Jim Vaught

NCI-Frederick, Фредерик, Maryland, United States

Are you Jim Vaught?

Claim your profile

Publications (5)22.01 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: A standard mouthwash protocol (a single 10-mL swish of mouthwash for 45 see) was modified in an attempt to increase the amount of human buccal cell DNA per collection and to reduce the percentage of low yielding human DNA collections (<4 mu g). A group of 22 healthy individuals donated a buccal sample each week for several weeks according to the standard protocol without or with one of the following modifications: (1) decreasing the volume of mouthwash, (2) having participants externally rub or not rub their cheeks before donating a specimen, (3) donating two consecutive specimens at each collection, (4) substituting saline for mouthwash, and (5) having individuals expectorate into mouthwash. There was no significant difference in the amount of human DNA collected when 10 mL or 5 mL of mouthwash was used. Externally rubbing cheeks before donating did not significantly alter the amount of human DNA collected, regardless of whether it was one or two donations. Addition of a second donation resulted in 24% to 50% more human DNA than from only a single donation, regardless of whether 5 mL or 10 mL of mouthwash was used, with or without cheek rubbing. With two donations, the percentage of low-yielding human DNA samples was reduced up to 31%. Substituting saline for mouthwash resulted in a significantly lower amount of human buccal DNA collected, regardless of cheek rubbing, and a higher number of low-yielding samples. Expectorating directly into mouthwash while externally rubbing cheeks performed the best (17.70 mu g human DNA), followed by swishing 2-10 mL of mouthwash before expectorating (12.26 mu g). Both protocols had 95% of their samples yielding at least 4 mu g of human DNA without increasing cost; however, when selecting a collection protocol the age and health status of the cohort needs to be considered.
    Cell Preservation Technology 12/2007; 5(4):216-224. DOI:10.1089/cpt.2007.0512 · 1.41 Impact Factor
  • Jim Vaught · Mark Cosentino ·

    Cell Preservation Technology 12/2007; 5(4):178-179. DOI:10.1089/cpt.2007.9986 · 1.41 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Economical methods for collecting and storing high-quality DNA are needed for large population-based molecular epidemiology studies. Buccal cell DNA collected via saliva and stored on treated filter paper cards could be an attractive method, but modest DNA yields and the potential for reduced recovery of DNA over time were unresolved impediments. Consequently, buccal cell DNA collection via oral mouthwash rinsing became the method of choice in epidemiologic studies. However, the amount of genomic DNA (gDNA) required for genotyping continues to decrease, and reliable whole genome amplification (WGA) methods further reduced the mass of gDNA needed for WGA to 10 ng, diminishing the obstacle of low DNA yields from cards. However, concerns about yield and DNA quality over time remained. We located and analyzed 42 buccal cell saliva samples collected and stored on treated cards for 7 years at room temperature, -20 degrees C, and -80 degrees C. We recovered DNA from the treated cards, estimated the concentration by a human-specific quantitative real-time PCR assay, and evaluated the quality by PCR amplification of 268-, 536-, and 989-bp fragments of the beta-globin gene and by AmpFlSTR Identifiler assay analysis. Most DNA yields per 3-mm punch were <10 ng, and most PCR amplicons failed to amplify, where size of the amplicon was negatively associated with successful amplification. Using these methods, treated cards did not consistently provide sufficient quantities of buccal cell gDNA after 7 years of storage for genotyping or WGA.
    Cancer Epidemiology Biomarkers & Prevention 03/2006; 15(2):385-8. DOI:10.1158/1055-9965.EPI-05-0662 · 4.13 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Electron-beam (E-beam) irradiation, currently being used to sterilize mail addressed to selected ZIP codes in the United States, has significant negative effects on the genomic integrity of DNA extracted from buccal-cell washes. We investigated the yield, composition, and genotyping performance of whole genome amplified DNA (wgaDNA) derived from 24 matched samples of E-beam-irradiated and nonirradiated genomic DNA (gDNA) as a model for the effects of degraded gDNA on the performance of whole genome amplification. gDNA was amplified using the Multiple Displacement Amplification method. Three methods of DNA quantification analysis were used to estimate the yield and composition of wgaDNA, and 65 short tandem repeat and single nucleotide polymorphism genotyping assays were used to evaluate the genotyping performance of irradiated and nonirradiated gDNA and wgaDNA. Compared with wgaDNA derived from nonirradiated gDNA, wgaDNA derived from irradiated gDNA exhibited a significantly reduced yield of wgaDNA and significantly reduced short tandem repeat and single nucleotide polymorphism genotyping completion and concordance rates (P < 0.0001). Increasing the amount of irradiated gDNA input into whole genome amplification improved genotyping performance of wgaDNA but not to the level of wgaDNA derived from nonirradiated gDNA. Multiple Displacement Amplification wgaDNA derived from E-beam-irradiated gDNA is not suitable for genotyping analysis.
    Cancer Epidemiology Biomarkers & Prevention 04/2005; 14(4):1016-9. DOI:10.1158/1055-9965.EPI-04-0686 · 4.13 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Buccal cells were collected from 29 participants, by use of mouthwash rinses, and were split into equal aliquots, with one aliquot irradiated by electron-beam (E-beam) irradiation equivalent to the sterilizing dosage used by the U.S. Postal Service and the other left untreated. Aliquots were extracted and tested for DNA yields (e.g., TaqMan assay for quantifying human genomic DNA), genomic integrity, and amplification-based analysis of genetic variants (e.g., single-nucleotide polymorphisms [SNPs] and single tandem repeats [STRs]). Irradiated aliquots had lower median DNA yields (3.7 microg/aliquot) than untreated aliquots (7.6 microg/aliquot) (P<.0005) and were more likely to have smaller maximum DNA fragment size, on the basis of genomic integrity gels, than untreated aliquots (P<.0005). Irradiated aliquots showed poorer PCR amplification of a 989-bp beta-globin target (97% for weak amplification and 3% for no amplification) than untreated aliquots (7% for weak amplification and 0% for no amplification) (P<.0005), but 536-bp and 268-bp beta-globin targets were amplified from all aliquots. There was no detectable irradiation effect on SNP assays, but there was a significant trend for decreased detection of longer STRs (P=.01) in irradiated versus untreated aliquots. We conclude that E-beam irradiation reduced the yield and quality of buccal-cell specimens, and, although irradiated buccal-cell specimens may retain sufficient DNA integrity for some amplified analyses of many common genomic targets, assays that target longer DNA fragments (>989 bp) or require whole-genome amplification may be compromised.
    The American Journal of Human Genetics 09/2003; 73(3):646-51. DOI:10.1086/378077 · 10.93 Impact Factor