despite their unique anatomy, turtles follow the basic embryonic pattern during development. Rather than developing directly into a turtle-specific body shape with a shell, they first establish the vertebrates' basic body plan and then enter a turtle-specific development phase. During this late specialization phase, the group found traces of limb-related gene expression in the embryonic shell, which indicates that the turtle shell evolved by recruiting part of the genetic program used for the limbs.

"The work not only provides insight into how turtles evolved, but also gives hints as to how the vertebrate developmental programs can be changed to produce major evolutionary novelties." explains Dr. Irie.

Another unexpected finding of the study was that turtles possess a large number of olfactory receptors and must therefore have the ability to smell a wide variety of substances. The researchers identified more than 1000 olfactory receptors in the soft-shell turtle, which is one of the largest numbers ever to be found in a non-mammalian vertebrate.

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Turtle genome analysis sheds light on turtle ancestry and shell evolution

Now weve got the book, now weve got the words and the hard part is figuring out the logic and what all the sentences mean.

Howard Lipshitz

the University of Torontos head of molecular genetics

It was like Gods own jigsaw puzzle.

Built up over evolutionary eons, it featured 46 spiralling, ladder-like structures, some three billion pieces, and it took thousands of scientists working around the globe 13 years to complete.

But that, it turned out, was the easy part.

The Human Genome Project which was presented in its final form 10 years ago this month provided a map of mankinds DNA. But it also opened up a Pandoras box of boggling complexity in the biological sciences and medicine that will take decades more to unravel.

Its mind-blowing actually, says Dr. Jeff Wrana, a top cancer researcher at the University of Toronto.

Its one of those things, you know, be careful what you wish for. .

What genome cartographers had wished for at the projects 1990 inception what the genetic tea leaves had led them to expect was something far simpler than what they found.

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The Human Genome Project: How it changed biology forever

Public release date: 28-Apr-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

April 28, 2013, Shenzhen, China- The Joint International Turtle Genomes Consortium, led by investigators from RIKEN, BGI, and Wellcome Trust Sanger Institute, has completed the genome sequencing of soft-shell turtle (Pelodiscus sinensis) and green sea turtle (Chelonia mydas). These achievements shed new light on the origin of turtles and applied the classical evo-devo model to explain the developmental process of their unique body plan. The findings were published online in Nature Genetics.

The evolution of turtles is an enigma in science. Their distinct body design-with a sharp beak and protective hard shell has changed very little over the past 210 million years. As the smallest species of soft-shell turtles, Chinese soft-shell turtle was once commonly sold in pet shops. Green sea turtle is considered as the largest of all the hard-shelled sea turtles and is named because of the green fat beneath its shell. Its population sizes has been drastically reduced recently and it has been listed as an endangered species.

To reveal the evolutionary history of turtles and the mechanisms underlying the development of their unique anatomical features, researchers in this project sequenced and analyzed the genomes of soft-shell turtle and green sea turtle. They found the evidence that turtles are likely to be a sister group with the common ancestor of crocodilians and birds from whole genome phylogenetic analyses. The turtles were diverged from archosaurians approximately between 267.9 and 248.3 million years ago, which coincides with the time range of the Upper Permian to Triassic period that overlapped or followed shortly after the end of Permian extinction.

In the study, researchers performed the brief research on genes may be associated with the turtle-specific characteristics, and found some olfactory receptor (OR) gene families were highly expanded in both turtles. This finding suggests that turtles have developed superior olfaction ability against a wide variety of hydrophilic substances. In addition, many genes involved in taste perception, hunger-stimulating, and energy homeostasis regulating hormone ghrelin have been uniquely lost in turtles. Researchers suggested that the loss of these genes may be related to their low-metabolic rate.

The consortium also investigated the association of embryonic gene expression profiles (GXP) and their morphological evolution pattern, based on ENSEMBL soft-shell turtle gene-set. By integrating RNA-seq technology, comparative genomics method, and mathematical statistical approaches, researchers confirmed GXP divergence during embryogenesis of soft-shell turtle and chicken indeed follows the developmental hourglass model. They also revealed that the maximal conservation stage occurred at around the vertebrate phylotypic period, rather than at later stage that show the amniote-common pattern.

To clarify the morphological specifications of turtle embryogenesis in late development, especially the formation of the carapacial ridge (CR), researchers investigated into CR-specific miRNA expression, found existence of tissue-specific miRNAs and involvement of Wnt signaling. Also they revealed the Wnt expression involved in the carapacial ridge (CR) formation of the turtle shell, researchers annotated all the Wnt genes in the two turtle genomes, identifying a total of 20 Wnt genes. Intriguingly, they discovered Wnt5a is the only Wnt gene expressed in the turtle CR region, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty.

Zhuo Wang, Project Manager from BGI, said, "The genome-wide phylogenetic analysis of two turtles in our project, along with two crocodile genomic data additionally, makes clear the evolutionary history of turtles in diverging from other species and settles the disputes about the phylogenetic position of reptiles. The genomic analyses and embryonic gene expression profiles have been combined to reveal the fundamental evo-devo questions on turtle evolution and development. These works have been highly appreciated by the editor and reviewers. Besides the interesting story, the genomic data we released here will provide a platform for more scientists to initialize their genome-wide studies on turtles. "

Dr. Hongyan Zhang, Regional Director of BGI Tech Solutions Co., Ltd. for Japan, said, "The completed genome sequencing of soft-shell turtle and green sea turtle give an important hint to uncover the development and evolution mechanism of turtles. This scientific achievement is a joint effort supported by BGI's advanced sequencing technologies and excellent bioinformatics capabilities, the profound basis research background of developmental biology from RIKEN, and other partners' great contributions. We are looking forward to having more collaboration with other scientists for better exploring the secret of life together in the near future."

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Turtle genome analysis sheds light on the development and evolution of turtle-specific body plan