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Table 1 Locus-specific biases on the genomic coverage and error rate of the studied WGA systems using high gDNA input (10 ng)

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%
ChargeSwitch REPLI-g MDA 10 ng 93.8% 98.9% 99.7% 00.6% 01.5% 06.5%
ChargeSwitch GenomiPhi MDA 10 ng 89.7% 97.7% 99.5% 00.9% 02.7% 10.7%
ChargeSwitch Single Cell WGA Kit QPLS 10 ng 55.6% 68.6% 79.0% 25.9% 34.6% 45.7%
ChargeSwitch LMA LMA 10 ng 13.0% 50.2% 94.2% 37.4% 79.0% 96.2%
ChargeSwitch ExpressLink LMA 10 ng 23.6% 59.4% 87.0% 43.3% 71.1% 89.9%
ChargeSwitch LigaFast LMA 10 ng 19.9% 57.3% 86.3% 44.1% 72.4% 91.8%
ChargeSwitch Ovation SPIA 10 ng 66.3% 86.9% 96.9% 06.1% 18.9% 37.3%
Illustra mini Spin Kit Ovation SPIA 10 ng 91.8% 96.7% 98.4% 01.6% 03.3% 08.1%
  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.