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Human Nail Clippings as a Source of DNA for Genetic Studies.

Truong L, Park HL, Chang SS, Ziogas A, Neuhausen SL, Wang SS, Bernstein L, Anton-Culver H - Open J Epidemiol (2015)

Bottom Line: From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for -allele detection compared to DNA derived from matched blood samples.For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and -allele detection, respectively.Concordance was ~98% for both methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Epidemiology, Genetic Epidemiology Research Institute, University of California, Irvine, CA, USA.

ABSTRACT

Blood samples have traditionally been used as the main source of DNA for genetic analysis. However, this source can be difficult in terms of collection, transportation, and long-term storage. In this study, we investigated whether human nail clippings could be used as a source of DNA for SNP genotyping, -allele detection, and whole-genome amplification. From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for -allele detection compared to DNA derived from matched blood samples. For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and -allele detection, respectively. Concordance was ~98% for both methods. When combined with OmniPlex whole-genome amplification, human nail clippings could potentially be used as an alternative to whole blood as a less invasive and more convenient source of DNA for genotyping studies.

No MeSH data available.


(a) ERCC2, 751A/C, pre-WGA SNP genotyping represents the general allelic discriminating plots for DNA from blood (left) and from matched, non-amplified nail clippings (right). Samples from blood generally clustered more tightly. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control. (b) ERCC2, 751A/C, post-WGA SNP genotyping represents the general allelic discriminating plots for nail-extracted DNA samples amplified by MDA (left) and Omniplex (right). Amplified nail-extracted DNA samples generally scattered more on the graphs compared to non-amplified samples. Left: post-MDA with one undetermined (x) and one inconsistency (#2). Right: post-OmniPlex. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control.
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Figure 2: (a) ERCC2, 751A/C, pre-WGA SNP genotyping represents the general allelic discriminating plots for DNA from blood (left) and from matched, non-amplified nail clippings (right). Samples from blood generally clustered more tightly. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control. (b) ERCC2, 751A/C, post-WGA SNP genotyping represents the general allelic discriminating plots for nail-extracted DNA samples amplified by MDA (left) and Omniplex (right). Amplified nail-extracted DNA samples generally scattered more on the graphs compared to non-amplified samples. Left: post-MDA with one undetermined (x) and one inconsistency (#2). Right: post-OmniPlex. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control.

Mentions: In general, SNP genotyping of non-amplified nail-extracted DNA showed good clustering although it was it was not as tight as compared to blood-extracted DNA (Figure 2(a)), likely due to variation in concentrations of double-stranded DNA and higher level of contaminants in nail-extracted DNA. All SNP genotyping was successful in non-amplified nail-extracted DNA except that TGFβ and COMT were both read as “undetermined” for sample 4, the same sample that exhibited poor PCR amplification of COI and BRCA1 (Figure 1(a)). For TGFβ and COMT, a mismatch was also observed for each in 1 out of the 13 successful assays (sample 1). Otherwise, nail-extracted DNA showed perfect concordance with matched blood-extracted DNA for all 4 SNP assays. The mean concordance rate was 96.2% (Table 3).


Human Nail Clippings as a Source of DNA for Genetic Studies.

Truong L, Park HL, Chang SS, Ziogas A, Neuhausen SL, Wang SS, Bernstein L, Anton-Culver H - Open J Epidemiol (2015)

(a) ERCC2, 751A/C, pre-WGA SNP genotyping represents the general allelic discriminating plots for DNA from blood (left) and from matched, non-amplified nail clippings (right). Samples from blood generally clustered more tightly. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control. (b) ERCC2, 751A/C, post-WGA SNP genotyping represents the general allelic discriminating plots for nail-extracted DNA samples amplified by MDA (left) and Omniplex (right). Amplified nail-extracted DNA samples generally scattered more on the graphs compared to non-amplified samples. Left: post-MDA with one undetermined (x) and one inconsistency (#2). Right: post-OmniPlex. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499506&req=5

Figure 2: (a) ERCC2, 751A/C, pre-WGA SNP genotyping represents the general allelic discriminating plots for DNA from blood (left) and from matched, non-amplified nail clippings (right). Samples from blood generally clustered more tightly. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control. (b) ERCC2, 751A/C, post-WGA SNP genotyping represents the general allelic discriminating plots for nail-extracted DNA samples amplified by MDA (left) and Omniplex (right). Amplified nail-extracted DNA samples generally scattered more on the graphs compared to non-amplified samples. Left: post-MDA with one undetermined (x) and one inconsistency (#2). Right: post-OmniPlex. Allele X (red): homozygous wild-type (AA); Allele Y (blue): homozygous variant (CC); Both (green): heterozygous (AC); NTC (black): Non-Template Control.
Mentions: In general, SNP genotyping of non-amplified nail-extracted DNA showed good clustering although it was it was not as tight as compared to blood-extracted DNA (Figure 2(a)), likely due to variation in concentrations of double-stranded DNA and higher level of contaminants in nail-extracted DNA. All SNP genotyping was successful in non-amplified nail-extracted DNA except that TGFβ and COMT were both read as “undetermined” for sample 4, the same sample that exhibited poor PCR amplification of COI and BRCA1 (Figure 1(a)). For TGFβ and COMT, a mismatch was also observed for each in 1 out of the 13 successful assays (sample 1). Otherwise, nail-extracted DNA showed perfect concordance with matched blood-extracted DNA for all 4 SNP assays. The mean concordance rate was 96.2% (Table 3).

Bottom Line: From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for -allele detection compared to DNA derived from matched blood samples.For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and -allele detection, respectively.Concordance was ~98% for both methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Epidemiology, Genetic Epidemiology Research Institute, University of California, Irvine, CA, USA.

ABSTRACT

Blood samples have traditionally been used as the main source of DNA for genetic analysis. However, this source can be difficult in terms of collection, transportation, and long-term storage. In this study, we investigated whether human nail clippings could be used as a source of DNA for SNP genotyping, -allele detection, and whole-genome amplification. From extracted nail DNA, we achieved amplicons up to a length of ~400 bp and >96% concordance for SNP genotyping and 100% concordance for -allele detection compared to DNA derived from matched blood samples. For whole-genome amplification, OmniPlex performed better than Multiple Displacement Amplification with a success rate of 89.3% and 76.8% for SNP genotyping and -allele detection, respectively. Concordance was ~98% for both methods. When combined with OmniPlex whole-genome amplification, human nail clippings could potentially be used as an alternative to whole blood as a less invasive and more convenient source of DNA for genotyping studies.

No MeSH data available.