Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing
| Autor: | Rivka Adar, Yael Fried, Elena Ainbinder, Ofir Raz, Lilach Milo, Ehud Shapiro, Tamir Biezuner, Shiran Amir |
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| Rok vydání: | 2021 |
| Předmět: |
Science
Cell Genomics Computational biology Commercial kit Biology Cellular level Polymerase Chain Reaction Sensitivity and Specificity Genome Article 03 medical and health sciences 0302 clinical medicine medicine Humans Cells Cultured 030304 developmental biology Genetics Whole Genome Amplification 0303 health sciences 030219 obstetrics & reproductive medicine Multidisciplinary Whole Genome Sequencing Targeted resequencing Computational biology and bioinformatics Large cohort medicine.anatomical_structure Next-generation sequencing Medicine Microsatellite Single-Cell Analysis PCR-based techniques 030217 neurology & neurosurgery |
| Zdroj: | Scientific Reports bioRxiv Scientific Reports, Vol 11, Iss 1, Pp 1-8 (2021) |
| ISSN: | 2045-2322 |
| DOI: | 10.1038/s41598-021-96045-9 |
| Popis: | Advances in biochemical technologies have led to a boost in the field of single cell genomics. Observation of the genome at a single cell resolution is currently achieved by pre-amplification using whole genome amplification (WGA) techniques that differ by their biochemical aspects and as a result by biased amplification of the original molecule. Several comparisons between commercially available single cell dedicated WGA kits (scWGA) were performed, however, these comparisons are costly, were only performed on selected scWGA kit and more notably, are limited by the number of analyzed cells, making them limited for reproducibility analysis. We benchmarked an economical assay to compare all commercially available scWGA kits that is based on targeted sequencing of thousands of genomic regions, including highly mutable genomic regions (microsatellites), from a large cohort of human single cells (125 cells in total). Using this approach, we could analyze the genome coverage, the reproducibility of genome coverage and the error rate of each kit. Our experimental design provides an affordable and reliable comparative assay that simulates a real single cell experiment. Results demonstrate the needfor a dedicated kit selection depending on the desired single cell assay. |
| Databáze: | OpenAIRE |
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