The genetic makeup of domestic pigs was compared to those of 10 wild boars – from which domestic pigs are descended.
Researchers found important genetic differences between wild boar from Asia and Europe, which split from a common ancestor around a million years ago. These differences were also identified in genes of modern Western and Chinese breeds of domesticated pigs, adding weight to the theory that pigs were domesticated in western Eurasia and East Asia.

This improved understanding of the genetic differences that developed through domestication, will help to inform future breeding programmes.
By comparing 21,000 genes identified in pigs with their counterparts in human, mice, dogs, horse and cows, it has emerged that the immune response genes used to fight infection are rapidly evolving in pigs.

Further understanding of the fundamental biology of these genes and how and why they have evolved more rapidly, could help direct future breeding to improve pig health and the ability to fight disease.

Several examples were identified where the pig genes shared similarities with the form of gene identified in humans that have also been linked with diseases, such as diabetes, obesity and Alzheimer’s.

These findings demonstrate the potential of pigs as a biomedical model to provide a beneficial insight into common complex human diseases. Analysis from this study also gives an insight into the genes that enable high quality pork production, which can help producers in future breed high quality swine, improve sustainability and lower costs.

The study also provides an explanation for the renowned ability for pigs to seek out truffles, picking out their signature scent amongst the complex scents of a woodland floor and locating them underground.

With 1,301 unique olfactory receptor genes, the pig has more genes than have been identified in human, dog or mouse, but similar numbers to those in the rat. This highlights the importance of a heightened sense of smell in scavenging animals.

Dr Mario Caccamo, head of bioinformatics for TGAC in Norfolk, who joined the project while at the Wellcome Trust Sanger Institute in Cambridge, led the assembly of the pig genome sequence and is one of the primary authors on the Nature paper.

Dr Caccamo said: “The publication of the swine genome reference is the culmination of a great team effort involving a large consortium of scientists from across the world.

“Our contribution at TGAC was focused on the generation of the final sequence assembly in collaboration with colleagues at the Welcome Trust Sanger Institute and the Beijing Genomics Institute (BGI).”

Professor Jane Rogers, Director of TGAC, contributed to the initiation of the project and led the sequencing whilst at the Wellcome Trust Sanger Institute.

Professor Rogers said “From the outset, this genome project was developed with the technical challenges in mind of providing a resource that would enable researchers to use the genome to make comparisons between the genes in pigs and humans that are involved in health, for example, genes involved in infectious disease defence mechanisms.

“Whilst the genome is not complete, it provides an excellent foundation for such work and I hope researchers around the world will use and continue to improve it over time.”

The study, published in Nature was led by scientists at the Roslin Institute at the University of Edinburgh, and the Wellcome Trust Sanger Institute in Cambridge, Wageningen University and the University of Illinois.

The International Swine Genome Sequencing Consortium is comprised of researchers from more than 40 institutes in 12 countries and was funded by the United States Department of Agriculture, the European Commission, the Biotechnology and Biological Sciences Research Council (BBSRC), the Wellcome Trust and pig industry groups in Europe and the United States.

New research published in the journal Science Translational Medicine this week makes the case for a two-day whole-genome sequencing for newborns in a neonatal intensive care unit (NICU).

After 50 hours, the test delivers to doctors a wealth of information about what could be causing newborns’ life-threatening illnesses. This would allow them to more efficiently and quickly tailor therapies to the babies, when possible, and identify problematic genetic variants that multiple family members may share.

“We think this is going to transform the world of neonatology, by allowing neonatologists to practice medicine that’s influenced by genomes,” said Stephen Kingsmore, the study’s senior author and director for the Center for Pediatric Genomic Medicine at Children’s Mercy Hospitals and Clinics in Kansas City, Missouri, at a press conference Tuesday.

There are more than 3,500 diseases caused by a mutation in a single gene, Kingsmore said, and only about 500 have treatments. About one in 20 babies born in the United States annually gets admitted to a neonatal intensive care unit, he said. Genetic-driven illnesses are a leading cause of these admissions at Kingsmore’s hospital.

One example of how a genetic test would help newborns is a condition called severe Pompe disease, Kingsmore said. Children with this disorder die if they are not treated by age 1. They will live longer, at least four years, if they receive an enzyme replacement therapy.

The study shows how two software programs, called SAGA and RUNE, work together to help physicians pinpoint the genes that could be causing problems in the children. A company called Illumina developed a rapid genome sequencing device that incorporates the programs.

Researchers reported diagnoses as a result of this genetic test in the study for six children. Two of these tests were done retrospectively, after the children had died.

The test extends beyond the ill baby; genome sequencing can also identify genetic traits in multiple family members, the researchers said. Carol Saunders, the study’s lead author, explained at the news conference how one baby and his 6-year-old brother both have a congenital heart defect and heterotaxy, meaning some internal organs are located on the wrong side of the body–read the full article

- Big data technology breaks the genome interpretation bottleneck

- An in silico genetic testing “lab in a box”

- More than a dozen leading institutions join early access program

CAMBRIDGE, MA –  September 27, 2012 – Knome Inc. announced today that it is taking orders for the knoSYS™100, the first plug-and-play, fully integrated hardware and software system designed to help researchers in medical and academic institutions interpret human whole genomes. The knoSYS™100 was developed to help geneticists discover relevant genetic variation, investigate diseases of unknown cause, and create next generation in silico gene tests. Units will begin shipping in Q4, 2012.

Starting at $125,000, the knoSYS™100 is based on Knome’s big data informatics technology. The system will accept next generation sequence data from leading sequencers, including those sold by Illumina, Life Technologies, and Complete Genomics.

Breaking the genome interpretation bottleneck          

The difficulty and cost associated with human genome sequencing has largely been addressed, with the cost of sequencing a whole genome expected to decline to under $1,000 in 2013. But it still takes a team of researchers weeks to months to annotate, compare, and interpret genome data. This slow pace and the lack of robust tools have significantly limited the ability of researchers to scale the process of interpreting human genomes.

With an average throughput of one genome per day, the knoSYS™100 eliminates the current informatics bottleneck in whole genome interpretation—matching the speed of today’s fastest sequencers.

“In the first half of this year, we saw the demand for genome interpretation surge as researchers in many of the world’s leading medical institutions started preparing for the broad utilization of whole genome interpretation for patient care,” said Martin Tolar, MD, PhD, Chief Executive Officer of Knome. “All of these institutions face the same issue—how to industrialize genome interpretation so that it is not only accurate, but fast.”

More than a dozen of the world’s top medical institutions have joined an early access program to pilot Knome’s genome interpretation technology, including: ARUP Laboratories, Cedars-Sinai Medical Center, Cincinnati Children’s Hospital, The Hospital for Sick Children (SickKids) in Toronto, Hyundai Cancer Institute at CHOC Children’s, University of Liverpool, and University of Verona.

An in silico genetic testing “lab in a box”

In addition to providing geneticists with query and visualization applications for conducting in-depth research into sets of whole genomes, the knoSYS™100 ships with tools and libraries that allow developers to create in silico gene tests that can be run at the push of a button.

“The advent of fast and affordable whole genome interpretation will fundamentally change the genetic testing landscape,” said George Church, PhD, professor of genetics at Harvard University and co-founder of Knome. “The genetic testing lab of the future is a software platform where gene tests are apps. This will shift genetic testing from a fixed, lengthy process to a rapid and highly dynamic one that makes full use of the data contained in the entire genome.”

Developers can use the tools and libraries included with the knoSYS™100 to replicate existing single gene tests in software. They can also go further, creating next generation superpanels that examine thousands of genes, as well as incorporate artificial intelligence algorithms; deep reference data on protein interaction and expression; statistical functions; and the power of kindred, population, and tumor/non-tumor comparison.

“In silico superpanels allow hundreds of conditions to be tested simultaneously and open the door to the development of a new class of molecular diagnostics for complex, multi-gene disorders,” said Dr. Church. “Moving from a world of assays to apps will expand the definition of what a gene ‘test’ actually is, raising important questions but also presenting tremendous opportunities to help improve human well-being.”

As a demonstration of capability, the knoSYS™100 will include several superpanels for research into cancer, epilepsy, heart disorders, and other conditions.

The system

The knoSYS™100  is an integrated hardware and software system constructed around Knome’s core big data informatics technology, used since 2008 to interpret thousands of whole human genomes and exomes for medical, pharmaceutical, and academic research projects. The components of the knoSYS™ 100 include:

• State-of-the-art informatics engine: a robust and scalable informatics engine (kGAP™) that quickly transforms sequence data produced by different sequencing platforms into standardized, richly annotated, and easily comparable data sets. kGAP draws on an ever-growing, Knome-curated and harmonized knowledge base of reference information from more than a dozen different third-party data sources.
• Advanced genome interpretation applications: query and data visualization applications that allow power users to access kGAP-enhanced genomes in order to conduct in-depth research to find the variants, genes, gene sets, and pathways that underlie disease, drug response and tumor growth.
• Functionality for developing next generation gene tests: tools and scripting libraries that enable medical researchers to create and share next generation, in silicogene panels on whole genomes and exomes processed through kGAP.
• Genomics supercomputer: the knoSYS™100 is optimized for the intensive processing and I/O requirements of whole genome informatics. At nearly 600 lbs. and running at over 1.2 teraFLOPS, it includes four 2.4GHz 8-core/16 thread Intel^® Xeon^® E5-2665 processors, and 18TB to 54TB of useable disk storage and Gigabit Ethernet—all contained in a secure, sound-proofed enclosure that can be placed in a laboratory environment.

Since the knoSYS™100 is installed on-premises and is maintained behind the client’s firewall, it is well-suited for institutions that do not wish to send genome data to third parties or the cloud due to privacy, consent, or confidentiality concerns.

“There are close to 2,000 next gen sequencers in labs around the world generating enormous amounts of data,” said Knome Chief Executive Officer Martin Tolar, MD, PhD. “Every one of those sequencers should have a knoSYS™100 right next to it. To further facilitate the application of genomics in patient care, we are investing over $50 million in R&D over the next several years. This is where we intend to make a lasting contribution to molecular-based, precision medicine.”

About Knome

Knome Inc. is a leading provider of human genome interpretation systems and services. We help clients in two dozen countries identify the genetic basis of disease, tumor growth, and drug response. Designed to accelerate and industrialize the process of interpreting whole genomes, Knome’s big data technologies are helping to pave the healthcare industry’s transition to molecular-based, precision medicine.

Media contacts:

Barbara Yates, The Yates Network

barbara@theyatesnetwork.com

781-258-6153

“We went to check on him, just like any parents go and check on their kids just to make sure they’re breathing,” says Terry, 34, of Spring, Texas. “And we found him in his crib, and he wasn’t breathing. He was blue.”

She and her husband were horrified. They rushed Christian to the hospital and learned he had several medical problems.

That terrifying night was the beginning of a long, frustrating odyssey. For the next six years, Sara Terry and her husband went from doctor to doctor trying to figure out what was behind Christian’s strange constellation of problems: developmental delay, low muscle tone, sleep apnea and a heart murmur, among others.

The Terrys got every test every specialist could think of, but no one could answer the big question: What’s wrong with Christian?

“With a child who goes undiagnosed, you don’t know how to treat it, and you don’t know maybe what their life expectancy is, or what you can expect from this child,” Terry says. “Or how you could push them, or what you can do with them. So it can be very difficult. And you don’t know if you’re doing everything you can for them.”

The Terrys finally ended up at the Baylor College of Medicine in Houston. A doctor there told them about something they’d never heard of: whole genome sequencing, which can test for every genetic syndrome that’s known.

The Terrys agreed, and sent off their son’s sample for testing — and waited.

Until recently, genetic tests only scanned small parts of someone’s DNA, such as the parts carrying genes that can cause Huntington’s or Alzheimer’s or breast cancer.

Whole genome sequencing spells out the entire genetic code — all 3 billion letters.

“For those of us in the field, it is sort of a holy grail,” says Arthur Beaudet, who chairs Baylor’s genetics department. “We now have the ability to get very complete genetic information about individuals and interpret in the context of whatever problems they may have.”

It wasn’t all that long ago that it took hundreds of scientists years, and billions of dollars, to do this on just one genome.

But now, a few lab techs using high-speed sequencers can unravel anyone’s DNA for just thousands of dollars, in weeks.

“To me, it’s a spectacular advance,” Beaudet says. “It changes everything, in the sense that we really begin to understand at an individual patient level exactly which gene is altered, and we can begin to think about ways to intervene.”

So far, doctors are using sequencing mostly on two kinds of patients. The first are patients like Christian, with mysterious illnesses no one can seem to sort out.

“Any patient who has one of these rare diseases will tell you about the misery and the agony of this process, which is going from doctor to doctor, undergoing test after test after test, and getting equivocal answers to what’s wrong with them or their child,” says Leslie Biesecker of the National Human Genome Research Institute–read the entire article here

Or read the article here