PubMed: Targeted next-generation sequencing by specific capture of multiple genomic l

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Targeted next-generation sequencing by specific capture of multiple genomic loci using low-volume microfluidic DNA arrays.

Anal Bioanal Chem. 2008 Oct 29;

Authors: Bau S, Schracke N, Kränzle M, Wu H, Stähler PF, Hoheisel JD, Beier M, Summerer D.

We report a flexible method for selective capture of sequence fragments from complex, eukaryotic genome libraries for next-generation sequencing based on hybridization to DNA microarrays. Using microfluidic array architecture and integrated hardware, the process is amenable to complete automation and does not introduce amplification steps into the standard library preparation workflow, thereby avoiding bias of sequence distribution and fragment lengths. We captured a discontiguous human genomic target region of 185 kb using a tiling design with 50mer probes. Analysis by high-throughput sequencing using an Illumina/Solexa 1G Genome Analyzer revealed 2150-fold enrichment with mean per base coverage between 4.6 and 107.5-fold for the individual target regions. This method represents a flexible and cost-effective approach for large-scale resequencing of complex genomes.

PMID: 18958448 [PubMed - as supplied by publisher]



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[seqer]

7% specificity? This does not sound impressive... This further highlights the problems of microarray-based enrichment methods, particularly for smaller size of non-contiguous regions.

[mrothe]

At least its a start. When you look at the first Nimblegen papers they are also not better. I think the microarray based enrichement is the way of choice for targeted resequencing.

Regards

[seqer]

Although Nimblegen papers are not great, but their metrics are better than this (e.g., ~50% specificity). Also, I don't see the reason why microarray based enrichment is the choice. Different methods have pros and cons, but to me, the solid phase capturing has fainter future.