Category Archives: Genome

09- Human Genome and Cancer - Interview with Dr. William Hahn
For additional information visit http://www.cancerquest.org Dr. William Hahn is an Associate Professor of Medicine at Harvard Medical School. Dr. Hahn #39;s research focuses on how cancer forms. He is interested in the mechanisms that allow cancer cells to reproduce indefinitely, including an enzyme called telomerase. He also works to develop new model systems to study cancer. In this interview, Dr. Hahn discusses his research and the impact of the human genome project on cancer researchers. In this interview segment, Dr. Hahn discusses his work with the human genome and how he is using cancer genomics to develop a better understanding of cancer. To learn more about cancer and watch additional interviews, please visit the CancerQuest website at http://www.cancerquest.org

By: CancerQuest

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09- Human Genome and Cancer - Interview with Dr. William Hahn - Video

An international team of scientists has sequenced the genome of the chickpea, a critically important crop in many parts of the world, especially for small-farm operators in marginal environments of Asia and sub-Saharan Africa, according to an announcement from researchers at UC Davis, and the International Crops Research Institute for the Semi-Arid Tropics in India.

The researchers published this week in the online version of the journal Nature Biotechnology the reference genome of the chickpea variety known as CDC Frontier and the genome sequence of 90 cultivated and wild chickpea lines from 10 different countries.

"The importance of this new resource for chickpea improvement cannot be overstated," said Douglas Cook, a UCD professor of plant pathology.

"The sequencing of the chickpea provides genetic information that will help plant breeders develop highly productive chickpea varieties that can better tolerate drought and resist disease -- traits that are particularly important in light of the threat of global climate change," he said.

Cook is one of three lead authors on the chickpea genome sequencing project, along with Rajeev Varshney of the International Crops Research Institute for the Semi-Arid Tropics and Professor Jun Wang, director of the Beijing Genomics Institute of China.

The chickpea plant, whose high-protein seed is also referred to as a garbanzo bean, is thought to have originated in the Middle East nearly 7,400 years ago.

India grows,

The announcement of the chickpea genome sequencing is the culmination of years of genome analysis by the International Chickpea Genome Sequencing Consortium, led by the International Crops Research Institute for Semi-Arid Tropics. The consortium includes 49 scientists from 23 organizations in 10 countries.

Funding for the sequencing project was provided by the U.S. National Science Foundation; Saskatchewan Pulse Growers of Canada; Grains Resource Development Corporation of Australia; Indo-German Technology Corporation of Germany and India; National Institute for Agricultural and Food Research and Technology of Spain; U.S. Department of Agriculture; Ministry of Education, Youth and Sports of the Czech Republic; University of Cordoba, Spain; Indian Council of Agricultural Research; BGI of China; and International Crops Research Institute for the Semi-Arid Tropics.

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UC Davis helps global team sequence chickpea genome

Novel Microscale Epigenomics Technology developed by GIS makes it possible to study the epigenome of rare cell populations and biopsy samples

Scientists at A*STARs Genome Institute of Singapore (GIS) have successfully developed a method to map the epigenome using 100 times fewer cells than was previously possible. The discovery, published in the journal Developmental Cell, means that it is now possible to study the epigenome of parts of the body with rare cell populations such as germ cells (which differentiate into the egg or sperm), and clinical biopsy samples (to advance the study, diagnosis and prevention of cancer).

This is an extremely important advancement since the proper regulation of the epigenome is essential for normal growth and health, while any abnormality in the regulation could be the cause of diseases such as cancers.

The genome, which refers to the complete set of DNA (deoxyribonucleic acid) in a cell, is identical in every cell of an individuals body. Chemical markers (also known as epigenetic markers) target the genome and influence which genes get turned on or off. It is the turning on or off of the genes that gives rise to the existence of different cells in the body, even though the genomes are identical. The epigenome refers to the record of these chemical changes that occur to the DNA.

Chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq) is a commonly used method to study the epigenome of cells. In ChIP-Seq, DNA fragments that are associated with specific epigenetic marks are baited out, sequenced and mapped to a reference genome. However, the conventional method typically requires large quantities of cells, which makes it difficult to study rare cell populations of the body or in precious clinical biopsy samples.

This limitation prompted the GIS scientists to miniaturize the ChIP method such that it is now possible to map the epigenome using much fewer cells (1,000 to 100,000 cells). The conventional method required one million to 10 million cells.

The scientists further applied this technology on a small number of mouse germ cells, which are the embryonic precursors of the sperm and egg, and uncovered many interesting epigenomic features that provide insight into the biology of the germ cells.

GIS Executive Director Prof Ng Huck Hui said, Epigenomics is an exciting frontier for human biology research. While the sequence of human genome tells us the code for life, it doesnt tell us how this code is utilized. The mystique of the epigenome lies in the multiple forms it takes and the remarkable information that it harbours. At the Genome Institute of Singapore, we are investing efforts to develop new microscale technologies to analyse the epigenomes of human cells and tissues.

"The new ChIP-seq protocol allows us to map the epigenomes of very small populations of cells that are not accessible by conventional methods, said GIS Principal Investigator Dr Shyam Prabhakar. It's akin to having a more powerful microscope that provides a more fine-grained view of critical biological processes. We are very excited about using this new technique to peer into the inner workings of tiny groups of cells that have a massive impact on human health. For example, tumours in cancer patients are known to be heterogeneous at the fine scale - some sub-regions are relatively benign, while others are lethal. The new protocol will help us characterize this fine-scale variation, and hopefully lead to more precise treatments for cancer and a host of other diseases."

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:: 11, Feb 2013 :: A*STAR’S GENOME INSTITUTE OF SINGAPORE DEVELOPS ADVANCED METHOD TO STUDY EPIGENOME OF CELLS ...

DNASTAR - Illumina Reference Guided Genome Assembly
See how to align Illumina data for a bacterial genome against a reference sequence using Lasergene Genomics Suite

By: DNASTARInc

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DNASTAR - Illumina Reference Guided Genome Assembly - Video

When the workday ends at BGIs factory in Shenzhen, the headquarters of the largest genome mapping company in the world, its like a bell has gone off at math camp. The companys scientists and technicians spill out of the doorways of the building, baby-faced and wearing jeans and sneakers. Some still have braces. Several young women link arms and skip toward a bus line. Others head next door to the dorm or over to the canteen where young couples are holding hands across plastic trays. This work we do is tiring and requires focus, says Liu Xin, a 26-year-old team leader in the bioinformatics division, as he sinks into a couch in one of BGIs conference rooms. So its good that they allow us to date.

Liu is one of a small army of recent college graduates at BGIs largest facility, a former shoe factory. Two gray buildings, the factory and the dorm, are wedged between one of Shenzhens industrial zonesa grid of high-rises, apartment buildings, and several hospitals and medical equipment companiesand a lush, jungly hill thats in the process of being bulldozed. Liu is stocky and serious, glad that he already has a steady girlfriend so he can focus on his career. He arrived at BGI three years ago, a biology major from Peking University with little experience in the study of the genome, the term for the entirety of an organisms genetic information. Now hes one of the senior people in his department. He works 12-hour days and oversees the sequencing of multiple genomes at a time. He specializes in plantshis team is currently sequencing a species of orchid. The bioinformatics teams around him are picking through the genomes of animals, microbial organisms, humans, and anything else that comes with a genetic code. Everyone is just out of college, he says. I am now more sophisticated than most of the newcomers.

Ten years after the mapping of the human genome, BGI has established itself as the worlds largest commercial genetic sequencer. The ranks of Chinas college graduates are expanding faster than the country can employ them, and BGI is leveraging this cheap, educated labor pool. At the factory in Shenzhen, more than 3,000 employees (average age, 26) spend their days preparing DNA samples, monitoring sequencing machines, and piecing together endless strings of As, Cs, Ts, and Gs, the building blocks of genetic material.

This is big data analysis, says Wang Jun, BGIs 36-year-old executive director. Wang, who regularly wears tennis shoes and untucked polo shirts, has published more than 35 articles in Science and Nature magazines and also teaches at the University of Copenhagen. Genomics, he says, is a new field and experts are being created from scratch. We dont need Ph.D.s to do this work, Wang says. Instead, he believes genomics is best learned the old-fashioned way. You just throw them in, he says of BGIs technicians. The best way is hands-on experience. When the first draft of the human genome was released in 2000 as part of the international Human Genome Project, it seemed inevitable that scientists would soon crack the codes of disease, health, and human development. But the genome has proved more complicated. What scientists produced in 2000 was a long list of nucleotides, the combinations of markers in DNA that specify the makeup of an organism. It was just a list, and only a fraction of it is understood. Scientists were quick to identify fragments of the genome that translate into proteins, which control things like eye color, but these make up only 1.5percent of the entire thing. As geneticists like to put it, they produced a map without a legend. This is where BGI comes in.

Photograph by Luke Casey for Bloomberg BusinessweekExecutive director Wang Jun (left)

The company was founded in 1999 with state funding to lead Chinas participation in the Human Genome Project. We didnt think about any business model; we basically didnt plan further than the human genome, says Wang, who was brought on in the early days of BGI to provide expertise in computers. China, he points out, was the only developing country working on the international project, and although the BGI team contributed only 1percent of the finished project, it did it quickly and with little previous experience. Even Bill Clinton thanked us for our participation, he says. Wang joined the project when he was just 22 and worked under BGIs two founders, the scientists Wang Jian, then 45, and Yang Huanming, then 47.

For its next challenge, BGI decided to tackle rice, whose genome is significantly shorter than that of humans but still large enough to impress. We recruited a bunch of undergraduates, and lots of them had no working experience on any project, Wang Jun says. The schedule was tight; Wang and his team barely slept. We can do these kind of crazy things in BGI, he says. We can get 100 people together, very fresh, no experience at all, and get it done.

In 2002, BGI published a paper on the rice project in Science and again attracted attention and money from the Chinese government, though its a private company. The company was rewarded with entry into the state-run Chinese Academy of Sciences, a distinction that secured additional funding. As part of CAS, however, BGI was limited to only 90 scientists. Its leaders had their eyes on expansion. Our boss wanted to buy more sequencing machines, says Deng Wenxi, a 24-year-old communications officer at the BGI factory. But the Beijing government would not support us. In 2007 the company found a solution by way of Shenzhens city government, which offered the factory 10million yuan (about $1.6 million in todays exchange rates) to cover startup fees and 20million yuan in annual grants. The company changed its name from Beijing Genomics Institute to BGI Shenzhen and moved to the shoe factory. Beijing is more strict, says Deng. Shenzhen wanted to welcome us. The factory, she says, actually belongs to the Shenzhen government. When asked about the move, Wang Jun answers the question a little more vaguely, Well, he says, the weather is definitely nicer here.

Today, BGI organizes its operations into three categorieshealth care, agriculture, and the environment. When scientists look at the genome, theyre looking for variations from one individual to another, from species to species, or population to population. Theyre looking to understand which variations link to specific traits or diseases.

As Wang Jun says, decoding any genome is a big data endeavor, and theres no other research institution or for-profit sequencing company in the world that has the capacity of BGI. In health care, it offers straightforward sequencing services for universities and corporations globally, which ask BGI to sequence a genome and send it back for analysis. More often than not, BGI works in partnerships to map, analyze, and publish the findings.

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BGI's Young Chinese Scientists Will Map Any Genome

Public release date: 5-Feb-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

February 5, 2013, Shenzhen and Kunming, China - In a collaborative study published online today in Nature Communications, researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, and BGI have completed the genome sequencing of Chinese tree shrew, a small animal widely distributed in South Asia, Southeast Asia, and South and Southwest China. This work provides new insights for researchers to use tree shrew as a model in studying hepatitis C virus (HCV) and hepatitis B virus (HBV) infections, myopia, as well as social stress and depression.

Tree shrews are similar to squirrels in their external appearance and habits. They have a higher brain to body mass ratio than any other mammals, and even than humans. Currently, tree shrews have been considered as a useful experimental model for researchers to design and develop new animal models for human diseases. However, the lack of a high-quality genome has greatly hampered the deeper understanding of this animal's biological features, evolutionary mechanisms, among others.

In this study, researchers conducted whole genome sequencing on a male Chinese tree shrew from Yunnan Province of China, and yielded a high-quality reference genome about 2.86Gb. Compared to the previous version reportedly in 2007, a significantly improved annotation was also generated, which contains 22,063 genes that is similar with the number of human genes. To identify the phylogenetic position of tree shrew in Euarchontoglires, they compared the tree shrew genome with other genomes, including human's, and revealed a closer relationship between tree shrew and primates.

When identifying the genetic features shared between tree shrew and primates, researchers found 28 genes previously considered as primate specific genes also present in tree shrew genome such as psoriasin protein and NKG2D ligands, indicating the tree shrew's immune system may employ the same indicators as in humans to eliminate infected and damaged cells. They also found some unique genetic features of tree shrew, such as immunoglobulin lambda variable gene family strikingly expanded to 67 copies in tree shrews but only 36 copies in the human genome.

Tree shrew has a well-developed brain structure that is similar with primate's. Researchers in this study detected 23 known neurotransmitter transporters in the tree shrew genome that are associated with the corresponding features of depression. These transporters are highly conserved in amino acid sequence with the human counterparts. All the findings provide a genetic basis for researchers making tree shrews an attractive model for experimental studies of psychosocial stress and evaluation of pharmacological effect of antidepressant drugs.

To understand the genetic basis underlying the visual system of tree shrew, researchers investigated the relevant genes involved in visual system, and found the tree shrew genome encompassed the orthologues of almost all the 209 known vision-related human genes. However, the lack of two cone photoreceptors, the middle wave-length sensitive proteins, may lead to the trichromacy in higher primates. The absence of these proteins is consistent with the fact that tree shrew is short of green pigment and possess dichromats, which is similar to some lower primates. Due to tree shrew's adaptation to the diurnal life, researchers found a looser evolutionary constraint of dim-light vision. Rod photoreceptor rhodopsin had a faster evolutionary rate in the tree shrew lineage, which is responsible for the night vision. A variant p.F45C that causes incurable night blindness disease in humans was detected in tree shrew species, suggesting a potentially functional degeneration of this gene in tree shrews.

The previous reports showed human HBV and HCV could infect tree shrew. Through investigating tree shrew immune genes associated with viral hepatitis, researchers found most of the genes respond in HBV and HCV infection showed a relatively high sequence identity between tree shrew and human genomes. They found the tree shrew lost DDX58, a key gene to produce interferon to against virus, and TRIM5 has achieved five Trim5 copies. One of TRIM5 copy has a CypA retrotranposition that present in only several primate species, implying the potential importance of this fused transcript.

Professor Yong-Gang Yao from Kunming Institute of Zoology, the leading author of this paper, said, "Since 1970s, researchers of our institute carried out many studies on the biology of Chinese tree shrews, and we published the first monograph of tree shrew in 1991. Currently, we are focused on establishing animal models of human diseases using this animal. The available genome data will greatly facilitate our efforts and speed up the process to design and develop new tree shrew models for human diseases, drug screening and safety testing"

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The genome of Chinese tree shrew provides new insights into facilitating biomedical researches

Pastor Chui Human Genome in Meltdown
This is a 7.5-minute sermon from science. Researchers show that the human genome has been succumbed to deleterious mutations for only about 5000 years to 10000 years for both European Americans and African Americans. Therefore, this is compatible with young ages for humans on earth. Calculations of human populations also indicate that humans have been on earth for a short time. Otherwise we may expect multitudes of human fossils as abundant as dinosaur fossils. Thank God for that.

By: Christopher Chui

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Pastor Chui Human Genome in Meltdown - Video

Introduction to genome
The product genome was conceived because research shows that the top 4% of sales professionals sell over 90% of products and services globally. genome provides a suite of on-line tools based on the very latest psychological research enabling us to effectively identify the DNA of the top performing sales professionals. Six core competencies that underpin selling excellence have been identified and, following extensive research examining the psychology behind these core competencies, genome exposes a set of sub-competencies that prove instrumental in driving superior sales performance. genome is a 3 stage on-line system consisting of the assessment (DNA), analysis (MATCH) and development (MENTOR) of sales professionals.

By: PA genome

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Introduction to genome - Video

LAS CRUCES Are you ready for a vanilla dessert chile pepper? How about pepper plants with leaves and stems as brilliantly colored (and maybe even as spicy) as their spectacular fruits?

Nobody has to tell those of us in the Chile Capital of the World that our favorite pepper is something special.

But mapping the entire genome of the chile pepper has brought us new information about just how unique chiles are, along with some exciting new potentials, Paul Bosland reported at the Chile Pepper Institute's 2013 New Mexico Chile Leaders Dinner, Monday at Stan Fulton Center.

"This puts NMSU and the Chile Pepper Institute on the cutting edge with a new level of research," said Bosland, a New Mexico State University Regents professor and director of the Chile Pepper Institute.

It might even be argued that chiles are more sophisticated and complex than the humans who eat them.

"We've now determined that the chile pepper has approximately 3.5 billion base pairs, which are the building blocks that make up the DNA double helix, compared to tomatoes which have about 950 million (homo sapiens have about 3 billion). The Human Genome Project determined we have about 20,000 genes. Chile peppers have about 37,000 genes.

"Whether that means chiles are more evolved than we are, I don't know," quipped Bosland.

The chile genome project, a cooperative effort with a leading South Korea university laboratory, could have some very serious benefits.

To complete the first-ever

"It's a very expensive, incredibly advanced machine that only takes a few days to do the same amount of genetic processing work that previously took 600 machines 10 years to accomplish," Bosland reported.

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Genome mapping unlocks new possibilities for chile peppers

Feb. 6, 2013 A group of international scientists has sequenced the draft genome sequence of the rubber tree Hevea brasiliensis, the major commercial source of natural rubber. The manuscript describing the draft genome is published in BMC Genomics.

Scientists have sequenced the draft genome sequence of the rubber tree Hevea brasiliensis, the major commercial source of natural rubber. Rubber is an indispensible commodity that is used in manufacture worldwide, billions dollar industry. The plant has played a vital role in the world economy since 1876. Currently Asia accounts for about 93% of global supply of rubber.

The manuscript describing the draft genome is published in BMC Genomics. The team identify around 12.7% of the almost 70,000 genes as unique, and outline those associated with rubber biosynthesis, rubber wood formation, disease resistance and allergenicity.

The rubber industry is affected by rubber blight -- a fungal disease -- and natural rubber allergenicity, a global medical concern for those repeatedly exposed to latex-containing products (e.g., gloves).

Ahmad Yamin Rahman and colleagues believe that this draft genome information will accelerate the development of high-yielding natural rubber plants. This will lead to assistance in latex production, wood development, disease resistance and allergenicity.

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Tapping into the rubber plant genome