Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays

BMC Genomics. 2018 Mar 6;19(1):182. doi: 10.1186/s12864-018-4572-6.


Background: The recommended genomic DNA input requirements for whole genome single nucleotide polymorphism microarrays can limit the scope of molecular epidemiological studies. We performed a large-scale evaluation of whole genome amplified DNA as input into high-density, whole-genome Illumina® Infinium® SNP microarray.

Results: Overall, 6622 DNA samples from 5970 individuals were obtained from three distinct biospecimen sources and genotyped using gDNA and/or wgaDNA inputs. When genotypes from the same individual were compared with standard, native gDNA input amount, we observed 99.94% mean concordance with wgaDNA input.

Conclusions: Our results demonstrate that carefully conducted studies with wgaDNA inputs can yield high-quality genotyping results. These findings should enable investigators to consider expansion of ongoing studies using high-density SNP microarrays, currently challenged by small amounts of available DNA.

Keywords: CCSS clinical trial; Genome-wide association study; High-density microarray; Whole genome amplification.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural

MeSH terms

  • DNA / analysis
  • DNA / blood
  • DNA / genetics*
  • Genome, Human*
  • Genomics
  • Genotype
  • Humans
  • Mouth Mucosa / metabolism*
  • Neoplasms / blood
  • Neoplasms / genetics*
  • Nucleic Acid Amplification Techniques
  • Oligonucleotide Array Sequence Analysis / methods
  • Polymorphism, Single Nucleotide*
  • Saliva / metabolism*


  • DNA