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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
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Comparison of single cell sequencing data between two whole genome amplification methods on two sequencing platforms
DaYang Chen1,2, HeFu Zhen3,2, Yong Qiu2
1BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083, China.
Scientific Reports
|March 23, 2018
Summary
Comparing whole genome amplification kits for single-cell low-coverage whole genome sequencing (SLWGS) revealed platform-dependent performance. PicoPLEX offered higher reproducibility on HiSeq2000, while WGA4 excelled in uniformity on Ion Proton for copy number variation detection.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Single-cell low-coverage whole genome sequencing (SLWGS) is crucial for accurate copy number variation (CNV) detection.
- Whole genome amplification (WGA) methods and sequencing platforms significantly impact SLWGS performance.
- Optimizing experimental conditions is key for reliable CNV analysis in single or multiple cells.
Purpose of the Study:
- To compare the performance of two WGA kits (PicoPLEX and GenomePlex Single Cell WGA Kit/WGA4) for SLWGS.
- To evaluate GC-bias, reproducibility, uniformity, and CNV detection accuracy across different WGA kits and sequencing platforms (HiSeq2000 and Ion Proton).
- To provide guidance for researchers selecting optimal experimental conditions for SLWGS applications.
Main Methods:
- Comparative analysis of single-cell and multiple-cell sequencing data.
- Utilized HiSeq2000 and Ion Proton sequencing platforms.
- Employed PicoPLEX and GenomePlex Single Cell WGA (WGA4) kits for whole genome amplification.
- Evaluated metrics including GC-bias, reproducibility, uniformity, and copy number variation detection sensitivity and specificity.
Main Results:
- On the HiSeq2000, PicoPLEX WGA Kit showed higher reproducibility and lower error rates but increased GC-bias compared to the WGA4 kit.
- On the Ion Proton, the WGA4 kit demonstrated superior uniformity and reduced GC-bias, albeit with lower reproducibility than PicoPLEX.
- CNV detection performance (sensitivity and specificity) varied between WGA kits and platforms, influenced by cell number.
Conclusions:
- The choice of WGA kit and sequencing platform critically affects SLWGS outcomes for CNV detection.
- PicoPLEX is favored for reproducibility on HiSeq2000, while WGA4 offers better uniformity on Ion Proton.
- Researchers should carefully consider these factors to optimize experimental design for specific SLWGS applications.
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