Category Archives: Genome

Deborah Marshall: Is the human genome worth $1000?
Dr Deborah Marshall is a health economist from the University of Calgary. She asks the question, is the human genome worth $1000? Dr Marshall #39;s talk was part...

By: genomeatlantic

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Deborah Marshall: Is the human genome worth $1000? - Video

Q?rius Presentation: The Dog Genome: Shedding Light on Human Disease - Elaine Ostrander
March 15, 2014 - Part of the "Genome: Unlocking Life #39;s Code" exhibition events. Dogs have been called a person #39;s best friend, but they also can tell us a lot...

By: GenomeTV

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Q?rius Presentation: The Dog Genome: Shedding Light on Human Disease - Elaine Ostrander - Video

March. 21 (UPI) -- Humans may be the most complex living organisms on earth, but their genome is dwarfed in size by the loblolly pine.

The tree's genome -- seven times longer than the human genome -- recently become the longest genome ever sequenced, thanks to a group of hard-working plant scientists.

Its a huge genome," David Neale, a professor of plant sciences at the University of California, Davis, told redOrbit. "But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order."

Neale led the effort to sequence the genome and detailed the team's findings in articles published in the latest issues of both GENETICS and the journal Genome Biology.

Neale and his colleagues hope their work will help scientists better understand how plants evolve. Their research may also help tree experts breed new and improved loblolly pines -- the hardy tree accounts for the vast majority of America's paper products, and is being developed as a new biofuel source.

Loblolly pine plays an important role in American forestry," said Sonny Ramaswamy, director of USDAs National Institute of Food and Agriculture -- the agency that funded the research project. "Now that weve unlocked its genetic secrets, loblolly pine will take on even greater importance as we look for new sources of biomass to drive our nations bioeconomy and ways to increase carbon sequestration and mitigate climate change."

The project has been ongoing since 2012, but now that scientists have found more efficient computerized techniques for sorting through the massive amounts of genetic data, scientists say they'll soon be able to sequence even larger genomes.

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Newly mapped loblolly pine genome is seven times longer than a human's

The New York Genome Center and IBM Watson Group Announce Collaboration to Advance Genomic Medicine
The New York Genome Center (NYGC) and IBM announced an initiative to accelerate a new era of genomic medicine with the use of IBM #39;s Watson cognitive system. ...

By: IBM Research

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The New York Genome Center and IBM Watson Group Announce Collaboration to Advance Genomic Medicine - Video

Quick Interview with Genome Scientist Konrad Karczewski at SXSW
As our 6th day of SXSW was coming to an end, we were hanging with my friend Konrad after he had just given a workshop on analyzing personal genomes, when we ...

By: MRM McCann

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Quick Interview with Genome Scientist Konrad Karczewski at SXSW - Video

PUBLIC RELEASE DATE:

20-Mar-2014

Contact: Kevin Jiang kevin.jiang@uchospitals.edu 773-795-5227 University of Chicago Medical Center

Although genome-wide association studies have linked DNA variants in the gene SCN10A with increased risk for cardiac arrhythmia, efforts to determine the gene's direct influence on the heart's electrical activity have been unproductive. Now, scientists from the University of Chicago have discovered that these SCN10A variants regulate the function of a different gene, SCN5A, which appears to be the primary gene responsible for cardiac arrhythmia risk. The SCN10A gene itself plays only a minimal role in the heart, according to the study, published in the Journal of Clinical Investigation on March 18.

"Significant effort has been invested into understanding the function of SCN10A in cardiac rhythm control, with underwhelming results," said study co-leader Ivan Moskowitz MD, PhD, associate professor of pediatrics, pathology and human genetics at the University of Chicago. "It turns out that the genetic variation within SCN10A that confers arrhythmia risk actually functions on a different gene. This study highlights the fact that DNA variation associated with disease can have regulatory impact on functional targets located a considerable distance away."

Mutations within the SCN10A gene are linked with increased risk of Brugada Syndrome, which causes cardiac arrhythmias and is a leading cause of death amongst youth in some parts of the world. Genome-wide association studieslarge scale experiments that look for genetic variants across the human genome with statistical associations to certain traits or diseaseswere used to identify these variants, but follow-up studies have been unable to determine their function.

Curious about previous ambiguous results, Moskowitz and his colleagues looked for other genes with links to SCN10A. First, they discovered that the region of SCN10A that conferred arrhythmia risk physically contacted a neighboring geneSCN5Awhich is well-known to have an important role in cardiac arrhythmias and sudden cardiac death. They then showed that these contacts are functional, and that by removing the implicated sequences from SCN10A, expression of SCN5A was profoundly diminished.

When they analyzed large-scale human data, the team found that the SCN10A variant originally identified for Brugada Syndrome risk was associated with lowered levels of SCN5A. But the variant had no detectable effect on the levels of SCN10A.

Taken together, the evidence suggests that any link between SCN10A and cardiac arrhythmia is due to its connection with SCN5A expression. Through the results of this study, Moskowitz believes scientists will now focus on the correct gene, SCN5A, to better understand genetic risk for cardiac arrhythmia and hopes this will lead to more accurate diagnostics and potential therapies in the future.

This study also illustrates how highly-publicized genome-wide association studies can be misleading for researchers. Study co-leader Marcelo Nobrega, PhD, an associate professor of human genetics at the University of Chicago, published a similar finding for a gene associated with obesity, on March 12th in Nature.

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Genome-wide association studies mislead on cardiac arrhythmia risk gene

Using haploid DNA and advanced computer technology, researchers have finally managed to sequence the genome of the loblolly pine tree.

After fitting 16 billion separate fragments together, scientists have finally managed to sequence the genome of the loblolly pine tree, the largest ever genome sequenced so far.

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The scientists, who published their papers in GENETICS and the journal Genome Biology, used DNA extracted from a single haploid seed of a Loblolly pine tree.

To obtain the DNA, the scientists first had to remove the embryo from the seed, says Indiana University's KeithanneMockaitis, an author on the paper. What remains is then a haploid, whose cells have just one set of chromosomes.

Using next-generation sequencing technology, researchers obtained billions of shorter sequence of bases. The challenge now was to sift through the data, identify the overlapping sequences, and assemble them together a computational puzzle called "genome assembly."

In the case of loblolly pine, the huge size of the genome made this process difficult.

The "challenge isn't just collecting all the sequence data. The problem is assembling that sequence into order," said David Neale, a professor of plant sciences at the University of California, Davis, who led the loblolly pine genome project.

"You have this big pile of tiny pieces and now you have to reassemble the book," said Steven Salzberg, professor of medicine and biostatistics at Johns Hopkins University, one of the directors of the loblolly genome assembly team, who was also an author on the papers.

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Scientists sequence a genome seven times bigger than yours

The human genome is the complete set of genetic information for humans (Homo sapiens). This information is encoded as DNA sequences within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. Human genomes include both protein-coding DNA genes and noncoding DNA. Haploid human genomes (contained in egg and sperm cells) consist of three billion DNA base pairs, while diploid genomes (found in somatic cells) have twice the DNA content. While there are significant differences among the genomes of human individuals (on the order of 0.1%), these are considerably smaller than the differences between humans and their closest living relatives, thechimpanzees(approximately 4%[1]) and bonobos.

karyotype, showing the organization of the genome into chromosomes. This drawing shows both the female (XX) and male (XY) versions of the 23rd chromosome pair. Chromosomes are shown aligned at their

The Human Genome Project produced the first complete sequences of individual human genomes. As of 2012, thousands of human genomes have been completely sequenced, and many more have been mapped at lower levels of resolution. The resulting data are used worldwide in biomedical science, anthropology, forensics and other branches of science. There is a widely held expectation that genomic studies will lead to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution.

Although the sequence of the human genome has been (almost) completely determined by DNA sequencing, it is not yet fully understood. Most (though probably not all) genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and RNA products. Recent results suggest that most of the vast quantities of noncoding DNA within the genome have associated biochemical activities, including regulation of gene expression, organization of chromosome architecture, and signals controlling epigenetic inheritance.

The haploid human genome contains approximately 20,000 protein-coding genes, significantly fewer than had been anticipated.[2][3]Protein-coding sequences account for only a very small fraction of the genome (approximately 1.5%), and the rest is associated with non-coding RNA molecules, regulatory DNA sequences, LINEs, SINEs, introns, and sequences for which as yet no function has been elucidated.[4]

The total length of the human genome is over 3 billion base pairs. The genome is organized into 22 paired chromosomes, the X chromosome (one in males, two in females) and, in males only, one Y chromosome, all being large linear DNA molecules contained within the cell nucleus. It also includes the mitochondrial DNA, a comparatively small circular molecule present in each mitochondrion. Basic information about these molecules and their gene content, based on a reference genome that does not represent the sequence of any specific individual, are provided in the following table. (Data source: Ensembl genome browser release 68, July 2012)

Table 1 (above) summarizes the physical organization and gene content of the human reference genome, with links to the original analysis, as published in the Ensembl database at the European Bioinformatics Institute (EBI) and Wellcome Trust Sanger Institute. Chromosome lengths were estimated by multiplying the number of base pairs by 0.34 nanometers, the distance between base pairs in the DNA double helix. The number of proteins is based on the number of initial precursor mRNA transcripts, and does not include products of alternative pre-mRNA splicing, or modifications to protein structure that occur after translation.

The number of variations is a summary of unique DNA sequence changes that have been identified within the sequences analyzed by Ensembl as of July, 2012; that number is expected to increase as further personal genomes are sequenced and examined. In addition to the gene content shown in this table, a large number of non-expressed functional sequences have been identified throughout the human genome (see below). Links open windows to the reference chromosome sequence in the EBI (E), NCBI (N), or UCSC (U) genome browsers. The table also describes prevalence of genes encoding structural RNAs in the genome.

MiRNA, or MicroRNA, functions as a post-transcriptional regulator of gene expression. Ribosomal RNA, or rRNA, makes up the RNA portion of the ribosome and is critical in the synthesis of proteins. Small nuclear RNA, or snRNA, is found in the nucleus of the cell. Its primary function is in the processing of pre-mRNA molecules and also in the regulation of transcription factors. SnoRNA, or Small nucleolar RNA, primarily functions in guiding chemical modifications to other RNA molecules.

The content of the human genome is commonly divided into coding and noncoding DNA sequences. Coding DNA is defined as those sequences that can be transcribed into mRNA and translated into proteins during the human life cycle; these sequences occupy only a small fraction of the genome (<2%). Noncoding DNA is made up of all of those sequences (ca. 98% of the genome) that are not used to encode proteins.

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Human genome - Wikipedia, the free encyclopedia

According to the study, the sequencing of the loblolly pine's genome was completed by using a faster and more efficient analytical process, including advanced computer technology. The genome sequence of the tree, which is the most commercially important tree species in the U.S., is expected to help scientists breed improved varieties of the pine and better understand the evolution and diversity of plants.

Its a huge genome, David Neale of the University of California, Davis, who led the research, said in a statement. But the challenge isnt just collecting all the sequence data. The problem is assembling that sequence into order.

The loblolly pine is one of several pines native to the southeastern U.S., spreading eastward from central Texas to Florida, and northward to Delaware and southern New Jersey. The tree is milled for building lumber and paper, while it is also the primary source of pulpwood and saw timber for the country's forest products industry.

To tackle the enormous size of the loblolly pine genome, which has 22 billion base pairs compared to only 3 billion in the human genome, scientists used a new method that could speed up genome assembly by compressing the raw sequence data 100-fold, according to the study, which has been published in two papers in the March 2014 issue of Genetics, and in one paper in the open access journal, Genome Biology.

As part of the study, scientists also looked for genes that control resistance to fusiform rust, a disease that infects southern pines and renders them unfit for use. According to scientists, they found a whole family of resistant genes in the loblolly pines genome.

Commercially, it is the most economically devastating disease of the southern pines, John M. Davis of the University of Florida, said in a statement. If growers didnt have genetic resistance, we would have no pine plantations its that important.

Floridas nearly 16 million acres of timberland supported economic activities that generated $14.7 billion in economic impact in recent years while providing nearly 90,000 full- and part-time jobs. A molecular understanding of genetic resistance is a valuable tool for forest managers as it allows them to select trees that can develop into healthy groves.

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Largest Genome Sequenced: Loblolly Pine's Genetic Code Is 7 Times Larger Than A Humans

The massive genome of the loblolly pine -- around seven times bigger than the human genome -- is the largest genome sequenced to date and the most complete conifer genome sequence ever published. This achievement marks the first big test of a new analysis method that can speed up genome assembly by compressing the raw sequence data 100-fold.

The draft genome is described in the March 2014 issue of the journal Genetics and the journal Genome Biology.

Loblolly pine is the most commercially important tree species in the United States and the source of most American paper products. The tree is also being developed as a feedstock for biofuel. The genome sequence will help scientists breed improved varieties and understand the evolution and diversity of plants. But the enormous size of the pine's genome had been an obstacle to sequencing efforts until recently. "It's a huge genome. But the challenge isn't just collecting all the sequence data. The problem is assembling that sequence into order," said David Neale, a professor of plant sciences at the University of California, Davis, who led the loblolly pine genome project and is an author on the GENETICS and Genome Biology articles.

Modern genome sequencing methods make it relatively easy to read the individual "letters" in DNA, but only in short fragments. In the case of the loblolly, 16 billion separate fragments had to be fit back together -- a computational puzzle called genome assembly.

"We were able to assemble the human genome, but it was close to the limit of our ability; seven times bigger was just too much," said Steven Salzberg, professor of medicine and biostatistics at Johns Hopkins University, one of the directors of the loblolly genome assembly team, who was also an author on the papers.

The scale of the problem can be compared to shredding thousands of copies of the same book and then trying to read the story. "You have this big pile of tiny pieces and now you have to reassemble the book," Salzberg said.

The key to the solution was using a new method to pre-process the gargantuan pile of sequence data so that it could all fit within the working memory of a single super-computer. The method, developed by researchers at the University of Maryland, compiles many overlapping fragments of sequence into much larger chunks, then throws away all the redundant information. Eliminating the redundancies leaves the computer with 100 times less sequence data to deal with.

This approach allowed the team to assemble a much more complete genome sequence than the draft assemblies of two other conifer species reported last year. "The size of the pieces of consecutive sequence that we assembled are orders of magnitude larger than what's been previously published," said Neale. This will enable the loblolly to serve as a high-quality "reference" genome that considerably speeds along future conifer genome projects.

The loblolly genome data have also been freely available throughout the project, with public releases starting back in June 2012. "Our project has had great benefits to the community long before publication," said Neale.

The new sequence confirmed that the loblolly genome is so large because it is crammed full of invasive DNA elements that copied themselves around the genome. Approximately 82% of the genome is made up of these and other repetitive fragments of sequence.

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Loblolly pine genome is largest ever sequenced: Seven times bigger than the human genome