Table 2.
Comparison of Commercial Amplicon-Based and Hybrid Capture-Based Target Enrichment Methods. A snapshot summary of some published studies comparing commercial target enrichment products, their vendors, enrichment approaches, workflow, samples tested, and their overall performance is provided.
| Commercial Enrichment Methods Compared |
Enrichment Approach |
Genome Targets and Sample Types | Findings | Reference |
|---|---|---|---|---|
| Fluidigm Access array (Fluidigm) | Microfluidic PCR | DNA from 8 human bladder cancer cell lines (both fresh and formalin-fixed samples). 24 mutations in 6 genes (BRAF, FGFR3, KRAS, NRAS,
PIK3CA, and TP53) Fresh and formalin-fixed and paraffin-embedded DNA samples. |
Complete concordance of results for fresh DNA SureSeq panel performed the best followed by Fluidigm and IonAmpliseq |
[46] |
| SureSeq panel | ||||
| (Oxfore Gene Technology) | Hybrid-capture | |||
| Ion AmpliSeq | ||||
| (ThermoFisher Scientific) | PCR amplicon-based | |||
| SureSelect (Agilent Technologies) | Hybrid capture | Single nucleotide variants (SNVs) and copy number variations (CNVs) in a panel of 257 cancer-related genes. Cancer cell lines and tumor samples (breast, melanoma, lung, and colon cancer) |
Comparable cost of workflow across the methods High level of concordance observed for SNV and CNV detection across methods SureSelect and SeqCap showed better library complexity and overall sequencing uniformity |
[47] |
| Haloplex (Agilent Technologies) | Hybrid capture | |||
| Nextera (Illumina Inc) | Hybrid capture | |||
| SeqCap EZ (Roche Nimblegen) | Hybrid capture | |||
| SureSelect (Agilent Technologies) | Hybrid capture | Whole-Exome Sequencing | Hybrid capture methods provided better library complexity, uniformity of coverage, analytical sensitivity, and specificity | [48] |
| Haloplex (Agilent Technologies) | Hybrid capture | |||
| SeqCap EZ (Roche Nimblegen) | Hybrid capture | |||
| Ion AmpliSeq | ||||
| (ThermoFisher Scientific) | PCR amplicon-based | |||
| TruSight (Illumina Inc) | Hybrid capture |
BRCA1 and BRCA2 sequencing FFPE tumor samples |
TruSight performed better with regards to uniformity of sequencing, analytical specificity, and detection of mutations and CNVs | [49] |
| TruSeq custom amplicon | ||||
| (Illumina Inc) | PCR amplicon-based | |||
| Avenio CtDNA panel (Roche) | Hybrid capture | Screening circulating cell-free tumor DNA (ctDNA) for cancer-related markers | QiaSeq had shorter workflow (1 day) in comparison to Avenio (3 days) Avenio fared better in enriching targets of interest (99% vs. 85% for QIASeq). Analytical sensitivity for Avenio (92.3%) was better than QiaSeq (86.4%). Detection sensitivity for low-level variants (≤ 5%) was better for Avenio (75%) vs. QiaSeq (53.8%) |
[51] |
| QIAseq Human Comprehensive Cancer | ||||
| panel (Qiagen) | PCR amplicon-based |