PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

NYU Courant researchers weigh methods to more accurately measure genome sequencing

2012-02-06
(Press-News.org) Lost in the euphoria of the 2003 announcement that the human genome had been sequenced was a fundamental question: how can we be sure that an individual's genome has been read correctly?

While the first full, individual genome was sequenced a decade ago, given the vast genetic variation across the world's seven billion people, not to mention the differences in makeup even among close relatives, the question of accurate sequencing for individuals has continued to vex researchers.

With companies now projecting they can sequence a genome for a $1,000, down from $25,000 just a few years ago, and efforts to develop "personalized" medicines, this matter is taking on increased significance in today's marketplace. These cheaper endeavors rely on newer technologies, which assume that scientists can continue to use the standard shotgun approach of randomly chopping down the genome into smaller pieces and then reassembling them algorithmically. Specifically, today's lower cost is achieved by breaking the DNA into even tinier pieces and rapidly and cheaply reading a massive amount of them. But it is not clear how to assess the accuracy of the newer assembly algorithms and the basic shotgun approach, especially if the accuracy of the earlier genomic data is questionable.

Among the particular challenges in confirming the accuracy of the sequencing of an individual's genome is matching a person's phenotype, or physical trait, with his or her genotype, or genetic makeup. This has served, in particular, as a barrier to successful development of personalized medicines, which were predicted shortly after the first sequencing of the human genome, but have yet to truly materialize.

In an article in the journal PLoS One, researchers at New York University's Courant Institute of Mathematical Sciences evaluate some current methods to sequence individual genomes—a study that serves as a "stress test" of the efficacy of these practices.

The researchers employed testing procedures that aim to identify key, or representative, features of the genome as well as how each of these features is related to others.

"Most current technologies, when assembling a genome, make several kinds of mistakes when they encounter a repeated region—where a substring of the letters that make up DNA strands re-occur in many locations in the genome," explained Bud Mishra, a professor of computer science and mathematics and the study's senior author. "The input random reads tend to collect in one such location, and also show much higher discrepancies among themselves."

To test the viability of these procedures, the NYU researchers relied on a collection of features from an open-source software, AMOS, developed by a public consortium of genomicists and bioinformaticists. If a method has accurately sequenced an individual's entire genome, the researchers hypothesized, then the components of that method's creation should "fit together," and will be consistent with other auxiliary data like "mate pairs," "optical maps," or "strobed sequences," all of which constitute long-range information from the genome. Currently, the use of mate pairs is quite common in sequence assembly and validation algorithms, but not the other two.

While they found shortcomings in all examined methods for sequencing an individual's genome, some assemblers showed promise. The NYU researchers' conclusions were derived from a procedure called Feature-Response Curve (FRCurve), which effectively shows a global picture of how different assemblers are able to deal with different regions and different structures in a large complex genome. In this way, it also points out how an assembler might have traded off one kind of quality measure at the expense of another kind. For instance, it shows how aggressively a genome assembler might have tried to pull together a group of genes into a contiguous piece of the genome, while incorrectly rearranging their correct order and copy-numbers.

"Such errors have important consequences, especially if the technology is being used to study the genome of a tumor, which often can be highly heterogeneous, making each tumor cell's genome rearranged and mutated very differently from its neighbors'," explained Mishra.

###

The study's other co-authors were NYU summer visitor Francesco Vezzi, now at Italy's University of Udine, and NYU graduate student Giuseppe Narzisi, now at Cold Spring Harbor Laboratory.

The study was supported by the National Science Foundation and Abraxis BioScience, LLC.

END



ELSE PRESS RELEASES FROM THIS DATE:

Parasites or not? Transposable elements in fruit flies

2012-02-06
Nearly all organisms contain pieces of DNA that do not really belong to them. These "transposable elements", so called because they are capable of moving around within and between genomes, generally represent a drain on the host's resources and in certain cases may lead directly to disease, e.g. when they insert themselves within an essential host gene. The factors that govern the spread of transposable elements within a population are broadly understood but many of the finer points remain unclear. New work at the University of Veterinary Medicine, Vienna (Vetmeduni ...

Sediments from the Enol lake reveal more than 13,500 years of environmental history

Sediments from the Enol lake reveal more than 13,500 years of environmental history
2012-02-06
A team of Spanish researchers have used different geological samples, extracted from the Enol lake in Asturias, to show that the Holocene, a period that started 11,600 years ago, did not have a climate as stable as was believed. The Holocene period, which includes the last 11,600 years of our history, has always been described as a stable period in terms of climatic conditions, especially when compared to the abrupt changes that occurred in the last ice age, which ended around 10,000 years ago, giving way to the Holocene. A study carried out by researchers from the Pyrenean ...

Jointly utilizing LTE networks

Jointly utilizing LTE networks
2012-02-06
Smartphones and tablets are some of the big sellers of the past year. Mobile Internet usage has increased rapidly with the sales success: according to a study of the industry association VATM, in 2011 the average data volume per mobile Internet user increased by 82 percent in Germany. In contrast to its predecessor UMTS, with the new LTE mobile radio standard, the clearly higher data rates and the shorter signal transmission times, providers want to cover the expected traffic. That is why the expansion of the LTE network is being pursued aggressively. Providers are setting ...

Making sense of addiction terminology

2012-02-06
London, UK – A new editorial released this week offers clarity and structure on confusing drug and alcohol addiction terminology for prescribers, users and regulators. "Through a glass darkly: can we improve clarity about mechanism and aims of medications in drug and alcohol treatments?" is published in the Journal of Psychopharmacology, the official journal of the British Association for Psychopharmacology, published by SAGE. David Nutt and Anne Lingford-Hughes of Imperial College London's Neuropsychopharmacology Unit together with Jonathan Chick from Queen Margaret ...

Collective action

Collective action
2012-02-06
If you wanted to draw your family tree, you could start by searching for people who share your surname. Cells, of course, don't have surnames, but scientists at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, have found that genetic switches called enhancers, and the molecules that activate those switches – transcription factors – can be used in a similar way, as clues to a cell's developmental history. The study, published today in Cell, also unveils a new model for how enhancers function. Looking at fruit fly embryos, Guillaume Junion and Mikhail ...

Judder-free videos on the smartphone

2012-02-06
The journey for the family holiday can be a long one. To avoid the incessant "Are we there yet?", stressed parents gladly hand their smartphones to the back seat – so the kids can watch videos or movies on the internet. While modern technology provides for entertainment, it occasionally reaches its limits and then the whining returns: The movies sometimes judder, or are completely interrupted. The cause may be twofold: If the user is standing at the basin of a valley and has poor reception, the data stream transmission rate is inadequate and the cellphone cannot download ...

Surface of Mars an unlikely place for life after 600 million year drought, say scientists

2012-02-06
Mars may have been arid for more than 600 million years, making it too hostile for any life to survive on the planet's surface, according to researchers who have been carrying out the painstaking task of analysing individual particles of Martian soil. Dr Tom Pike, from Imperial College London, will discuss the team's analysis at a European Space Agency (ESA) meeting on 7 February 2012. The researchers have spent three years analysing data on Martian soil that was collected during the 2008 NASA Phoenix mission to Mars. Phoenix touched down in the northern arctic region ...

Global extinction: Gradual doom is just as bad as abrupt

Global extinction: Gradual doom is just as bad as abrupt
2012-02-06
A painstakingly detailed investigation shows that mass extinctions need not be sudden events. The deadliest mass extinction of all took a long time to kill 90 percent of Earth's marine life, and it killed in stages, according to a newly published report. Thomas J. Algeo, professor of geology at the University of Cincinnati, worked with 13 co-authors to produce a high-resolution look at the geology of a Permian-Triassic boundary section on Ellesmere Island in the Canadian Arctic. Their analysis, published Feb. 3 in the Geological Society of America Bulletin, provides strong ...

Soy isoflavone supplements did not provide breast cancer protections

2012-02-06
PHILADELPHIA -- Soy isoflavone supplements did not decrease breast cancer cell proliferation in a randomized clinical trial, according to a study published in Cancer Prevention Research, a journal of the American Association for Cancer Research. Lead researcher Seema A. Khan, M.D., professor of surgery at the Robert H. Lurie Comprehensive Cancer Center of Northwestern University, said the results of this study are consistent with the findings of previous studies that were designed to test cancer prevention benefits of dietary supplements. "Simply put, supplements are ...

Dignity counts when caring for older people

2012-02-06
Older people feel that their health problems pose a challenge to their sense of independence, dignity and identity and sometimes the health care they are given makes things worse. According to research funded by UK Research Councils' New Dynamics of Ageing programme (NDA), healthcare providers must avoid taking a 'blanket view' of how to help older people cope with the ageing process. The study carried out by Dr Liz Lloyd and her colleagues found that people were often surprised by the impact that illness and growing old had on their lives. Their sense of 'self' was ...

LAST 30 PRESS RELEASES:

Signs identified that precede sudden arrhythmic death syndrome in young people

Discovery of bacteria's defence against viruses becomes a piece of the puzzle against resistance

Pre-eclampsia is associated with earlier onset and higher incidence of cardiovascular risk factors

Warwick astronomers discover doomed pair of spiralling stars on our cosmic doorstep

Soil conditions significantly increase rainfall in world’s megastorm hotspots

NK cells complexed with bispecific antibody yield high response rates in patients with lymphoma

Planetary health diet and mediterranean diet associated with similar survival and sustainability benefits

Singapore launches national standard to validate antimicrobial disinfectant products

Molecular stool test could improve detection of tuberculosis in adults with HIV

Suspected fibrocartilaginous embolus in Asian small-clawed otter (Aonyx cinereus)

Enhancing heat transfer using the turbulent flow of viscoelastic fluids

Exercise as an anti-ageing intervention to avoid detrimental impact of mental fatigue

UMass Amherst Nursing Professor Emerita honored as ‘Living Legend’

New guidelines aim to improve cystic fibrosis screening

Picky eaters by day, buffet by night: Butterfly, moth diets sync to plant aromas

Pennington Biomedical’s Dr. Leanne Redman honored with the E. V. McCollum Award from the American Society for Nutrition

CCNY physicists uncover electronic interactions mediated via spin waves

Researchers’ 3D-printing formula may transform future of foam

Nurture more important than nature for robotic hand

Drug-delivering aptamers target leukemia stem cells for one-two knockout punch

New study finds that over 95% of sponsored influencer posts on Twitter were not disclosed

New sea grant report helps great lakes fish farmers navigate aquaculture regulations

Strain “trick” improves perovskite solar cells’ efficiency

How GPS helps older drivers stay on the roads

Estrogen and progesterone stimulate the body to make opioids

Dancing with the cells – how acoustically levitating a diamond led to a breakthrough in biotech automation

Machine learning helps construct an evolutionary timeline of bacteria

Cellular regulator of mRNA vaccine revealed... offering new therapeutic options

Animal behavioral diversity at risk in the face of declining biodiversity

Finding their way: GPS ignites independence in older adult drivers

[Press-News.org] NYU Courant researchers weigh methods to more accurately measure genome sequencing