Category Archives: Transhuman News

The Genomics of Attention Deficit Hyperactivity Disorder - Maximillian Muenke
Nov. 2, 2012 - Genomics in Medicine Lecture Series More: http://www.genome.govFrom:GenomeTVViews:9 0ratingsTime:01:06:31More inFilm Animation

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The Genomics of Attention Deficit Hyperactivity Disorder - Maximillian Muenke - Video

Genome Lab SNP Stream Genotyping System Display
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Genome Lab SNP Stream Genotyping System Display - Video

SAN DIEGO & SAN FRANCISCO--(BUSINESS WIRE)--

Please replace the release (dated November 5, 2012) with the following corrected version due to multiple revisions.

The corrected release reads:

BIONANO GENOMICS LAUNCHES IRYS, A NOVEL PLATFORM FOR COMPLEX HUMAN GENOME ANALYSIS

Speed, Simplicity Enable Routine Use of Genetic Information in Wide-Ranging Applications

BioNano Genomics today announced the commercial rollout of its breakthrough Irys System, an intuitively designed genome mapping system that empowers genomics researchers with a new way of analyzing genomic DNA. Irys makes it possible to routinely and accurately detect genomic structural variation and to finish genome assemblies.

(Note to editors: See associated image.)

Irys reveals genome architecture in its native state, thereby adding a completely new repertoire to the genomics tool kit. The Irys System allows researchers and clinicians to access meaningful biological information that is disrupted or completely lost when samples are analyzed by the methods used today such as next-generation sequencing or microarrays, said BioNano Genomics President and CEO Dr. R. Erik Holmlin, who announced the launch of Irys from the American Society of Human Genetics (ASHG) Annual Meeting, being held in San Francisco, Nov. 6-10. BioNano Genomics is excited about introducing a new approach that makes it easy to observe genomic architecture and context. We believe this capability will add unprecedented insight into biology and usher in a new wave of discoveries.

The fully automated Irys benchtop instrument uses the IrysChip to uncoil and confine long DNA molecules in proprietary Nanochannel Arrays where they are uniformly linearized in a highly parallel display for high-resolution, single-molecule imaging. Irys does not employ DNA fragmentation or amplification, which are typical with next-generation sequencing. The result is sequence information over extremely long reads ranging from hundreds of kilobases to a megabase, where the samples valuable structural information is preserved. Irys makes it possible for researchers to directly observe structural variants including replications, deletions, translocations and inversions. The simplicity, affordability and speed of Irys, which can analyze several gigabases per hour, make it an ideal genome mapping solution for labs of any size, said Todd Dickinson, VP Commercial Operations, and we envision broad application throughout genomics and epigenomics, especially in biomedical research and ultimately molecular diagnostics.

Complex genomes contain highly repetitive sequences and prove challenging for whole genome assembly, said Pui-Yan Kwok, MD, PhD, Henry Bachrach Distinguished Professor at the UCSF School of Medicine and senior author of a study published in Nature Biotechnology, which demonstrated the utility of the Irys platform for structural variation analysis and de novo assembly of next generation sequencing (NGS) data. The BioNano approach to genome mapping readily resolves these issues, and allowed us to achieve haplotype-resolved de novo assembly of the notoriously difficult human MHC region. We are thrilled with the quality of data we are getting with the Irys system and are now deploying this new technology broadly across our research program.

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CORRECTING and REPLACING BioNano Genomics Launches Irys, a Novel Platform for Complex Human Genome Analysis

SAN DIEGO & SAN FRANCISCO--(BUSINESS WIRE)--

BioNano Genomics today released its breakthrough Irys System, an intuitively designed genome mapping system that empowers genomics researchers with a new way of achieving more accurate and comprehensive discoveries, including structural variation analysis and sequence assemblies.

(Note to editors: See associated image.)

Irys is a novel, automated platform that uses single-molecule imaging to visualize extremely long nucleic acids and reveal genome architecture in its native state, thereby significantly extending the reach of existing genomic technologies.

The Irys System allows researchers and clinicians to access meaningful biological information that is often disrupted or completely lost when molecules are sheared, said BioNano Genomics President and CEO Dr. R. Erik Holmlin, who announced the launch of Irys at the American Society of Human Genetics (ASHG) Annual Meeting, being held in San Francisco Nov. 6-10. BioNano Genomics is pleased to introduce a new approach that allows one to easily observe architecture and context across the whole genome, providing unprecedented insight into biology.

The fully automated Irys benchtop instrument uses a proprietary IrysChip to uncoil and confine long DNA molecules into nanochannels, uniformly linearizing them for high-resolution, single-molecule imaging. The Irys System does not require DNA fragmentation and amplification steps that are typical of next-generation sequencing resulting in extremely long reads of hundreds of kilobases to megabases. Because of this, the samples valuable structural information is preserved, making it possible for researchers to directly observe structural variants including translocations and inversions.

The simplicity, affordability and speed of Irys, which can analyze several gigabases of data per hour, make it an ideal genome mapping solution for labs of any size, said Todd Dickinson, Vice President of Commercial Operations for BioNano Genomics. We envision broad applications throughout biomedical research and ultimately molecular diagnostics.

Complex genomes contain highly repetitive sequences and prove challenging for whole genome assembly, said Pui-Yan Kwok, MD, PhD, Henry Bachrach Distinguished Professor at the University of California, San Francisco School of Medicine and senior author of a study published in Nature Biotechnology, which demonstrated the utility of the Irys platform for structural variation analysis and de novo assembly of next generation sequencing (NGS) data. The BioNano approach to genome mapping readily handled these issues, and allowed us to achieve haplotype-resolved de novo assembly of the notoriously difficult human MHC region. We are thrilled with the quality of data we are getting with the Irys system and are now deploying this new technology broadly across our research program.

Dr. Kwok will join Dr. Holmlin and other experts at ASHG to lead an educational workshop about Irys at 12:45 p.m. on Nov. 8 at Moscone Center, Room 301. Register to attend the workshop to learn more about the new system, or visit BioNano Genomics Booth 924/926 on the ASHG expo floor.

About BioNano Genomics

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BioNano Genomics Launches Irys, a Novel Platform for Complex Human Genome Analysis

After decades of hard work, the barley genome, or genetic code, has been cracked.

The barley genome is twice the size of our own human genome and was successfully ordered and assembled by an international group of scientists ranging from many different scientific disciplines.

The International Barley Sequencing Consortium is the group of scientist who cracked the genetic code of the 5.3 billion lettered barley genome, and the research was published in the most recent edition of Nature.

This consortium was created in 2006 and is a collaboration of scientists from 22 different organizations in nine different countries.

Roger Wise, research plant geneticist for United States Department of Agriculture-Agricultural Research Service and collaborator professor of plant pathology at Iowa State was one of these scientists.

This project was absolutely huge, and this is reflected by the well over 60 authors on the paper, Wise said.

Records indicate that barley has been around and developing for more than 10,000 years, originating in modern-day Middle East.

Today, barley ranks fourth among the cereals in worldwide production, behind wheat, rice and corn.

According to the National Barely Growers Association, 320 million bushels of barley were produced each year in the United States from 1994 till 2003, averaging $760 million dollars in the agricultural economy.

This research is the first of many steps to bring an increase in yields, improve pest and disease resistance, and enhance nutritional value to barley.

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Barley genome gives insight into future pest and disease resistance

BEVERLY, Mass.--(BUSINESS WIRE)--

BIOBASE GmbH announced today that it has been selected by Cypher Genomics to aid in whole genome interpretation. Researchers at Cypher Genomics will incorporate the knowledgebase in Genome TraxTM to assist in their interpretation of next generation sequencing variants to provide rich genomic knowledge from sequencing data.

Cypher Genomics provides comprehensive automated software solutions for medical geneticists, computational biologists, clinicians, and researchers looking to extract maximal value from whole genome sequencing. Genome TraxTM enables the ability to interpret next generation-sequencing (NGS) data and convert the genomic data to actionable genomic knowledge.

Genome TraxTM prioritizes human genome variants in whole genome or exome data that merit further investigation. The tool maps NGS data to known features such as HGMD disease mutations and TRANSFAC regulatory sites. In addition, Genome TraxTM identifies novel mutations that are likely to affect the function of candidate disease genes, and enables users to filter out the millions of irrelevant variants.

"Genome TraxTM provides the most comprehensive database of human disease associations and is an invaluable resource in both clinical and research-grade genetics and genomics activities," explains Dr. Ali Torkamani, Chief Science Officer, at Cypher Genomics.

"Cypher Genomics will interpret genomes with cutting-edge precision and enable the use of genomics in diagnosis, discovery, and treatment. Genome TraxTM frees them to focus on their deep expertise in computer science, quantitative genetics, and medicine, to deliver state-of-the-art genome processing to their customers," stated Frank Schacherer, CTO, BIOBASE.

Excerpt from:
Cypher Genomics Selects BIOBASE Genome TraxTM Knowledgebase for Variant Analysis

Scientists have recently completed their work sequencing the barley genome, which could lead to better or less-expensiveScientists with the International Barley Genome Sequencing Consortium have recently completed their work sequencing the barley genome, which is even larger than the human genome.

The goal of this research is to gain a better understanding of barley and how to make its cultivars the various types of barley that have been selectively grown for their specific characteristics higher in dietary fibre, more resistant to diseases and climate change, and possibly to create better or less-expensive beer.

[ Related: Wheat, soybeans, potatoes could be replaced in warmer climate ]

The data, published last month in Nature, is a draft-work, showing that roughly two-thirds of the total sequence of genes has been mapped. Nils Stein (what a great name for a barley researcher!) is head of the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), and the lead researcher of this work. He hopes that this will give them a better knowledge of how gene expression is controlled in the barley plant, which could lead to ways for plant breeders to have more control over them in the production of new cultivars.

Stein and his team also compared the genomes of two-row barley and six-row barley. Two-row barley is lower in protein content than six-row barley, and is traditionally used for English ales and German beers, whereas six-row barley is used in American lagers, especially when corn or rice are used as adjuncts. They found that many of the active genes of these cultivars are located where they are not accessible when using selective breeding methods, however according to Popular Science, Stein says that gene modification techniques might be used to specifically target those genes.

[ Related: Cloned cow produces super nutritious, hypo-allergenic milk for kids ]

This completed sequence may also make an excellent model for understanding more complicated genome sequences, like that of wheat, which could then lead to better disease resistance and environmental tolerances for one of the most important staple foods we grow.

For all the latest in science and weather, follow @ygeekquinox on Twitter.

Original post:
Barley genome breakthrough might lead to better, cheaper beer

Public release date: 7-Nov-2012 [ | E-mail | Share ]

Contact: Cathy Yarbrough press@ashg.org 858-243-1814 American Society of Human Genetics

Whole genome sequencing of the DNA code of three prenatal samples provided a detailed map of the locations of their chromosomal abnormalities in 14 days, scientists reported today at the American Society of Human Genetics (ASHG) 2012 meeting in San Francisco.

"Such a relatively brief timeframe will enable physicians to predict diagnosis of serious congenital disorders prenatally to counsel the parents and plan perinatal care of infants with chromosomal rearrangements," said Zehra Ordulu, M.D., Brigham and Women's Hospital and Harvard Medical School medical research fellow in obstetrics, gynecology and reproductive biology, who presented the study.

In the study, whole genome sequencing was used after current prenatal diagnostic methods of karyotyping and array comparative genomic hybridization (aCGH) to provide nucleotide level precision were conducted.

Karyotyping and aCGH studies of the prenatal samples provided the first clues of "balanced de novo chromosomal rearrangements," and prompted the investigation by genomic sequencing.

Clinical consequences of such chromosome rearrangements, which are defined as the relocation of chromosome segments without any loss or gain in genomic material, are rare, not inherited and challenging to predict without knowledge of the precise breakpoints.

"Unlike karyotyping, aCGH and other standard methods, whole genome sequencing provided the information to detect the 'breakpoints" in the chromosomes at which the rearrangements occurred and thereby to determine the genomic regions altered," said Cynthia C. Morton, Ph.D., William Lambert Richardson Professor in obstetrics, gynecology and reproductive biology, professor of pathology at Brigham and Women's Hospital and Harvard Medical School and incoming president-elect of ASHG.

"Early detection of a genetic disorder is of significant importance for informing genetic counseling and for managing the pregnancy, birth and further clinical follow-up," said Dr. Morton, who headed the study.

"This study foretells an empowered prenatal diagnostic environment in which DNA sequencing becomes the standard of care," she added.

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Whole genome sequencing of de novo balanced rearrangements in prenatal diagnosis