Wednesday, 8 August 2012

PubMed Highlight: Detection of ultra-rare mutations by next-generation sequencing.

Another smart protocol that increases mutation detection accuracy through strand-specific sequencing

Detection of ultra-rare mutations by next-generation sequencing.
Proc Natl Acad Sci U S A. 2012 Aug 1;

Authors: Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, Hiatt JB, Loeb LA

Next-generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of ∼1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when "deep sequencing" genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, we have developed a method termed Duplex Sequencing. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors result in mutations in only one strand and can thus be discounted as technical error. We determine that Duplex Sequencing has a theoretical background error rate of less than one artifactual mutation per billion nucleotides sequenced. In addition, we establish that detection of mutations present in only one of the two strands of duplex DNA can be used to identify sites of DNA damage. We apply the method to directly assess the frequency and pattern of random mutations in mitochondrial DNA from human cells.

Thursday, 2 August 2012

Illumina move aggressively in the Desktop Sequenchers battlefield

A furious commercial fight is going on in the NGS market on desktop sequenchers, with both Illumina and Life Tech constantly and rapidly updating their technologies, while pointing out at the rival pitfalls. It seems now that a new era in the NGS Desktop War has began. Besides trying to convince the customers with data reports, graphs and commentaries, Illumina is now moving forward proposing some interesting trade-in programs. Basically, they would trade your existing sequencher (PGM, or 454 GS FLX) in change for their MiSeq, giving a consistent discount (around 50,000$ as some users reported).
By now Life Technologies responded that they are evaluating the trade-in option, but they have no concrete plans in the short period. 
More details and some interesting story from users sharing their experiences with NGS platforms and the Illumina's trade-in can be found on InSequence.

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