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Genome-wide scans using archived neonatal dried blood spot samples.

Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM - BMC Genomics (2009)

Bottom Line: Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects.The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary.This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip.

View Article: PubMed Central - HTML - PubMed

Affiliation: Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark. mvh@ssi.dk

ABSTRACT

Background: Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference.

Results: Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% - 99.73% (mean 99.56%, N = 16), and conflicts with reference DNA in only three per 10,000 genotype calls.

Conclusion: Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.

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Related in: MedlinePlus

Plot of the normalized values measure for the A allele and B allele. The same 16 samples were amplified using the GPlex4 and the REPLI-g WGA kits. The "Illumina cluster" plot shows how the GPlex4 (blue dots) and the REPLI-g (green dots) wgaDNA genotypes compare to the Illumina cluster file. The "GPlex4 cluster" plot shows how a custom-made cluster file based on GPlex4 samples (blue dots) improves both fit and call-rate of the loci. The "REPLI-g cluster" plot shows how a custom-made cluster file based on REPLI-g samples (green dots) improves both fit and call-rate of the loci.
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Figure 1: Plot of the normalized values measure for the A allele and B allele. The same 16 samples were amplified using the GPlex4 and the REPLI-g WGA kits. The "Illumina cluster" plot shows how the GPlex4 (blue dots) and the REPLI-g (green dots) wgaDNA genotypes compare to the Illumina cluster file. The "GPlex4 cluster" plot shows how a custom-made cluster file based on GPlex4 samples (blue dots) improves both fit and call-rate of the loci. The "REPLI-g cluster" plot shows how a custom-made cluster file based on REPLI-g samples (green dots) improves both fit and call-rate of the loci.

Mentions: Based on the results displayed in Additional file 1, the combinations of DNA extraction by the ENA kit and WGA by the REPLI-g and GPlex4 kits were selected for further evaluation. For this, 16 new subjects were employed. After DNA-extraction, WGA and subsequent genome-wide scans (GWS), the results were analysed using both a standard Human610-Quadv1B Cluster, provided by Illumina, and WGA kit specific tailored cluster files. The rationale for the tailored cluster files is demonstrated in Figure 1. Generally, the wgaDNA samples cluster nicely, but not always in the area defined by the Illumina Human610-Quadv1B cluster file, which is based on gDNA samples. By creating tailored WGA-specific cluster files and using these for analysis, the genotype call-rates of both set-ups (REPLI-g and GPlex4) improved significantly (Wilcoxon paired test, p < 0.001) as seen in Table 1. Comparison of the call-rates indicated that the REPLI-g samples had a significantly higher call-rate than the GPlex4 samples (Wilcoxon's paired test, p < 0.001). Comparison of the amount of wgaDNA amplified by each kit revealed no significant difference (Wilcoxon's paired test, p > 0.050).


Genome-wide scans using archived neonatal dried blood spot samples.

Hollegaard MV, Grauholm J, Børglum A, Nyegaard M, Nørgaard-Pedersen B, Ørntoft T, Mortensen PB, Wiuf C, Mors O, Didriksen M, Thorsen P, Hougaard DM - BMC Genomics (2009)

Plot of the normalized values measure for the A allele and B allele. The same 16 samples were amplified using the GPlex4 and the REPLI-g WGA kits. The "Illumina cluster" plot shows how the GPlex4 (blue dots) and the REPLI-g (green dots) wgaDNA genotypes compare to the Illumina cluster file. The "GPlex4 cluster" plot shows how a custom-made cluster file based on GPlex4 samples (blue dots) improves both fit and call-rate of the loci. The "REPLI-g cluster" plot shows how a custom-made cluster file based on REPLI-g samples (green dots) improves both fit and call-rate of the loci.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713266&req=5

Figure 1: Plot of the normalized values measure for the A allele and B allele. The same 16 samples were amplified using the GPlex4 and the REPLI-g WGA kits. The "Illumina cluster" plot shows how the GPlex4 (blue dots) and the REPLI-g (green dots) wgaDNA genotypes compare to the Illumina cluster file. The "GPlex4 cluster" plot shows how a custom-made cluster file based on GPlex4 samples (blue dots) improves both fit and call-rate of the loci. The "REPLI-g cluster" plot shows how a custom-made cluster file based on REPLI-g samples (green dots) improves both fit and call-rate of the loci.
Mentions: Based on the results displayed in Additional file 1, the combinations of DNA extraction by the ENA kit and WGA by the REPLI-g and GPlex4 kits were selected for further evaluation. For this, 16 new subjects were employed. After DNA-extraction, WGA and subsequent genome-wide scans (GWS), the results were analysed using both a standard Human610-Quadv1B Cluster, provided by Illumina, and WGA kit specific tailored cluster files. The rationale for the tailored cluster files is demonstrated in Figure 1. Generally, the wgaDNA samples cluster nicely, but not always in the area defined by the Illumina Human610-Quadv1B cluster file, which is based on gDNA samples. By creating tailored WGA-specific cluster files and using these for analysis, the genotype call-rates of both set-ups (REPLI-g and GPlex4) improved significantly (Wilcoxon paired test, p < 0.001) as seen in Table 1. Comparison of the call-rates indicated that the REPLI-g samples had a significantly higher call-rate than the GPlex4 samples (Wilcoxon's paired test, p < 0.001). Comparison of the amount of wgaDNA amplified by each kit revealed no significant difference (Wilcoxon's paired test, p > 0.050).

Bottom Line: Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects.The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary.This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip.

View Article: PubMed Central - HTML - PubMed

Affiliation: Section of Neonatal Screening and Hormones, Statens Serum Institut, Copenhagen, Denmark. mvh@ssi.dk

ABSTRACT

Background: Identification of disease susceptible genes requires access to DNA from numerous well-characterised subjects. Archived residual dried blood spot samples from national newborn screening programs may provide DNA from entire populations and medical registries the corresponding clinical information. The amount of DNA available in these samples is however rarely sufficient for reliable genome-wide scans, and whole-genome amplification may thus be necessary. This study assess the quality of DNA obtained from different amplification protocols by evaluating fidelity and robustness of the genotyping of 610,000 single nucleotide polymorphisms, using the Illumina Infinium HD Human610-Quad BeadChip. Whole-genome amplified DNA from 24 neonatal dried blood spot samples stored between 15 to 25 years was tested, and high-quality genomic DNA from 8 of the same individuals was used as reference.

Results: Using 3.2 mm disks from dried blood spot samples the optimal DNA-extraction and amplification protocol resulted in call-rates between 99.15% - 99.73% (mean 99.56%, N = 16), and conflicts with reference DNA in only three per 10,000 genotype calls.

Conclusion: Whole-genome amplified DNA from archived neonatal dried blood spot samples can be used for reliable genome-wide scans and is a cost-efficient alternative to collecting new samples.

Show MeSH
Related in: MedlinePlus