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.
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>or=1 ng/microL 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/microL 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.
Agalliu
Ilir
I
Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA. iagalliu@aecom.yu.edu
Schweitzer
Peter A
PA
Leanza
Suzanne M
SM
Burk
Robert D
RD
Rohan
Thomas E
TE
D015331:Cohort Studies; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D005260:Female; D015894:Genome, Human; D005838:Genotype; D006197:Hair / Q000737:chemistry*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009061:Mouth Mucosa / Q000166:cytology; D021141:Nucleic Acid Amplification Techniques / Q000379:methods*; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D011446:Prospective Studies; D012680:Sensitivity and Specificity; D013048:Specimen Handling
D004247:DNA