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Ultralow Amounts of DNA from Long-term Archived Serum Samples Produce Quality Genotypes

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December 12, 2019

Trine B. Rounge, Marianne Lauritzen, Sten Even Erlandsen, Hilde Langseth, Oddgeir Lingaas Holmen & Randi E. Gislefoss

European Journal of Human Genetics (2019)

Sample characteristics and genotyping results from Janus Serum Bank samples analyzed with Axiom arrays (n = 64) and HumanCoreExome arrays (n = 24, with slightly increased yields) across six groups with different preanalytical treatment
Sample characteristics and genotyping results from Janus Serum Bank samples analyzed with Axiom arrays (n = 64) and HumanCoreExome arrays (n = 24, with slightly increased yields) across six groups with different preanalytical treatment

Abstract

While genotyping studies are scavenging for suitable samples to analyze, large serum collections are currently left unused as they are assumed to provide insufficient amounts of DNA for array-based genotyping. Long-term stored serum is considered to be difficult to genotype since preanalytical treatments and storage effects on DNA yields are not well understood. Successful genotyping of such samples has the potential to activate large biobanks for future genome-wide association studies (GWAS). We aimed to evaluate genotyping of ultralow amounts of DNA from samples stored up to 45 years in the Janus Serum Bank with two commercially available platforms. 64 samples, with various preanalytical treatments, were genotyped on the Axiom Array from Thermo Fisher Scientific and a subset of 24 samples with slightly higher yield were genotyped on the HumanCoreExome array from Illumina. Our results showed that about 80% of the serum samples produced call rates with the Axiom arrays that would be satisfactory in GWAS. The mean DNA yield was 5.8 ng as measured with PicoGreen, 3–6% of recommended yield. The failed samples had on average lower input amounts of DNA. All serum samples genotyped on the HumanCoreExome with a standard and FFPE protocol produced GWAS satisfactory call rates, with mean 97.57% and 98.35% call rates, respectively. The mean yield was 10.65 ng, 6% of the recommendations. Successful array-based genotyping of ultralow DNA yields from serum samples stored up to 45 years is possible. These results demonstrate the potential to activate large serum biobank collections for future studies.

More info at: https://www.nature.com/articles/s41431-019-0543-x

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