Illumina DNA test panel-based genotyping of whole genome amplified-DNA extracted from hair samples: Performance and agreement with genotyping results from genomic DNA from buccal cells

Ilir Agalliu, Peter A. Schweitzer, Suzanne M. Leanza, Robert D. Burk, Thomas E. Rohan

Research output: Contribution to journalArticle

5 Scopus citations

Abstract

Background: Hair is a DNA source that can be collected easily and inexpensively from participants in epidemiological studies. However, there is concern about DNA quality and quantity. Therefore, we assessed genotyping performance of whole genome amplified (WGA)-DNA extracted from hair using the GenomePlex® method and evaluated its agreement with genotyping results of buccal cell DNA from the same individuals, using the Illumina GoldenGate platform. Methods: The Illumina DNA test panel includes 360 highly validated single nucleotide polymorphisms (SNPs) selected from the Linkage IV Panel that are distributed across the entire genome. DNA was extracted from both archived hair and buccal cell samples obtained from 44 randomly selected subjects participating in a large cohort study in Canada. Results: The genotyping success rate was 97.7% for 44 paired samples. However, WGA-DNA from hair failed more during genotyping in comparison to buccal cell DNA. Hair samples with a pre-WGA-DNA ≥1 ng/μL quantified using the PicoGreen ® assay (n=33) showed an average genotyping completion rate of 98.8% and SNP concordance of 91.2% with genotyping performance of buccal cell DNA. In contrast, samples with a pre-WGA-DNA <1 ng/μL had lower genotyping completion rate (94%) and poor SNP concordance (49%). Conclusions: Results suggest that WGA-DNA obtained from hair can produce excellent genotyping call rates and show relatively good SNP concordance with results from buccal cell DNA using high-throughput technology. DNA quantity obtained from hair samples is a crucial determinant of genotyping performance. Larger studies are needed to examine the utility of hair DNA with different genotyping platforms.

Original languageEnglish (US)
Pages (from-to)516-522
Number of pages7
JournalClinical Chemistry and Laboratory Medicine
Volume47
Issue number5
DOIs
StatePublished - May 1 2009

Keywords

  • DNA test panel
  • GoldenGate assay
  • Hair
  • SNP concordance
  • Whole genome amplification

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Biochemistry, medical

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