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from GenomeWeb

Illumina Battles BGI Over Purchase of Complete Genomics

Illumina confirmed that it made a competing unsolicited bid for Complete Genomics at about 5 percent above BGI-Shenzhen’s offer for the Mountain View, Calif.-based next-generation sequencing services firm.

In a document filed with the US Securities and Exchange Commission late Friday, Illumina confirmed it was the company identified as “Party H” by Complete Genomics that made an offer of $3.30 per share to acquire it.

Complete Genomics disclosed the bid earlier this week in an SEC document, adding that it declined the offer after determining that it would likely be turned down by regulators. In another SEC document filed on Friday, Complete Genomics further said that its board determined BGI’s offer to be pro-competitive compared to Party H’s because among other things BGI’s offer “will preserve the company’s innovative technology in the market place.”

(read more…)

Helicos BioSciences Files for Chapter 11 Bankruptcy Protection

Helicos BioSciences filed for Chapter 11 bankruptcy protection on Thursday.

The Cambridge, Mass.-based single-molecule sequencing firm filed its petition in US Bankruptcy Court for the District of Massachusetts after years of struggling financially and trying to keep pace in the fast-moving next-generation sequencing space.

Under Chapter 11 bankruptcy, Helicos will be afforded the opportunity to reorganize its operations, and the company said that it continues to operate as a debtor in possession.

In a document filed with the US Securities and Exchange Commission today, Helicos said it filed for Chapter 11 protection after its board “determined that continued operation of the company outside of bankruptcy protection is not possible due to its lack of cash resources and no available funding operations.”

(read more…)

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from Genetic Engineering News- Third-Generation Sequencing Debuts
by Vicki Glaser

Helicos BioSciences

In Helicos’ tSMS technology, labeled nucleotides are mixed with nucleic-acid templates immobilized on a flow cell. Detection of the fluorescent signals emitted as a result of each base addition is performed in the HeliScope™ Genetic Analysis System. The Helicos system can sequence 105–180 megabases/hour with average read lengths of 33–36 bases from templates ranging in length from 25 to 5,000 bases.

It will enable a range of applications including chromatin profiling by direct sequencing of immunoprecipitated DNA, direct RNA sequencing, small RNA quantitation, digital gene expression, copy number variation assessment, and epigenetic analysis.

For direct RNA sequencing, the system can produce 300–400 million aligned reads/run with an average read length of 34 nucleotides (range 25–55) and a <5% per nucleotide error rate. Dr. Milos presented qualitative and quantitative data from RNA studies using tSMS to map the 3´ ends of RNA transcripts from yeast and human liver cells, producing a high-resolution map of 3´ polyadenylation sites. Another project under way is using direct RNA sequencing to study a pool of micro-RNAs and generate miRNA count distribution. Early results suggest that the technique yields greater quantitative accuracy than conventional cDNA-based methods.

Pacific BioSciences

In Pacific BioSciences SMRT™ sequencing technology, sequencing takes place on SMRT cells, each of which contains thousands of zero-mode waveguides (ZMWs). Each ZMW represents a hole tens of nanometers in diameter in a metal film that has been deposited on a silicon dioxide substrate.

The PacBio system generates both DNA sequence and epigenomic information directly from the real-time sequencing of genomic DNA. Single-molecule sensitivity enables faster results and longer read lengths.

Within about two years, the company plans to offer an application that will enable direct RNA sequencing in real time on the SMRT system without the need to convert RNA to cDNA. This application will provide insights into the epigenetics of RNA. An example was presented at the AGBT conference in which RNA sequencing using SMRT technology could distinguish pseudo-uridine from its native analog.

(read the full article…)

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Which sequencing platform/technology is best suited for RNA-Seq applications?

Platform                                  Votes

Roche/454 – GS FLX                        4
Illumina – Genome Analyzer            12
Illumina – HiSeq                             16
Applied Biosystems – SOLiD            6
Helicos – HeliScope                         2
Pacific Biosciences                          2

Total Votes                                   42

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From GenomeWeb

Illumina’s Q3 Revenues Jump 50 Percent on Strength of HiSeq
Illumina reported after the close of the market Tuesday that its third-quarter revenues jumped 50 percent, easily beating analysts’ consensus estimate.

Life Technologies’ Q3 Revenues Rise 8 Percent on Record SOLiD 4 Sales
The company’s CE and next-generation sequencing business saw strong results, while its PCR business suffered from difficult year-ago comparison figures, it said.

Roche’s Sequencing Business Grows 12 Percent YTD as Applied Science Sales Shrink in Q3
Roche said it has seen “robust uptake” in the European Union and Asia Pacific for the 454 GS Junior sequencer, a benchtop sequencer launched in May that is geared at small laboratories.

Helicos BioSciences Cuts 14 More Positions in Q3
The firm also cut 40 jobs in May amid its plans to restructure and focus on the molecular diagnostics market. Part of its restructuring includes the departure of J. William Efcavitch as chief technology officer.

The firm will cut another 14 positions, on top of the previously announced 40 jobs, as it aims to reduce its operating costs. Additionally, Lapidus steps down as Chairman.

Pacific Biosciences Files for IPO in Q3
The firm has raised around $370 million since its inception, and announced plans to go public in an offering that could potentially bring in $200 million.

The firm went on to sell 12.5 million shares at $16 per share, the mid-point of its estimated offering range, at the initial public offering in October.

Helicos BioSciences Corporation has now named all three major competitors in a lawsuit claiming willfull infringement on their patents which broadly cover sequencing-by-synthesis technology.  They claim that Pacific Biosciences, Life Technologies, and Illumina have all incorporated Helicos’ patented technology “at the heart of” their respective sequencing systems and products.

The patents cover sequencing-by-synthesis methods using labeled nucleotides. The nucleotides are labeled with detectable markers, such as fluorescent markers, that enable determination of each nucleotide incorporated into the DNA strand being extended by the polymerase. The patents describe processes that involve, for example, identifying each new nucleotide by observing its detectable label and neutralizing or removing the label before addition of the next nucleotide. The specific claims apply to both “real time” and “step and repeat” approaches.

“After a careful examination of the sequencing products and technologies offered by Illumina and Life Technologies, we are convinced that they, in addition to Pacific Biosciences, infringe the Helicos patents, which are in full force and effect up through 2028,” stated Dr. Ivan Trifunovich, President and CEO of Helicos.

Recently, Helicos had stated a strategic initiative to vigorously protect their next-generation sequencing IP.

(Read the press release… )

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• SEQanswers – RNA Sequencing

  • Identifying small RNA sequence within whole genome sequence May 21, 2013
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  • novoalign mapping May 15, 2013
    Hi, I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads I am new to novoalign(went through the... […]
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  • Design of expt across multiple lanes May 15, 2013
    Hi, I am performing an RNA-seq experiment to look at differential expression. The design is as follows: 2 populations x 3 biological... […]
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• Biostar – RNA-Seq

  • What are the best practices for SNP identification in RNA seq transcriptome data
    I have 20 RICE RNA seq tranascriptome data hiseq 2000 platform paired end reads. I aligned fasta reads with BWA and remove PCR duplicates with PICARD. Later I call SNP with samtools using various parameters. I would like to clarify what parameters should I used while alinging to reference rice genome for looking SNP location 100 bp upstream and 250 bp downst […]
  • How do TopHat options -g , --supress-hits, and Bowtie options interplay?
    Hi, I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now? I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments. Now, the description sounds mo […]
  • What happened to -k in TopHat for multiple-mapping reads?
    Selecting -g n in tophat does not discard reads mapping more than n, but instead only reports n alignments for those out all all their TOP scoring alignments. I think there used to be an option -k that would allow one to discard reads that topped x alignments -- whatever happened to that? I only see -g in the tophat 2 manual, no reporting options like before […]
  • Does tophat use the library-type information for mapping, or just for the XS flag?
    When I specify library-type to TopHat, i.e., first-strand, second-strand, unstranded, TopHat appends a value + or - to the XS:A tag, which is useful for subsequent analyses, such as annotation. However, does this information influence the "mappability" of reads, or is this unaffected? My guess is that the information will be considered for mapping […]
  • Purpose of Y-shaped adapters in Illumina Sequencing?
    Hi all, Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. What are the advantages of this? My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that: -Upon primer a […]
  • Cell Type composition in a tissue based on gene marker expression
    I am not sure if the following would even make sense.... Tissues are composed of composite cell types, and often there are studies such as microarray/NGS where we perform a collective sampling of cells from these tissues. Information about the composition (say percentage of cell type) is not taken into consideration. In some case (such as brain/cancer), ther […]