Table 1

Comparison of standard versus improved solution hybrid selection methods

Manual standard SHS protocol

Automated improved SHS protocol



Process step

Standard method

Drawbacks

Improved method

Advantages


Shearing of genomic DNA

Covaris S2

Single sample

Optimized Covaris E210

Multi-sample, improved yield, tight size range

Enzymatic cleanups

Individual spin columns

Low throughput, 50 to 60% recovery, manual

'With-bead' SPRI

High throughput, 80 to 90% recovery, automated

Solution hybrid selection capture

Manual, column- based

Labor intensive (6 samples/FTE/week)

Fully automated

Walkaway, high throughput (1,200 samples/4FTE/week)

Final PCR enrichment

Denature, followed by PCR

Sample loss through transfers

Direct 'off-bead' PCR

Improved final yield

In process quality control checkpoints

Agilent Bioanalyzer

Limited visibility until sequence results

Many

In process results: key predictors of sample, library and sequencing quality


FTE, full time employee; SHS, solution hybrid selection; SPRI, solid phase reversible immobilization.

Fisher et al. Genome Biology 2011 12:R1   doi:10.1186/gb-2011-12-1-r1

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