Category Archives: Genome

Yaniv Erlich

DANA SMITH

Late at night, a video camera captures a man striding up to the locked door of the information-technology department of a major Israeli bank. At this hour, access can be granted only by a fingerprint reader but instead of using the machine, the man pushes a button on the intercom to ring the receptionist's phone. As it rings, he holds his mobile phone up to the intercom and presses the number 8. The sound of the keypad tone is enough to unlock the door. As he opens it, the man looks back to the camera with a shrug: that was easy.

Yaniv Erlich the star of this 2006 video considers this one of his favourite hacks. Technically a penetration exercise conducted to expose the bank's vulnerabilities, it was one of several projects that Erlich worked on during a two-year stint with a security firm based near Tel Aviv. Since then, the 33-year-old computational biologist has been bringing his hacker ethos to biology. Now at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, he is using genome data in new ways, and in the process exposing vulnerabilities in databases that hold sensitive information on thousands of individuals around the world.

In a study published in January1, Erlich's lab showed that it is possible to discover the identities of people who participate in genetic research studies by cross-referencing their data with publicly available information. Previous studies had shown that people listed in anonymous genetic data stores could be unmasked by matching their data to a sample of their DNA. But Erlich showed that all it requires is an Internet connection.

Erlich's work has exposed a pressing ethical quandary. As researchers increasingly combine patient data with other types of information everything from social-media posts to entries on genealogy websites protecting anonymity becomes next to impossible. Studying these linked data has its benefits, but it may also reveal genetic and medical information that researchers had promised to keep private and that, if made public, might hurt people's employability, insurability or even personal relationships.

Such revelations may make the scientific community uncomfortable and undermine the public's trust in medical research. But Erlich and his colleagues see their work as a way to alert the world about flawed systems, keep researchers honest and ultimately strengthen science. In March, for instance, the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, claimed that the genome sequence that it had published for the HeLa cell line would not reveal anything about Henrietta Lacks the source of the cells or her descendants. Erlich issued a tart response: Nice lie EMBL! he tweeted. The sequence was later pulled from public databases, and the EMBL admitted that it would indeed be possible to glean information about the Lacks family from it, even though much of the HeLa genetic data had already been published as part of other studies.

Most scientists would not go anywhere close to these questions, out of a sense of what it might mean for the field, or for them personally, says David Page, director of the Whitehead Institute, who has advised Erlich about his research. But this is not about publicity-seeking this is about fearlessness, and a kind of interest in how all the parts of the Universe fit together that mark all of Yaniv's work.

Erlich was inspired to teach himself programming as a child in Israel after seeing the 1983 film WarGames, in which a teenager accidentally hacks into government computer systems and nearly launches global thermonuclear war. Erlich thought that he would study maths and physics at university, but after a friend told him that there was a lot of maths in biology, he decided to major in computational neuroscience. In 2006, following his graduation, Erlich moved to the United States to earn his PhD in genetics at Cold Spring Harbor Laboratory in New York.

Under his adviser, molecular biologist Greg Hannon, Erlich devised what he called DNA Sudoku: a sequencing method that could be used on tens of thousands of specimens analysed simultaneously. It allowed scientists to use computational techniques to find a gene carrying a rare mutation from this mixed batch of DNA and assign it to the right specimen2. Erlich is now using the technique to find disease-causing mutations in young Ashkenazi Jews to inform their decisions about potential marriage partners.

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Privacy protections: The genome hacker

HGP10 Symposium: Whole Genome Sequencing in Newborn Screening - Jeff Botkin
April 25, 2013 - The Genomics Landscape a Decade after the Human Genome Project More: http://www.genome.gov/27552257.

By: GenomeTV

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HGP10 Symposium: Whole Genome Sequencing in Newborn Screening - Jeff Botkin - Video

MENLO PARK, Calif., May 6, 2013 (GLOBE NEWSWIRE) -- Researchers from Pacific Biosciences of California, Inc., (PACB), the U.S. Joint Genome Institute and the University of Washington have published a new method for assembling high-quality genomes from Single Molecule, Real-Time (SMRT(R)) DNA sequencing. Published in the May 5 edition of Nature Methodsi, the paper by Chin et al. describes the hierarchical genome assembly process (HGAP) and demonstrates the method for efficient, automated de novo assembly from genomic DNA to a finished genome sequence for several microorganisms and a human bacterial artificial chromosome (BAC) clone. As part of the paper, the authors also describe a new consensus algorithm, Quiver, that achieves highly accurate de novo genome sequence results exceeding 99.999% (QV 50) accuracy.

Finished genomes are crucial for understanding microbes and advancing the field of microbiology.ii Previous attempts for obtaining the complete genome sequence of microbes in an automated, high-throughput manner have challenged researchers. For example, with second-generation sequencing methods, short read lengths inhibit the ability to resolve long repeats, resulting in unfinished, fragmented draft assemblies. Further, extreme sequence contexts, such as GC- or AT-rich regions, or palindromic sequences, lead to gaps in draft genome assemblies that cannot be covered using these second-generation methods. As a result, Sanger sequencing has typically been employed for finishing microbial genomes, but due to its laborious and low-throughput nature this process is slow and expensive.

More recently, hybrid-assembly approaches have been described in which long PacBio reads were used in combination with short-read dataiii,iv. Building on these advances, in this new paper the authors utilize just a single, long-insert shotgun DNA library in conjunction with SMRT Sequencing, thereby removing the need for additional sample preparation and sequencing data sets required for previously described hybrid strategies. A paper describing a similar strategy and assembly results by S. Koren, A. Phillippy, and colleagues from the National Biodefense Analysis and Countermeasures Center, Frederick, MD, and the United States Agriculture Department has been deposited in a pre-print archive.

"This approach can close the large gap that currently exists between 'draft' and high-quality 'finished' genomes," said Jonas Korlach, senior author on the paper and Chief Scientific Officer at Pacific Biosciences. "Further, the ability to automatically and cost-effectively assemble genomes independent of the availability of a reference sequence can be critical in the rapid characterization of new pathogen strains."

Evan Eichler, co-author on the paper, Howard Hughes Medical Investigator and Professor at the Department of Genome Sciences at the University of Washington, said, "I am excited by the ability of SMRT DNA Sequencing and HGAP for finishing complex regions of the human genome. This approach has demonstrated the potential to cost-effectively generate high-quality finished sequence from large-insert clones of these regions, such as BACs. Short-read sequencing technologies simply cannot adequately access and assemble through these complex regions of genomes."

Pacific Biosciences recently launched the PacBio(R) RS II -- a new SMRT Sequencing system that provides the industry's highest consensus accuracy and longest reads with double the throughput from the previous version of the system. The PacBio RS II allows scientists to rapidly and cost-effectively generate finished genome assemblies, reveal and understand epigenomes, and characterize genomic variation. The PacBio RS II system, including consumables and software, provides a simple, fast, end-to-end sequencing workflow for applications such as infectious disease and microbiology, agriculture, and understanding rare diseases.

More information is available at http://www.pacb.com.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (PACB) offers the PacBio(R) RS II High Resolution Genetic Analyzer to help scientists solve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT(R)) technology, the company's products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems.

i Chin et al. (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods doi 10.1038/nmeth.2474.

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New Assembly Method Published for Rapid and Automated Genome Sequencing Using Long-Read, Single Molecule, Real-Time ...

Let #39;s Play project altered beast part 1 - first genome chip
An introduction video to Project altered beast rarely abbreviated in (PAB) for the ps2 - if you wish to skip straight to the game 1:53 The story follows a ma...

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Let's Play project altered beast part 1 - first genome chip - Video

May 5, 2013 A new study led by researchers from Harvard School of Public Health (HSPH) and the Wellcome Trust Sanger Institute in the UK has, for the first time, used genome sequencing technology to track the changes in a bacterial population following the introduction of a vaccine. The study follows how the population of pneumococcal bacteria changed following the introduction of the 'Prevnar' conjugate polysaccharide vaccine, which substantially reduced rates of pneumococcal disease across the U.S. The work demonstrates that the technology could be used in the future to monitor the effectiveness of vaccination or antibiotic use against different species of bacterial pathogens, and for characterizing new and emerging threats.

The study appears online May 5, 2013 in Nature Genetics.

"This gives an unprecedented insight into the bacteria living and transmitting among us," said co-author William Hanage, associate professor of epidemiology at HSPH. "We can characterize these bugs to an almost unimaginable degree of detail, and in so doing understand better what helps them survive even in the presence of an effective vaccine."

Pneumococcal disease is caused by a type of bacteria called Streptococcus pneumoniae, which is present in many people's noses and throats and is spread by coughing, sneezing, or other contact with respiratory secretions. The circumstances that cause it to become pathogenic are not fully understood. Rates of pneumococcal disease -- an infection that can lead to pneumonia, meningitis, and other illnesses -- dropped in young children following the introduction of a vaccine in 2000. However, strains of the bacteria that are not targeted by the vaccine rapidly increased and drug resistance appears to be on the rise.

The research, led by HSPH co-senior authors Hanage; Marc Lipsitch, professor of epidemiology; and Stephen Bentley, senior scientist at the Wellcome Trust Sanger Institute, aimed to better understand the bacterial population's response to vaccination. Whole genome sequencing -- which reveals the DNA code for each bacterial strain to an unprecedented level of detail -- was used to study a sample of 616 pneumococci collected in Massachusetts communities from 2001 to 2007.

This study confirmed that the parts of the bacterial population targeted by the vaccine have almost disappeared, and, surprisingly, revealed that they have been replaced by pre-existing rare types of bacteria. The genetic composition of the new population is very similar to the original one, except for a few genes that were directly affected by the vaccine. This small genetic alteration appears to be responsible for the large reduction in the rates of pneumococcal disease.

"The widespread use of whole genome sequencing will allow better surveillance of bacterial populations -- even those that are genetically diverse -- and improve understanding of their evolution," said Lipsitch. "In this study, we were even able to see how quickly these bacteria transmit between different regions within Massachusetts and identify genes associated with bacteria in children of different ages."

"In the future, we will be able to monitor evolutionary changes in real-time. If we can more quickly and precisely trace the emergence of disease-causing bacteria, we may be able to better target interventions to limit the burden of disease," said Bentley.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

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Genome sequencing provides unprecedented insight into causes of pneumococcal disease

May 5, 2013 The U.S. Department of Energy Joint Genome Institute (DOE JGI) is among the world leaders in sequencing the genomes of microbes, focusing on their potential applications in the fields of bioenergy and environment. As a national user facility, the DOE JGI is also focused on developing tools that more cost-effectively enable the assembly and analysis of the sequence that it, as well as other genome centers, generates.

Despite tremendous advances in cost reduction and throughput of DNA sequencing, significant challenges remain in the process of efficiently reconstructing genomes. Existing technologies are good at cranking out short fragments (reads) of DNA letters that are computationally stitched back together (assembled) into longer pieces, so that the order of those letters can be determined and the function of the target sequence discerned. However, genome assembly, the equivalent of trying to put together a multi-million piece jigsaw puzzle without knowing what the picture on the cover of the box is, remains challenging due to the very large number of very small pieces, which must be assembled using current approaches.

As reported May 5 online in the journal Nature Methods, a collaboration between the DOE JGI, Pacific Biosciences (PacBio) and the University of Washington has resulted in an improved workflow for genome assembly that the team describes as "a fully automated process from DNA sample preparation to the determination of the finished genome."

The technique, known as HGAP (Hierarchical Genome Assembly Process), uses PacBio's single molecule, real-time DNA sequencing platform, which generates reads that can be up to tens of thousands of nucleotides long, even longer than those provided by the workhorse technology of the Human Genome Project era, the Sanger sequencing technology, which produced reads of about 700 nucleotides. The Sanger process involved creating multiple DNA libraries, conducting multiple runs, and combining the data, so that gaps in the code were covered and accuracies of a DNA base assignment were very high. Post-Sanger methods still typically require multiple libraries and often a mix of technologies to produce optimal results. Instead, with HGAP, "only a single, long-insert shotgun DNA library is prepared and subjected to automated continuous long-read SMRT sequencing, and the assembly is performed without the need for circular consensus sequencing," the team reported.

This de novo assembly method was tested using three microbes previously sequenced by the DOE JGI. The data collected were compared against the reference sequences for these microbes and the team found that the HGAP method produced final assemblies with >99.999% accuracy.

"We are always on the lookout for new approaches that will improve upon the efficient delivery of high-quality data to our growing community of researchers," said Len Pennacchio, DOE JGI's Deputy Director of Genomic Technologies. "This technique is one of many improvements that we are pursuing in parallel to achieve additional economies of scale."

The DOE JGI's sequencing efforts account for more than 20% of the more than 20,000 worldwide genome projects (microbes, plants, fungi, algae, and communities of microbes) completed or currently in the queue, and most of those are focused on the biology of environmental, energy, and carbon processing.

"We enjoyed a very productive collaboration with JGI on this project and benefited tremendously from the expertise of JGI's scientists in both the fields of microbiology and microbial genome assembly and annotation," said Jonas Korlach, Chief Scientific Officer at Pacific Biosciences. "This expertise provided us with the ability to adapt our single molecule sequencing assembly methods to produce a higher level of finished quality than was previously possible using a gold-standard Sanger finishing approach, and at a speed and price point competitive with alternative next generation sequencing and assembly methods. We look forward to seeing what scientific advances will be enabled by this method as JGI's User Community assesses JGI's capabilities to assemble their microbial genomes using this new approach."

The team will now seek to extend the utility of this new assembly method beyond microbes to the genomes of more complex organisms.

Disclaimer: This article is not intended to provide medical advice, diagnosis or treatment. Views expressed here do not necessarily reflect those of ScienceDaily or its staff.

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New cost-effective genome assembly process

HGP10 Symposium: Fruits of the Genome Sequences for Society - David Botstein
April 25, 2013 - The Genomics Landscape a Decade after the Human Genome Project More: http://www.genome.gov/27552257.

By: GenomeTV

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HGP10 Symposium: Fruits of the Genome Sequences for Society - David Botstein - Video

Dance Yrself Clean, Genome with Charlie Otto
5/1/13 Tonic Room, Chicago.

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Dance Yrself Clean, Genome with Charlie Otto - Video

Piano Improv: Dai Dai Genome - Week 4 [ dj-Jo ]
Original Song: http://www.youtube.com/watch?v=nCdimH0iDZM This song has been one of my favorite Hatsune Miku songs ever since I started listening to vocaloid...

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Piano Improv: Dai Dai Genome - Week 4 [ dj-Jo ] - Video

HGP10 Symposium: Applying Genome Science to Medical Care
April 25, 2013 - The Genomics Landscape a Decade after the Human Genome Project More: http://www.genome.gov/27552257.

By: GenomeTV

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HGP10 Symposium: Applying Genome Science to Medical Care - Video