Posts Tagged ‘genome sequencing’

New Sequencing Technology Reveals Thousands of Unknown Genome Variations

 :: Posted by American Biotechnologist on 11-10-2014

Thousands of never-before-seen genetic variants in the human genome have been uncovered using a new genome sequencing technology. These discoveries close many human genome mapping gaps that have long resisted sequencing.

The technique, called single-molecule, real-time DNA sequencing (SMRT), may now make it possible for researchers to identify potential genetic mutations behind many conditions whose genetic causes have long eluded scientists, said Evan Eichler, professor of genome sciences at the University of Washington, who led the team that conducted the study.

“We now have access to a whole new realm of genetic variation that was opaque to us before,” Eichler said.

Eichler and his colleague report their findings Nov. 10 in the journal Nature.

To date, scientists have been able to identify the genetic causes of only about half of inherited conditions. This puzzle has been called the “missing heritability problem.” One reason for this problem may be that standard genome sequencing technologies cannot map many parts of the genome precisely. These approaches map genomes by aligning hundreds of millions of small, overlapping snippets of DNA, typically about 100 bases long, and then analyzing their DNA sequences to construct a map of the genome.

This approach has successfully pinpointed millions of small variations in the human genome. These variations arise from substitution of a single nucleotide base, called a single-nucleotide polymorphisms or SNP. The standard approach also made it possible to identify very large variations, typically involving segments of DNA that are 5,000 bases long or longer. But for technical reasons, scientists had previously not been able to reliably detect variations whose lengths are in between — those ranging from about 50 to 5,000 bases in length.

The SMRT technology used in the new study makes it possible to sequence and read DNA segments longer than 5,000 bases, far longer than standard gene sequencing technology.

This “long-read” technique, developed by Pacific Biosciences of California, Inc. of Menlo Park, Calif., allowed the researchers to create a much higher resolution structural variation map of the genome than has previously been achieved. Mark Chaisson, a postdoctoral fellow in Eichler’s lab and lead author on the study, developed the method that made it possible to detect structural variants at the base pair resolution using this data.

To simplify their analysis, the researchers used the genome from a hydatidiform mole, an abnormal growth caused when a sperm fertilizes an egg that lacks the DNA from the mother. The fact that mole genome contains only one copy of each gene, instead of the two copies that exist in a normal cell. simplifies the search for genetic variation.

Using the new approach in the hydatidiform genome, the researchers were able to identify and sequence 26,079 segments that were different from a standard human reference genome used in genome research. Most of these variants, about 22,000, have never been reported before, Eichler said.

“These findings suggest that there is a lot of variation we are missing,” he said.

The technique also allowed Eichler and his colleagues to map some of the more than 160 segments of the genome, called euchromatic gaps, that have defied previous sequencing attempts. Their efforts closed 50 of the gaps and narrowed 40 others.

The gaps include some important sequences, Eichler said, including parts of genes and regulatory elements that help control gene expression. Some of the DNA segments within the gaps show signatures that are known to be toxic to Escherichia coli, the bacteria that is commonly used in some genome sequencing processes.

Eichler said, “It is likely that if a sequence of this DNA were put into an E. coli, the bacteria would delete the DNA.” This may explain why it could not be sequenced using standard approaches. He added that the gaps also carry complex sequences that are not well reproduced by standard sequencing technologies.

“The sequences vary extensively between people and are likely hotspots of genetic instability,” he explained.

For now, SMRT technology will remain a research tool because of its high cost, about $100,000 per genome.

Eichler predicted, “In five years there might be a long-read sequence technology that will allow clinical laboratories to sequence a patient’s chromosomes from tip to tip and say, ‘Yes, you have about three to four million SNPs and insertions deletions but you also have approximately 30,000-40,000 structural variants. Of these, a few structural variants and a few SNPs are the reason why you’re susceptible to this disease.’ Knowing all the variation is going to be a game changer.”

Thanks to University of Washington Health Sciences for contributing this story.

Whole genome sequencing and you

 :: Posted by American Biotechnologist on 11-12-2012

As professionals, it is our job to be advocate for science and to educate the public about the benefits of scientific research and advancements (especially if you want the government to continue funding your lab). Want a good tool to explain genome sequencing to your friends and family? Check it out.

A RADical technology for genome sequencing

 :: Posted by American Biotechnologist on 04-27-2011

Take millions of puzzle pieces containing partial words and put them back together into full words, sentences, paragraphs and chapters until the book these random parts came from is rebuilt.

Eric A. Johnson

That daunting process in not unlike sequencing an organism’s genome, says University of Oregon biologist Eric A. Johnson, a member of the UO Institute of Molecular Biology. His lab developed a patent-pending technology for discovering differences between genomes called restriction-site associated DNA markers, or RAD. They have now shown that RAD can also be used to help put a genome sequence together.

The original RAD technique, unveiled in 2005, led to the UO spinoff company Floragenex, which uses the technology in plant genetics. More recently, Johnson and UO colleague William A. Cresko used it to identify genetic differences in threespine stickleback, a fish, which evolved separately after environmental conditions had isolated some of the saltwater fish into freshwater habitats.

Now, after three years of research, adapting it along the way as sequencing tools advanced, Johnson, Cresko and three UO colleagues provide a proof-of-principle paper in the April issue of PLoS One, a publication of the Public Library of Science. The National Institutes of Health-funded research documents that the new method, called RAD paired-end contigs, works and provides accurate sequencing results.

“The RAD sequence is a placeholder that identifies one small region of a genome,” Johnson said. “We showed that this technique lets us gather together appropriate nearby sequences and piece them together.” In just seconds, a section is completed, he said. In a matter of hours, he added, an entire genome’s sequence emerges.

Using the book analogy, Johnson said: “We first asked if we can piece together one short sentence at a time instead of ordering all the words in the whole book at once. Next, can we put together one paragraph at a time? That’s like going from, say, 1,000 letters of the genome in a row to 5,000 at a time. Here, we show that we can do this. We can put the book back together.”

A RAD marker in the book analogy might be a word at the start of each sentence. Using that marker as an anchor, the rest of the words in the sentence are easily separated from all the words in the book, and then the words in the sentence are put in the right order, on an on until all the content is organized correctly, Johnson said. The end product, he added, contains few, if any, leftover or unexplained fragments, a problem occurring with current technologies that rely on clusters of computers, requiring extensive memory, to complete sequencing projects.

RAD technology can be applied to study the genetics of organisms for which genomes have not been completed, Johnson said.

The PLoS One paper detailed how RAD works on stickleback and the bacterium e-coli. Both involve small and rather simple genomes. There already is interest in its potential application in human genome sequencing, Johnson said.

At about the same time the PLoS One paper was being published, Johnson, who also is the chief scientific officer of Floragenex, was part of a company-sponsored, one-day RAD Sequencing and Genomics Symposium in Portland, Ore., on April 19. Nine researchers from five institutions (UO, Oregon State University, University of British Columbia, University of Tennessee and University of Washington) described how they are applying RAD in their sequencing projects.

“It was quite gratifying to hear them speak about this technology and how it is working for them,” Johnson said.

RAD technology also is being used in a three-year project — funded by a $1 million grant from the W.M. Keck Foundation and led by Cresko and UO colleague Hui Zong — to identify genetic changes that occur from the formation of a single mutation to full-fledged cancer. The project could lead to a new generation of molecular diagnostics to detect cancers in their earliest stages.

Citation: Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA (2011) Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads. PLoS ONE 6(4): e18561. doi:10.1371/journal.pone.0018561

Source: University of Oregon via EurekAlert!

Gaggle Genome Browser: The Google Map of Genomics

 :: Posted by American Biotechnologist on 09-07-2010

Advances in next gen sequencing has been accompanied by an onslaught of genomic data which has in-turn required new tools for processing and navigating very large data sets. The gaggle genome browser was developed by the Baglia lab at the Institute for Systems Biology in Seattle, Washington. The browser allows for users to navigate through available genomic data from a variety of organisms. The tool is very user friendly and has cursor functions similar to google maps (in fact, you might think of the genome browser as the genomic version of google maps).

Below is a brief introduction to the gaggle genome browser by Mary from the OpenHelix blog.

Sequencing Sitting Bull-Frivolous Funding or Good PR

 :: Posted by American Biotechnologist on 08-23-2010

According to a report in ScienceNews, the famous Sioux chief Sitting Bull may be joining the small but growing number of people who have had their DNA sequenced. In reporting this story, GenomeWeb quoted Blaine Bettinger at The Genetic Genealogist who named Albert Einstein, Abraham Lincoln, Ötzi and Juanita the Peruvian Ice Maiden (a 600-year-old mummy) as other famous personalities whose DNA should also be sequenced as a memento of the past.

What intrigued me most about this story was not the “wow” factor associated with sequencing a famous person’s DNA, nor was it the ethical issue of sequencing someone’s genome without their permission as proposed by The Genetic Genealogist. What got me thinking about this story was a comment by S. Pelech on GenomeWeb where s/he laments that despite the decreasing costs associated with whole genome sequencing, money spent on sequencing the genomes of long-dead celebrities would be better spent on research initiatives that would be of more benefit to human health.

In general, I agree with S. Pelech that “trimming the fat” from the system and concentrating our resources on more practical research projects would be a prudent use of scare research funds. In siding with S. Pelech, I am assuming that his beef is with the use of public grant funds for what I like to call “extracurricular” research. I do not believe that we should be dictating how private funds are used in any research environment.

On the other hand, the glitz and glamor associated with sequencing Albert Einstein or Sitting Bull’s genome will likely increase public awareness of genome sequencing projects (or at least keep the field in the forefront of the public consciousness) and may ultimately lead to more public support for other genomic project and increased funding down the road. After all, government funding of science is generally determined by public perception. If the public is in support of increasing research funding then the government will be more likely to follow suit (especially with campaign promises during election season).

So to summarize my thoughts, I believe that although we should focus our dollars of funding “practical” research projects, there is room for supporting “eye candy” research if it helps keep the public focused on scientific research.

What are your thoughts?