Comparison of commercially available target enrichment methods for next-generation sequencing

Area of Science:

• Genomics and Bioinformatics
• Molecular Biology and Genetics

Background:

• Targeted genomic enrichment is crucial for efficient next-generation sequencing (NGS) by focusing on specific genomic regions.
• Custom-targeted genomic enrichment methods from Agilent Technologies and Roche NimbleGen were evaluated for their performance in DNA NGS.

Purpose of the Study:

• To compare the effectiveness of custom-targeted genomic enrichment methods from Agilent and NimbleGen for DNA NGS.
• To assess the sensitivity, specificity, and coverage of both companies' assays in capturing identical genomic locations.

Main Methods:

• Two leading companies, Agilent and NimbleGen, designed and performed custom-targeted genomic enrichment assays on the same genomic sample (3.5 Mb target region).
• Captured material was sequenced using Genome Analyzer IIx systems in two independent laboratories.
• Sequencing data were analyzed for coverage, sensitivity, specificity, and single-nucleotide polymorphism (SNP) detection.

Main Results:

• Enrichment success was highly dependent on capture probe design, with Agilent samples showing higher coverage variability.
• NimbleGen samples yielded 2546 SNPs, while Agilent samples yielded 2071 SNPs within the targeted regions.
• Both companies identified unique SNPs, with a comparable number of SNPs found within the overlapping target regions.

Conclusions:

• Roche NimbleGen's custom-targeted genomic enrichment method demonstrated superior performance in terms of SNP discovery and coverage consistency compared to Agilent's.
• The design of capture probes significantly impacts the success of targeted sequencing projects.
• Both platforms showed potential for variant discovery, but NimbleGen provided a more comprehensive SNP detection.