Limits...
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.


GSTM1 -allele detection and reference assays in real-time PCR reactions. (a) Quadruplicate reactions of whole blood showed 4 samples with GSTM1 alleles (#1, 7, 9, 14). (b) Both duplicates of non-amplified nail DNA showed no product for sample #4 and inconsistency in the duplicates for sample #2. (c) Duplicate reactions of nail DNA post-MDA WGA showed failed amplification in both duplicates for sample #3, whereas samples #2 and #5 each had one failed duplicate. (d) Duplicates of nail DNA post-Omni- Plex WGA with complete consistency in all 14 samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4499506&req=5

Figure 3: GSTM1 -allele detection and reference assays in real-time PCR reactions. (a) Quadruplicate reactions of whole blood showed 4 samples with GSTM1 alleles (#1, 7, 9, 14). (b) Both duplicates of non-amplified nail DNA showed no product for sample #4 and inconsistency in the duplicates for sample #2. (c) Duplicate reactions of nail DNA post-MDA WGA showed failed amplification in both duplicates for sample #3, whereas samples #2 and #5 each had one failed duplicate. (d) Duplicates of nail DNA post-Omni- Plex WGA with complete consistency in all 14 samples.

Mentions: Of the 14 whole blood samples tested, 10 samples were for GSTM1, with all 10 replicates showing excellent consistency across the 14 samples (Figure 3(a)). No-template control (NTC) showed zero activity for both reference and GSTM1 assays. Non-amplified nail-extracted DNA correctly identified the allele (Figure 3(b)) except that one sample failed (sample 4) and another one was inconsistent between duplicates (sample 2). The alleles of GSTM1 were also correctly identified in samples amplified by MDA or OmniPlex except for three MDA-amplified samples (samples 2, 3, and 5) in which the assay failed (Figure 3(c) and Figure 3(d)). Overall, all nail-extracted DNA samples, amplified or not, had an excellent concordance rate (100%) for -allele detection, but OmniPlex had the best success rate (100%) (Table 4).


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)

GSTM1 -allele detection and reference assays in real-time PCR reactions. (a) Quadruplicate reactions of whole blood showed 4 samples with GSTM1 alleles (#1, 7, 9, 14). (b) Both duplicates of non-amplified nail DNA showed no product for sample #4 and inconsistency in the duplicates for sample #2. (c) Duplicate reactions of nail DNA post-MDA WGA showed failed amplification in both duplicates for sample #3, whereas samples #2 and #5 each had one failed duplicate. (d) Duplicates of nail DNA post-Omni- Plex WGA with complete consistency in all 14 samples.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: GSTM1 -allele detection and reference assays in real-time PCR reactions. (a) Quadruplicate reactions of whole blood showed 4 samples with GSTM1 alleles (#1, 7, 9, 14). (b) Both duplicates of non-amplified nail DNA showed no product for sample #4 and inconsistency in the duplicates for sample #2. (c) Duplicate reactions of nail DNA post-MDA WGA showed failed amplification in both duplicates for sample #3, whereas samples #2 and #5 each had one failed duplicate. (d) Duplicates of nail DNA post-Omni- Plex WGA with complete consistency in all 14 samples.
Mentions: Of the 14 whole blood samples tested, 10 samples were for GSTM1, with all 10 replicates showing excellent consistency across the 14 samples (Figure 3(a)). No-template control (NTC) showed zero activity for both reference and GSTM1 assays. Non-amplified nail-extracted DNA correctly identified the allele (Figure 3(b)) except that one sample failed (sample 4) and another one was inconsistent between duplicates (sample 2). The alleles of GSTM1 were also correctly identified in samples amplified by MDA or OmniPlex except for three MDA-amplified samples (samples 2, 3, and 5) in which the assay failed (Figure 3(c) and Figure 3(d)). Overall, all nail-extracted DNA samples, amplified or not, had an excellent concordance rate (100%) for -allele detection, but OmniPlex had the best success rate (100%) (Table 4).

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.