Targeted Resequencing of Whole Genome Amplified Samples
RainDance is the first company to support the use of whole genome amplified (WGA) DNA samples for sequence enrichment. This capability will enable researchers to conduct studies with sample quantities that were previously too small for targeted resequencing.
The application has been validated using standard WGA reaction conditions for three commercially available WGA kits. The protocol for processing WGA samples is exceptionally easy to perform and works seamlessly with our Sequence Enrichment Solution and RDT 1000 system. It uses the solution’s proven hardware, consumables, and reagents.
| Sample Type | Target Bases with >20X Coverage |
Overall Concordance to HapMap |
Homozygous SNP Concordance |
Heterozygous SNP Concordance |
| No amplification | 93.8% | 98.7% | 99.1% | 97.1% |
| Qiagen Repli-G Mini Kit |
92.5% | 98.7% | 99.0% | 97.1% |
| BioHelix Corp. Rapisome pWGA Kit |
93.7% | 98.7% | 99.0% | 97.1% |
| GE GenomiPhi V2 DNA Amplification Kit |
75.2% | 98.3% | 98.7% | 96.4% |
A custom 4000 primer pair library designed to amplify 4000 exons representing a total of 1.64 Mb of target sequence was used to evaluate the performance of non-amplified vs. amplified genomic DNA.
50 ng aliquots of a Yoruba HapMap sample (NA18858) were amplified following manufacturer’s suggested protocols using three different whole genome amplification kits:
- REPLI-g Mini Kit, Qiagen
- Rapisome pWGA Kit, BioHelix Corporation
- GenomiPhi V2 DNA Amplification Kit, GE Healthcare
The amplified DNA samples were compared to unamplified DNA (2 μg) in the sequence enrichment assay to evaluate SNP concordance and allelic representation. Sequencing was performed on an Illumina GAII platform using 36 bp reads.
