By Julia Karow
Researchers at the University of Washington have developed a method to generate both short reads and long-range information about their position on a DNA molecule using a standard Illumina flow cell.
The method combines the benefits of high-throughput sequencing and optical mapping in a single platform, according to Jerrod Schwartz, a postdoctoral fellow in Jay Shendure's lab at the UW department of genome sciences, who has been developing the technique for the past year or so.
Schwartz presented an outline of the optical sequencing approach last month at the Advances in Genome Biology and Technology meeting in Marco Island, Fla. A paper providing more details is currently under review at a scientific journal.
One of the limitations of short-read sequencing technologies today is that they provide no long-range contiguity, or positional information about a read on a DNA molecule. This has limited their use for the high-quality and low-cost de novo assembly of mammalian genomes, according to Schwartz.
His new method creates sequencing libraries from long DNA molecules directly on an Illumina flow cell, providing long-range information based on the distance between DNA clusters generated near the ends of the molecules.
He starts by adding flow cell adaptors to the ends of DNA fragments, currently up to about 8 kilobases long. The fragments are then added to a standard Illumina flow cell, where their ends hybridize to the surface primers.
A transposase that is loaded with the second flow cell adaptor is then added. It fragments the hybridized DNA and ligates the adaptors onto the newly created ends. This generates two smaller DNA fragments in close proximity to each other that have both flow cell adaptors attached to them.
After generating clusters through Illumina's bridge amplification protocol, both DNA fragments can be sequenced. Clusters that are close to each other on the flow cell are likely to derive from the same DNA molecule, so the relative position of the reads can be inferred.
In a variation of this method, Schwartz and his colleagues have stretched out long DNA molecules on the flow cell using an electric field. The distance between their ends, where reads are generated, relates to the length of the sequence between the reads.
Ultimately, Schwartz said, the researchers want to create multiple clusters and reads along the backbone of the same DNA molecule.
They are currently starting to apply their method to longer DNA molecules, ranging in size from 10 to 40 kilobases, and it is not clear yet what the size limit will be, he said.
In proof-of-principle experiments, the researchers have shown that the method, "works pretty well," he said, adding that high-quality de novo genome assembly, haplotyping, and sequencing through "any kind of challenging region" are among possible applications.
Illumina is "definitely aware" of the method but Schwartz said he could not comment on whether the company is interested in developing it commercially.
Others have developed alternative approaches to obtain both sequence and long-range positional information, but usually these involve more than one platform.
For example, researchers have started to combine long, low-accuracy reads from Pacific Biosciences' platform with more accurate short reads from Illumina, Ion Torrent, or 454 to improve the quality of de novo genome assemblies (IS 3/6/2012).
Optical mapping is another way to generate long-range information, and OpGen, which has commercialized the technology, recently introduced a human chromosome mapping service to help detect large structural variations that next-generation sequencing alone would miss (IS 2/28/2012).
Finally, nanopore sequencing technologies promise to provide sequence information for long DNA molecules, but it is not clear yet what the quality and cost will be.
HSBC Said to Withdraw Offer to Buy Dexia’s Denizbank of Turkey
By Howard Mustoe - Jan 9, 2012
HSBC Holdings Plc (HSBA), Europe’s biggest bank, withdrew its bid for Dexia SA-owned Denizbank AS (DENIZ), according to a person with knowledge of the matter.
The person asked not to be identified because the matter is private. Dexia Chief Executive Officer Pierre Mariani said in November the Paris- and Brussels-based bank would open Denizbank’s “data rooms” as part of the sales process. Last month, OAO Sberbank, Russia’s biggest bank, scrapped its plan to buy Denizbank of Turkey because of “uncertain market conditions.”
A spokesman for HSBC declined to comment and a phone message left with Denizbank CEO Hakan Ates wasn’t immediately returned.
HSBC in October was said to be interested in Denizbank, the first lender to founder with the European debt crisis, according to people with knowledge of the situation. London-based HSBC named Turkey as an area for growth at an investor day in May, together with Mexico, Singapore and Brazil.
“There are some very high-growth markets, which we will continue to invest in,” HSBC CEO Stuart Gulliver said in May.
Sky News reported HSBC had dropped plans to buy the bank earlier today.
Westlake Chemical may withdraw Georgia Gulf offer
Tue, Feb 21 2012
Feb 21 (Reuters) - Westlake Chemical Corp threatened to withdraw its sweetened $1.9 billion offer for Georgia Gulf, more than a month after the commodity chemicals maker made a bid for its smaller peer.
Earlier this month, Westlake raised the unsolicited bid by about 17 percent to $35 per share, but Georgia Gulf said it could produce more value for investors on its own.
"We know what Georgia Gulf is worth. We have not withdrawn our proposal so far. However, at some point if we do not see a real change in approach from management, we likely will," Westlake Chief Executive Albert Chao said on a conference call with analysts.
Westlake's shares fell 1 percent to $59.67 and Georgia Gulf's 3 percent to $33.49 on Tuesday on the New York Stock Exchange.
Valeant Pharmaceuticals International, Inc. (NYSE: VRX and TSX: VRX) today announced that it has withdrawn its offer to acquire ISTA Pharmaceuticals Inc. (Nasdaq: ISTA) for $7.50 per share in cash. Valeant had previously announced that the offer would only remain open until January 31, 2012, but withdrew the offer today due to lack of progress.
"As we stated last December, we were not interested in participating in a lengthy evaluation process and we are disappointed that the ISTA team was not willing to fully explore our proposal by January 31," stated J. Michael Pearson, chairman and chief executive officer. "We continue to be disciplined on our M&A strategy and we are actively working on other opportunities that we believe can create value for our shareholders. We wish the ISTA team well in their future endeavors."
Jonathan Rothberg’s Life Technologies launched his newest sequencing toy, a benchtop Ion Proton at this year’s CES. By sometime in 2012, Ion Proton can sequence a human genome for just $1000. And PC Magazine and Forbes called the Ion Proton the coolest gadget at the CES. Steve Jobs’ has played an indirect role in Jonathan Rothberg’s success and his coolest gadget.
In an interview regarding his alma matter Carengie Mellon University, the $1000 genome man Rothberg said he heard Steve Jobs speak at Carnegie Mellon during his senior year after the launch of the Macintosh. Steve Jobs shared the reason for his success to the student audience. And the secret to his success was a “Just Do It” attitude. This was years before Nike coined the phrase.
Life Technologies has received two orders in India. Public sector organization and Genotypic Technologies, India’s premium genomics service provider have placed orders with Life Technologies. Says, Dr Raja Mugasimangalam, CEO of Genotypic Technologies, “The simplicity of the technology and higher throughputs without upgrades as well as Life Technologies’ strong presence in India gives us the confidence to adopt this technology.”