COPSAC COPSAC COPSAC COPSAC
  • About COPSAC
    • Organization Diagram
    • Board of Directors
    • Research team
    • Scientific visitors
    • Hall of Fame
    • Expatriates
    • Research Students
    • Location
    • Funding
    • Press photos and logoes
    • Personal privacy policy
    • Open positions
  • COPSAC cohorts
    • COPSAC2000 cohort
    • COPSAC2010 cohort
    • COPSACSEVERE cohort
    • Available data
      • COPSAC2000 Clinic
      • COPSAC2000 Exposures
      • COPSAC2000 Omics
      • COPSAC2000 Biobank
      • COPSAC2010 Clinic
      • COPSAC2010 Exposures
      • COPSAC2010 Omics
      • COPSAC2010 Biobank
  • Dissemination
    • Publications
    • Theses
    • Research Awards and Honors
    • Literature for parents
  • Research Projects
    • COPSYCH
    • EAGLE Consortium
    • EarlyVir
  • Strategy
    • Author guidelines
  • Methods
  • ‌

Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source.

    Home Publications Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source.
    NextPrevious

    Robustness of genome-wide scanning using archived dried blood spot samples as a DNA source.

    By Dansk Børne Astma Center | Publications | Comments are Closed | 4 July, 2011 |

    BMC Genet. 2011 Jul 4

    Hollegaard MV1, Grove J, Grauholm J, Kreiner-Møller E, Bønnelykke K, Nørgaard M, Benfield TL, Nørgaard-Pedersen B, Mortensen PB, Mors O, Sørensen HT, Harboe ZB, Børglum AD, Demontis D, Ørntoft TF, Bisgaard H, Hougaard DM.

    Abstract
    BACKGROUND:
    The search to identify disease-susceptible genes requires access to biological material from numerous well-characterized subjects. Archived residual dried blood spot (DBS) samples, also known as Guthrie cards, from national newborn screening programs may provide a DNA source for entire populations. Combined with clinical information from medical registries, DBS samples could provide a rich source for productive research. However, the amounts of DNA which can be extracted from these precious samples are minute and may be prohibitive for numerous genotypings. Previously, we demonstrated that DBS DNA can be whole-genome amplified and used for reliable genetic analysis on different platforms, including genome-wide scanning arrays. However, it remains unclear whether this approach is workable on a large sample scale. We examined the robustness of using DBS samples for whole-genome amplification following genome-wide scanning, using arrays from Illumina and Affymetrix.

    RESULTS:
    This study is based on 4,641 DBS samples from the Danish Newborn Screening Biobank, extracted for three separate genome-wide association studies. The amount of amplified DNA was significantly (P < 0.05) affected by the year of storage and storage conditions. Nine (0.2%) DBS samples failed whole-genome amplification. A total of 4,586 (98.8%) samples met our criterion of success of a genetic call-rate above 97%. The three studies used different arrays, with mean genotyping call-rates of 99.385% (Illumina Infinium Human610-Quad), 99.722% (Illumina Infinium HD HumanOmni1-Quad), and 99.206% (Affymetrix Axiom Genome-Wide CEU). We observed a concordance rate of 99.997% in the 38 methodological replications, and 99.999% in the 27 technical replications. Handling variables such as time of storage, storage conditions and type of filter paper were shown too significantly (P < 0.05) affect the genotype call-rates in some of the arrays, although the effect was minimal.

    CONCLUSION:
    Our study indicates that archived DBS samples from the Danish Newborn Screening Biobank represent a reliable resource of DNA for whole-genome amplification and subsequent genome-wide association studies. With call-rates equivalent to high quality DNA samples, our results point to new opportunities for using the neonatal biobanks available worldwide in the hunt for genetic components of disease.

    PMID: 21726430

    No tags.
    NextPrevious

    CONTACT

    COPSAC
    Copenhagen Prospective Studies on Asthma in Childhood
    Copenhagen University Hospital, Herlev-Gentofte
    phone +45 3867 7360
    contact@copsac.com
    COPSAC • Copenhagen University Hospital, Herlev-Gentofte • Denmark © 2023
    • About COPSAC
      • Organization Diagram
      • Board of Directors
      • Research team
      • Scientific visitors
      • Hall of Fame
      • Expatriates
      • Research Students
      • Location
      • Funding
      • Press photos and logoes
      • Personal privacy policy
      • Open positions
    • COPSAC cohorts
      • COPSAC2000 cohort
      • COPSAC2010 cohort
      • COPSACSEVERE cohort
      • Available data
        • COPSAC2000 Clinic
        • COPSAC2000 Exposures
        • COPSAC2000 Omics
        • COPSAC2000 Biobank
        • COPSAC2010 Clinic
        • COPSAC2010 Exposures
        • COPSAC2010 Omics
        • COPSAC2010 Biobank
    • Dissemination
      • Publications
      • Theses
      • Research Awards and Honors
      • Literature for parents
    • Research Projects
      • COPSYCH
      • EAGLE Consortium
      • EarlyVir
    • Strategy
      • Author guidelines
    • Methods
    • ‌
    COPSAC