Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage

Abstract

Background: Blood specimen collection at an early study visit is often included in observational studies or clinical trials for analysis of secondary outcome biomarkers. A common protocol is to store buffy coat specimens for future DNA isolation and these may remain in frozen storage for many years. It is uncertain if the DNA remains suitable for modern genome wide association (GWA) genotyping.

Methods: We isolated DNA from 120 Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial buffy coats sampling a range of storage times up to 9 years and other factors that could influence DNA yield. We performed TaqMan SNP and GWA genotyping to test whether the DNA retained integrity for high quality genetic analysis.

Results: We tested two QIAGEN automated protocols for DNA isolation, preferring the Compromised Blood Protocol despite similar yields. We isolated DNA from all 120 specimens (yield range 1.1-312 ug per 8.5 ml ACD tube of whole blood) with only 3/120 samples yielding < 10 ug DNA. Age of participant at blood draw was negatively associated with yield (mean change -2.1 ug/year). DNA quality was very good based on gel electrophoresis QC, TaqMan genotyping of 6 SNPs (genotyping no-call rate 1.1% in 702 genotypes), and excellent quality GWA genotyping data (maximum per sample genotype missing rate 0.64%).

Conclusions: When collected as a long term clinical trial or biobank specimen for DNA, buffy coats can be stored for up to 9 years in a -80°C frozen state and still produce high yields of DNA suitable for GWA analysis and other genetic testing.

Trial registration: ClinicalTrials.gov NCT00000620.

Figures

Figure 1

Distribution of total DNA yield from 120 ACCORD buffy coat specimens. The histogram shows the number of samples within each interval of total DNA yield. The interval size is 25 ug, and the maximum and minimum yields were 1.1 ug and 312.2 ug.

Figure 2

Total DNA yield as a function of collection year from 120 ACCORD buffy coat specimens. The figure shows a Tukey boxplot of variation in DNA yield for each year of blood collection in the 120 ACCORD samples. The upper and lower edges (hinges) of the boxes are the third and first quartiles and the central line shows the median value of yield for a year. The lines radiating above and below the boxes visually show the range to the maximum and minimum yields. There are no outlier samples in any of the years with unusually large or small yields as defined by the usual robust test of more than 1.5 × interquartile range.