Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage
<p>Abstract</p> <p>Background</p> <p>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...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2011-06-01
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| Series: | Journal of Translational Medicine |
| Online Access: | http://www.translational-medicine.com/content/9/1/91 |
| _version_ | 1811260895596118016 |
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| author | Bowden Donald W Light Laney S Artale Jamie Chmielewski Jessica Farber Emily A Mychaleckyj Josyf C Hou Xuanlin Marcovina Santica M |
| author_facet | Bowden Donald W Light Laney S Artale Jamie Chmielewski Jessica Farber Emily A Mychaleckyj Josyf C Hou Xuanlin Marcovina Santica M |
| author_sort | Bowden Donald W |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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%).</p> <p>Conclusions</p> <p>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 -80degC frozen state and still produce high yields of DNA suitable for GWA analysis and other genetic testing.</p> <p>Trial Registration</p> <p>The Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial is registered with ClinicalTrials.gov, number <a href="http://www.clinicaltrials.gov/ct2/show/NCT00000620">NCT00000620</a>.</p> |
| first_indexed | 2024-04-12T18:54:30Z |
| format | Article |
| id | doaj.art-165f9ab66e894549b27c48691cbd702f |
| institution | Directory Open Access Journal |
| issn | 1479-5876 |
| language | English |
| last_indexed | 2024-04-12T18:54:30Z |
| publishDate | 2011-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Translational Medicine |
| spelling | doaj.art-165f9ab66e894549b27c48691cbd702f2022-12-22T03:20:22ZengBMCJournal of Translational Medicine1479-58762011-06-01919110.1186/1479-5876-9-91Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storageBowden Donald WLight Laney SArtale JamieChmielewski JessicaFarber Emily AMychaleckyj Josyf CHou XuanlinMarcovina Santica M<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Methods</p> <p>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.</p> <p>Results</p> <p>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%).</p> <p>Conclusions</p> <p>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 -80degC frozen state and still produce high yields of DNA suitable for GWA analysis and other genetic testing.</p> <p>Trial Registration</p> <p>The Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial is registered with ClinicalTrials.gov, number <a href="http://www.clinicaltrials.gov/ct2/show/NCT00000620">NCT00000620</a>.</p>http://www.translational-medicine.com/content/9/1/91 |
| spellingShingle | Bowden Donald W Light Laney S Artale Jamie Chmielewski Jessica Farber Emily A Mychaleckyj Josyf C Hou Xuanlin Marcovina Santica M Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage Journal of Translational Medicine |
| title | Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage |
| title_full | Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage |
| title_fullStr | Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage |
| title_full_unstemmed | Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage |
| title_short | Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage |
| title_sort | buffy coat specimens remain viable as a dna source for highly multiplexed genome wide genetic tests after long term storage |
| url | http://www.translational-medicine.com/content/9/1/91 |
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