Hitachi High Technologies America (HTA) will partner with ZS Genetics to commercialize ZS single-molecule DNA sequencing platform, the companies said today, through a collaboration whose value was not disclosed.

The companies said ZS Genetics proprietary third-generation technologies, based on high-resolution electron microscopy (EM), will allow users for the first time to sequence long reads50,000 or more base-pairsof single DNA molecules at high quality. The company expects to average hundreds of millions of base-pairs of sequencing data per hour.

ZS Genetics says its technology is designed to sequence entire human genomes in days by reading sequences of single DNA molecules that are hundreds of times longer than those read by any other existing technologies, without the need for amplification.

ZS Genetics third-generation sequencing processes DNA samples into single-stranded DNA that is then modified into double-stranded DNA with a few heavy atoms or modified deoxyribonucleotide triphosphates (dNTPs) per base pair. Each dNTP contains a unique label separately identifiable in the electron microscope image, which is captured and analyzed with software that recognizes the DNA and labels.

The technology typically sequences each sample 5 to 10 times, rather than 30 to 50 timesa reduction in oversampling that ZS Genetics says on its website will collapse the informatics costs of sequencing and improve the quality of genomes produced.

Privately held ZS Genetics plans to establish an early-access center in its Wakefield, MA, facility later this year for product and application development, in collaboration with select customer and supply-chain partners it did not name.

The companies did not disclose other details and terms of their strategic product development relationship.

The technical capabilities of our two companies are expected to produce a DNA sequencing platform capable of enabling unique scientific discovery, as well as offering a powerful tool to complement and broaden current short-read sequencing technologies, ZS Genetics CEO John A. McCarthy, Jr., said in a statement. The rapidly increasing complexity of scientific discovery continues to reinforce the need for higher quality and more scientifically rich DNA sequencing capabilities."

Added Phil Bryson, vp and gm of HTAs Nanotechnology Systems Division: We are confident that HTAs decades-long leadership in high-resolution EM for highly complex applications in R&D and industry can translate readily into this powerful and important new application for the life sciences industry.

HTA, a subsidiary of Hitachi High-Technologies Corp., sells and services semiconductor manufacturing equipment, analytical instrumentation, scientific instruments, and bio-related products, as well as industrial equipment, electronic devices, and electronic and industrial materials. HTA is a privately owned global affiliate company operating within the Hitachi Group Companies.

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Hitachi Partners with ZS Genetics to Commercialize Sequencing Platform - Genetic Engineering & Biotechnology News

SAN DIEGO, March 09, 2017 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc., a company focused on genome structure analysis, today highlighted results from a study demonstrating how combining genomic sequencing and mapping technologies, including Bionanos next-generation mapping (NGM), produced the most continuous de novo mammalian assembly to date, of the domestic goat (Capra hircus). The paper, Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome, was published online in advance of print in the March 6, 2017 issue of Nature Genetics (DOI:10.1038/ng.3802).

The paper described the use of single-molecule real-time long-read sequencing for contig formation (PacBios RSII), followed by scaffolding using chromatin interaction mapping (Phase Genomics Hi-C) and optical mapping data (Bionano Genomics Irys). The resulting assembly was polished with paired-end short-read sequencing for sequence accuracy (Illuminas HiSeq).

Hi-C has been gaining popularity for scaffolding de novo assembled genomes. By cross-linking remote regions of chromosomes, Hi-C has the potential to make scaffolds reaching chromosome arm lengths possible. However, this cross-linking does not always enable order and orientation of the contigs to be determined correctly. In the scaffolding of the goat genome described here, Hi-C introduced 7 times more errors than Bionano (21 vs. 3).

Since Bionano NGM is the only non-sequence based scaffolding method, it is the only technology capable of correcting errors inherent to both short-read and long-read sequencing. Bionano genome maps are created completely de novo, and therefore provide an entirely independent assembly with which to compare the sequence contigs. The Nature Genetics paper describes how Bionanos genome maps were able to correct 36 mis-assemblies in the PacBio contigs. Furthermore, Bionano allowed for precise sizing of 79% of the remaining gaps, which is not possible with Hi-C.

Erik Holmlin, Ph.D., CEO of Bionano, commented, This paper follows the recent release of multiple reference-quality human genomes, including the Chinese and Korean reference genomes, all of which included Bionano data to create the most contiguous and accurate assemblies possible. Since the time this study was conducted over 18 months ago, Bionano has significantly advanced its scaffolding tools and with the recently released Saphyr instrument, the cost to map a mammalian genome has decreased six-fold. This publication serves as important validation of NGM as a complementary genomic tool to combine with next-generation sequencing to reveal highly informative native structure of chromosomes.

Bionanos hybrid scaffold pipeline within the Bionano Access analysis and visualization software allows users to combine two genome maps, each created by labeling a different sequence motif with an NGS assembly. This combination typically doubles the contiguity achieved using one genome map, incorporates about 50% more contigs into the assembly, and provides an additional de novo assembly to be used in error correction. Using Saphyr, two mammalian genome maps can be created in a single run, for a total reagent and consumables cost of less than $2000 a fraction of the sequencing and scaffolding cost for the entire project described in this paper, which approached $100,000.

The generated assembly, ARS1, represents an approximate 400-fold improvement in genome continuity due to properly assembled gaps compared to the previously published goat assembly, and better resolves the full structure of large repeats longer than 1 kilobase (kb). ARS1 comprises just 31 scaffolds and 649 gaps covering 30 of the 31 haploid, acrocentric goat chromosomes (excluding only the Y chromosome), which compares favorably to the current human reference (GRCh38), which has 24 scaffolds, 169 unplaced or un-localized scaffolds, and 832 gaps in the primary assembly.

The researchers concluded that the assembly strategy using multiple complementary technologies achieved superior continuity and accuracy, is cost-effective compared to past finishing approaches, and sets a new standard for mammalian genome assembly quality.

The Bionano Access software, which includes two-enzyme hybrid scaffolding and related scaffold editing, will be released as a free download later this month.

Read More

About Bionano Genomics

Bionano Genomics, Inc. provides the Irys and Saphyr systems for next-generation mapping (NGM), which is the leading solution in physical genome mapping. NGM offers customers whole genome analysis tools that reveal true genome structure and enabling researchers to capture whats missing in their data to advance human, plant and animal genomic research. NGM uses NanoChannel arrays to image DNA at the single-molecule level with average single-molecule lengths of about 350,000 base pairs, which leads the genomics industry. The long-range genomic information obtained with NGM detects and deciphers structural variations (SVs), which are large, complex DNA segments involving repeats that are often missed by sequencing technologies and which are a leading cause of inaccurate and incomplete genome assembly.

As a stand-alone tool, NGM enables the accurate detection of SVs, many of which have been shown to be associated with human disease as well as complex traits in plants and animals. As a complementary tool to next-generation sequencing (NGS), NGM integrates with sequence assemblies to create contiguous hybrid scaffolds for reference-quality genome assemblies that reveal the highly informative native structure of the chromosome. NGM also provides the additional ability to verify, correct and improve a NGS-generated genome assembly.

Only Bionano provides long-range genomic information with the cost-efficiency and high throughput to keep up with advances in NGS.

NGM has been adopted by a growing number of leading institutions around the world, including: National Cancer Institute (NCI), National Institutes of Health (NIH), Wellcome Trust Sanger Institute, BGI, Garvan Institute, Salk Institute, Mount Sinai and Washington University. Investors in the Company include Domain Associates, Legend Capital, Novartis Venture Fund and Monashee Investment Management.

For more information, please visit http://www.BionanoGenomics.com.

Notes: Bionano Genomics is a trademark of Bionano Genomics, Inc. Any other names of actual companies, organizations, entities, products or services may be the trademarks of their respective owners.

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Nature Genetics Paper Demonstrates How Inclusion of Bionano Genomics' Next-Generation Mapping is Essential to ... - Yahoo Finance

By Tom Polansek | CHICAGO

CHICAGO The strain of bird flu that infected a chicken farm in Tennessee in recent days shares the same name as a form of the virus that has killed humans in China, but is genetically distinct from it, U.S. authorities said on Tuesday.

The U.S. Department of Agriculture identified the strain in Tennessee as H7N9, following a full genome sequencing of samples from the farm. It said all eight gene segments of the virus had North American wild bird lineage.

On Sunday, the USDA confirmed the farm in Tennessee was infected with highly pathogenic bird flu, making it the first case in a commercial U.S. operation in more than a year.

In China, at least 112 people have died from H7N9 bird flu this winter, Xinhua news agency said on Friday.

However, that virus has Eurasian lineage, U.S. flu experts said.

"Even though the numbers and the letters are the same, if you look at the genetic fingerprint of that virus, it is different," said Dan Jernigan, director of the influenza division at the National Center for Immunization and Respiratory Diseases at U.S. Centers for Disease Control and Prevention.

Jernigan said the risk to humans from the virus found in Tennessee is low. Genome sequencing shows the H7N9 virus did not have genetic features present in the virus in China that make it easier for humans to become infected, he said.

The virus found in Tennessee likely mutated to become highly pathogenic from a less dangerous, low pathogenic form, he said.

Disease experts fear a deadly strain of bird flu could mutate into a form that could be passed easily between people and become a pandemic.

Multiple outbreaks of the virus have been reported in poultry farms and wild flocks across Europe, Africa and Asia in the past six months. Most involved strains that were low risks for human health, but the sheer number of different types, and their simultaneous presence in so many parts of the world, has increased the risk of viruses mixing and mutating - and possibly jumping to people, according to disease experts.

China's Center for Disease Control and Prevention has said the majority of people infected by H7N9 in China reported exposure to poultry, especially at live markets.

Identifying the viruses in Tennessee and China both as H7N9 is similar to having two cars from different states with the same license plate number, said Carol Cardona, avian flu expert at the University of Minnesota.

The strain in Tennessee "is NOT the same as the China H7N9 virus that has impacted poultry and infected humans in Asia," the USDA emphasized in a statement.

"While the subtype is the same as the China H7N9 lineage that emerged in 2013, this is a different virus and is genetically distinct from the China H7N9 lineage," the USDA added.

U.S. officials are working to determine how the Tennessee farm, which was a supplier to Tyson Foods Inc, became infected. All 73,500 birds there were killed by the disease or suffocated with foam to prevent its spread.

Tyson, the world's biggest chicken company, is "hopeful this is an isolated incident," spokesman Worth Sparkman said.

Authorities have not identified the name of the farm or the town in Lincoln County, Tennessee, where it is located.

(Editing by Matthew Lewis and Bernard Orr)

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Cattle Genetics | BEEF Magazine

It wasnt until a few weeks after the albino ball python hatched that Justin Kobylka noticed it was distinctly marked with three smiley faces. He saw one a yellow blob that looks like a smiling emoji and thought it was cool. Then, when reviewing a photograph of the snake, he noticed they comprised a trio a pattern that he, a professional snake breeder, had never heard of. He was in the presence of a rare masterwork of genetic engineering.

I knew theoretically that you could get smiley faces one smiley face is not that uncommon, said Kobylka, who hatched his first batch of snakes in an incubator underneath his dorm room bed in college, in an interview with Inverse. I would likely be able to breed more in the future that have just one, but I dont know if I could get three ever again no matter how long I try. Its really a lucky thing.

This snakes existence is a mixture of luck and years worth of careful science. While the snakes unique pattern is what makes it viral worthy, what is less obvious is how difficult it is for a highly patterned albino that is, white-skinned ball python to even exist.

There are two recessive mutations, fairly common in the natural world, manifested this snake: albinism and pybalism, the characteristic of having high-color, high-contrast patterns like the smiley face. The first albino ball python that ever hatched was bred from double heterozygous parent snakes that both contained mutant alleles at both genes encoding these two traits. Because the odds are one in 16 that a snake carrying both mutations could hatch and each female only has six eggs a year, it could take two to three years for this breeding to even occur, Kobylka says.

Breeding gets easier once the first albino pyball is born: Using it in a second pairing with another double heterozygous parent, the odds drop to one in four. Still, theres no guarantee that the albino pyballs characteristic splotch pattern will form the shape of a smiley, let alone three times in a row; it occurs in only one in ten snakes. This is where Kobylkas luck factors in.

The special smilies are fun, but were just happy to be able to make an albino ball python, says Kobylka. Two years ago, making an albino ball python was a holy grail.

When these special snakes hatched, they were worth a pretty penny for collectors; they are valued between $30,000 to $40,000. Today, Kobylka can use an albino python in the actual pairing as a double homozygous animal as the parent, which drops the odds to another albino ball python hatching to one in four. While this easier breeding system has increased the quantity available, and has dropped the price to about $4,500 each.

Is it possible for you to get an emoji snake exactly like this? Probably not science isnt on your side and Kobylka is keeping this one.

Photos via Giphy

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This Very Rare Emoji Snake Is a Genetics Marvel - Inverse