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Table 2 Locus-specific biases on the genomic coverage and error rate of the studied WGA systems using low gDNA input (15 cells)

From: Impact of whole-genome amplification on the reliability of pre-transfer cattle embryo breeding value estimates

  Whole-genome amplification   Genomic coveragea(%) Error rateb(%)
gDNA extraction Kit/method Technology type gDNA input All replicates At least 2/3 replicates Any replicate All replicates At least 2/3 replicates Any replicate
ChargeSwitch Non-amplified (Reference) Non-amplified (Reference) 1.5 μg 97.7% 99.2% 99.6% 00.0% 00.0% 02.0%
Built-in REPLI-g MDA 15 cells 20.9% 73.1% 95.2% 18.4% 42.7% 86.2%
Built-in GenomiPhi MDA 15 cells 76.2% 90.7% 98.0% 03.9% 13.6% 26.9%
Built-in Single Cell WGA Kit QPLS 15 cells 56.7% 72.0% 83.5% 21.1% 31.3% 44.6%
ChargeSwitch LMA LMA 15 cells 07.6% 29.0% 63.8% 62.1% 87.0% 97.8%
ChargeSwitch ExpressLink LMA 15 cells 13.7% 43.3% 77.1% 53.0% 80.5% 94.6%
ChargeSwitch LigaFast LMA 15 cells 09.1% 32.5% 66.8% 58.0% 84.9% 96.9%
Quick gDNA MicroPrep Ovation SPIA 15 cells 11.7% 39.3% 75.1% 44.9% 77.0% 94.8%
  1. a: Genomic coverage or call rates is the proportion of target loci giving positive signals over background over the overall number of loci accounted for on Illumina’s Bovine 50 K SNP Chip. b: Error rate is the proportion of erroneous genotype calls relatively to the non-amplified reference; All replicates (%): % of loci which consistently covered in all performed replicates; At least 2/3 replicates (%): % of loci which consistently covered in At least 2/3 performed replicates; Any replicate (%): % of loci which consistently covered in any performed replicate; LMA: Ligation-Mediated Amplification; MDA: Multiple Displacement Amplification; QPLS: Quasi-random Primed Library Synthesis followed by PCR amplification; SPIA: Single Primer Isothermal Amplification.