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The key innovation of our method is multiplex capture and sequence that allows the simultaneous survey of both mutant, parental, and background strains in a single experiment.
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The cLPP multiplex capture of thousands of exons in a single tube can be performed within approximately 4 hours.
In the analysis of data from the multiplex capture of common coding SNPs using padlock probes (see below), we restricted the analysis to SNPs with 100 reads or more.
In order to build a cost-effective but comprehensive diagnostic approach, we performed multiplex capture of the regions of interest using patients' DNA followed by sequencing with an Illumina Genome Analyzer.
Using this approach we were able to multiplex DNA-target capture and SOLiD sequencing while retaining individual sequence information.
A molecular-barcoding strategy was used to multiplex DNA target capture and sequencing, while retaining individual sequence information.
We evaluated 289 patients who self-identified as African American with primary invasive breast cancer and with personal or family cancer history or tumor characteristics associated with high genetic risk for all classes of germline mutations in known breast cancer susceptibility genes using a validated targeted capture and multiplex sequencing approach.
Genomic DNA was used to simultaneously amplify several gene loci using multiplex PCR, in order to capture and analyze 15 mutational hot spots enriched for, but not exclusive to, targets of mutations thought to arise early in leukemogenesis (Table 1).
Furthermore, for the same cost as a single sample, we pursued a multiplex approach that let us both capture and then sequence multiple samples simultaneously.
These findings were enabled by employing the amplicon-rescued multiplex PCR technology, which allows the capture and amplification of Ig transcripts from a given B cell population in an inclusive and quantitative fashion.
To assess how these methods performed when used in conjunction with the ABI SOLID3+, we investigated three enrichment techniques: Nimblegen oligonucleotide hybridization array-based capture; Agilent SureSelect oligonucleotide hybridization solution-based capture; and Raindance Technologies' multiplexed PCR-based approach.
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