Roche Further Improves Cost Effectiveness and Application Versatility in Sequencing: New Long-Tag Paired End Reads and Multiplex Identifiers for the Genome Sequencer FLX System

454 Life Sciences, a part of Roche Applied Science, today announced the launch of new products and software for the ultra-high throughput Genome Sequencer FLX System (GS FLX). The new additions expand researchers’ ability to customize their sequencing projects to achieve highly scientifically meaningful results at very competitive price point.

The new 3K – Long Tag (3K-LT) Paired End protocol enables researchers to sequence 100 bases from each end of a 3000 base span on a single sequence read. Paired end data with long tags can significantly improve the de novo assemblies of complex genomes and can be used to identify structural variations at high resolution, including insertions, deletions, inversions, and copy number variations. The addition of 3K-LT Paired End reads to the previously available shotgun reads allows researchers to choose the type of read that delivers the most appropriate data for their application. Accurate results are achieved the first time, reducing misinterpretations and costly follow up experiments.

“454 Sequencing enabled us to efficiently identify over 1000 structural variations (SVs) in two individuals. Our study demonstrates that a large number of SVs are present in the human population and that SV plays a greater role in genetic diversity than SNPs. It will be essential to incorporate SV detection in human genome sequencing projects.” said Michael Snyder, PhD., Lewis B. Cullman Professor of Molecular, Cellular and Developmental Biology at Yale University. Snyder, an early access collaborator, used the Long-Tag Paired End reads for a study entitled "Paired-End Mapping Reveals Extensive Genomic Structural Variation in Humans," which appeared in the October 19, 2007 edition of Science.

The new Ligation Multiplex Identifier (MID) kit reduces the cost per sample, increases multiplexing, and simplifies the handling of multiple samples. Using the Ligation MIDs in the kits supplied by 454, up to 12 uniquely tagged samples can by amplified and sequenced together. Samples are tagged with a unique MID using a standard blunt-end ligation protocol. Each of the 12 Ligation MID adaptors contains a unique 10-base sequence that is recognized by the sequencing analysis software, allowing for automated sorting of MID-containing reads. When used in conjunction with the previously available gaskets (which physically divide a sequencing run into separate regions), up to 192 samples can be sequenced per run.

Enhancements to the supplied software include: automated detection of samples tagged with MIDs; improved de novo genome assembly using 3K-LT Paired End reads; improved algorithms for mutation detection, especially large insertions or deletions up to 50 bases; and a new Phred-like quality scoring system, developed in conjunction with The Broad Institute. The new quality scoring system more accurately scores read error and improves data compatibility with other 3rd party applications.

“The new products launched today represent a suite of enhancements to the current 454 Sequencing system, which give our customers expanded experimental options and a reduced cost per sample.” said Chris McLeod, President of 454 Life Sciences. “Paired End reads with long tags are critical for those researchers who want the an accurate and complete picture of the genome and for those who want to get a comprehensive view of genetic variation beyond SNPs.”