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1.  Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping 
BMC Medical Genomics  2012;5:19.
Background
The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility of using saliva-extracted DNA in comparison to blood-derived DNA, across two genotyping platforms: Applied Biosystems TaqmanTM and Illumina BeadchipTM genome-wide arrays.
Method
Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek®) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by Gen-Probe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed.
Results
Total DNA yields were lower from saliva (mean 24 μg, range 0.2–52 μg) than from blood (mean 210 μg, range 58–577 μg) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA.
Conclusion
We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.
doi:10.1186/1755-8794-5-19
PMCID: PMC3497576  PMID: 22647440
2.  Saliva sampling in global clinical studies: the impact of low sampling volume on performance of DNA in downstream genotyping experiments 
BMC Medical Genomics  2013;6:20.
Background
The collection of viable DNA samples is an essential element of any genetics research programme. Biological samples for DNA purification are now routinely collected in many studies with a variety of sampling methods available. Initial observation in this study suggested a reduced genotyping success rate of some saliva derived DNA samples when compared to blood derived DNA samples prompting further investigation.
Methods
Genotyping success rate was investigated to assess the suitability of using saliva samples in future safety and efficacy pharmacogenetics experiments. The Oragene® OG-300 DNA Self-Collection kit was used to collect and extract DNA from saliva from 1468 subjects enrolled in global clinical studies. Statistical analysis evaluated the impact of saliva sample volume of collection on the quality, yield, concentration and performance of saliva DNA in genotyping assays.
Results
Across 13 global clinical studies that utilized the Oragene® OG-300 DNA Self-Collection kit there was variability in the volume of saliva sample collection with ~31% of participants providing 0.5 mL of saliva, rather than the recommended 2 mL. While the majority of saliva DNA samples provided high quality genotype data, collection of 0.5 mL volumes of saliva contributed to DNA samples being significantly less likely to pass genotyping quality control standards. Assessment of DNA sample characteristics that may influence genotyping outcomes indicated that saliva sample volume, DNA purity and turbidity were independently associated with sample genotype pass rate, but that saliva collection volume had the greatest effect.
Conclusion
When employing saliva sampling to obtain DNA, it is important to encourage all study participants to provide sufficient sample to minimize potential loss of data in downstream genotyping experiments.
doi:10.1186/1755-8794-6-20
PMCID: PMC3698156  PMID: 23759220
Global study; Volume of saliva collection; DNA characteristics; Genotyping performance
3.  Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples 
Background
Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva.
Methods
Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP) in the catechol-0-methyltransferase gene (COMT rs4680) and one representative variable number of tandem repeats (VNTR) in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region) were selected for genetic analyses.
Results
The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days), repeated freeze-thaw cycles (up to 6 cycles), and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible.
Conclusions
Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using 10 ng of DNA per genotyping reaction, the obtained samples can be used for more than one hundred candidate gene assays. When saliva is collected with an absorbent device, most of the nucleic acid content remains in the device, therefore it is advisable to collect the device separately for later genetic analyses.
doi:10.1186/1471-2288-11-170
PMCID: PMC3267685  PMID: 22182470
4.  Quality of DNA extracted from saliva samples collected with the Oragene™ DNA self-collection kit 
Background
Large epidemiological studies in DNA biobanks have increasingly used less invasive methods for obtaining DNA samples, such as saliva collection. Although lower amounts of DNA are obtained as compared with blood collection, this method has been widely used because of its more simple logistics and increased response rate. The present study aimed to verify whether a storage time of 8 months decreases the quality of DNA from collected samples.
Methods
Saliva samples were collected with an OrageneTM DNA Self-Collection Kit from 4,110 subjects aged 14–15 years. The samples were processed in two aliquots with an 8-month interval between them. Quantitative and qualitative evaluations were carried out in 20% of the samples by spectrophotometry and genotyping. Descriptive analyses and paired t-tests were performed.
Results
The mean volume of saliva collected was 2.2 mL per subject, yielding on average 184.8 μg DNA per kit. Most samples showed a Ratio of OD differences (RAT) between 1.6 and 1.8 in the qualitative evaluation. The evaluation of DNA quality by TaqMan®, High Resolution Melting (HRM), and restriction fragment length polymorphism-PCR (RFLP-PCR) showed a rate of success of up to 98% of the samples. The sample store time did not reduce either the quantity or quality of DNA extracted with the Oragene kit.
Conclusion
The study results showed that a storage period of 8 months at room temperature did not reduce the quality of the DNA obtained. In addition, the use of the Oragene kit during fieldwork in large population-based studies allows for DNA of high quantity and high quality.
doi:10.1186/1471-2288-12-65
PMCID: PMC3422993  PMID: 22559914
5.  Saliva as an alternative source of high yield canine genomic DNA for genotyping studies 
BMC Research Notes  2009;2:219.
Background
The domestic dog presents an attractive model system for the study of the genetic basis of disease. The development of resources such as the canine genome sequence and SNP genotyping platforms has allowed for the implementation of canine genetic studies. Successful implementation of such studies depends not only on the quality of individual DNA samples, but also on the number of samples obtained. The latter can be maximized using a non-invasive DNA collection method that can increase study participation. We compared the DNA yield and quality obtained from blood and buccal swabs to those obtained using a non-invasive saliva collection kit (Oragene ®•ANIMAL kit). We also assessed the success rate of PCR amplification and genotyping accuracy of DNA isolated using these collection methods.
Findings
Comparison of DNA yields from matched saliva, blood and buccal swab samples showed that yields from saliva were significantly higher than those from blood (p = 0.0198) or buccal swabs (p = 0.0008). Electrophoretic analysis revealed that blood and saliva produced higher quality DNA than buccal swabs. In addition, a 1.1-kb PCR fragment was successfully amplified using the paired DNA samples and genotyping by PCR-RFLP yielded identical results.
Conclusion
We demonstrate that DNA yields from canine saliva are higher than those from blood or buccal swabs. The quality of DNA extracted from saliva is sufficient for successful amplification of a 1.1-kb fragment and for accurate SNP genotyping by PCR-RFLP. We conclude that saliva presents a non-invasive alternative source of high quantities of canine genomic DNA suitable for genotyping studies.
doi:10.1186/1756-0500-2-219
PMCID: PMC2781016  PMID: 19874604
6.  Impact of a Biospecimen Collection Seminar on Willingness to Donate Biospecimens among Chinese Americans: Results from a Randomized, Controlled Community-Based Trial 
Background
Biospecimen collection from diverse populations can advance cancer disparities research, but is currently underrepresented.
Methods
We partnered with a community-based clinic serving Cantonese-speaking Chinese Americans to develop and revise an educational seminar on biospecimen collection. Through a randomized controlled trial (n = 395), the intervention seminar was compared with a control seminar (cancer prevention) on change in willingness to donate biospecimens.
Results
At baseline, many were willing to donate a biospecimen (saliva, urine, hair, toenails, blood, unused cancerous tissue) whether healthy or hypothetically had cancer. Also, many would donate because future generations would benefit, and few had concerns about donation. In logistic regression analyses, there was an intervention effect for willingness to donate: urine if had cancer [OR, 2.2; 95% confidence interval (CI), 1.3–3.7], toenails if healthy (OR, 2.1; 95% CI, 1.4–3.2) or had cancer (OR, 2.3; 95% CI, 2.0–2.7), hair if healthy (OR, 1.8; 95% CI, 1.3–2.5) or had cancer (OR, 2.8; 95% CI, 1.9–4.0), and unused cancerous tissue (OR, 1.8; 95% CI, 1.2–2.9). There was also an intervention effect for donating because future generations would benefit (OR, 2.0; 95% CI, 1.4–3.0), and this attitude was a strong independent predictor for willingness to donate all biospecimens, whether healthy or had cancer (OR, 2.9–4.2).
Conclusion
Cantonese-speaking Chinese American participants of an educational seminar on biospecimen collection showed greater increases in willingness to donate biospecimens and donating for the benefit of future generations, than participants who attended a control seminar.
Impact
Donating for the benefit of future generations is a theme that should be incorporated in messages that encourage biospecimen donation for Chinese Americans.
doi:10.1158/1055-9965.EPI-13-0744
PMCID: PMC4049566  PMID: 24609848
7.  PCR detection of Plasmodium falciparum in human urine and saliva samples 
Malaria Journal  2006;5:103.
Background
Current detection or screening for malaria infection necessitates drawing blood by fingerprick or venipuncture, which poses risks and limitations for repeated measurement. This study presents PCR detection of Plasmodium falciparum in human urine and saliva samples, and illustrates this potential application in genotyping malaria infections.
Methods
Urine and saliva were obtained from 47 thick film positive and 4 negative individuals one day after collection of blood slides and filter paper blood spots. P. falciparum DNA was extracted from blood, urine and saliva, in separate groups, using the Chelex method or Qiagen DNEasy® kit (urine and saliva only). Blood, urine and saliva extracts were subjected to PCR in separate batches. Amplicons from the various sample types were examined for MSP2 polymorphisms and restriction fragment patterns on DHFR amino acid codon 59.
Results and discussion
Malaria infections exhibited primarily low-grade parasite densities, with a geometric mean of 775 asexual parasites/μl. Regularly matching polymorphic MSP2 genotypes were found between the corresponding urine, saliva and peripheral blood amplicons of each individual, with different inter-individual polymorphic genotypes. Amplicon yields were significantly dependent on DNA extraction method, parasite density and primer set (p < 0.001). A Qiagen® kit extraction had more than 2× higher amplicon yield than the Chelex method, for both urine and saliva. Amplicon yields were 1.6 fold higher from saliva than urine. For each unit increase in log parasite density, the probability of amplicon enhanced 1.8 fold. Highest amplicon yields were obtained from the primer set with the shortest PCR product.
Conclusion
P. falciparum infection is detectable by PCR on human urine and saliva samples. Subject to further refinement of extraction technique and amplicon yields, large-scale malaria parasite screening and epidemiological surveys could be possible without the need to collect blood and use of needles or sharps.
doi:10.1186/1475-2875-5-103
PMCID: PMC1654175  PMID: 17092335
8.  HSV-1 DNA in Tears and Saliva of Normal Adults 
Purpose.
To assess the frequency of shedding of herpes simplex virus type 1 (HSV-1) DNA in tears and saliva of asymptomatic individuals.
Methods
Fifty subjects without signs of ocular herpetic disease participated. Serum samples from all subjects were tested for HSV IgG antibodies by enzyme-linked immunosorbent assay (ELISA) and for HSV-1 by neutralization assay. HSV-1 DNA copy number and frequency of shedding were determined by real-time polymerase chain reaction (PCR) analysis of tear and saliva samples collected twice daily for 30 consecutive days.
Results
Thirty-seven (74%) of the 50 subjects were positive for HSV IgG by ELISA. The percentages of positive eye and mouth swabs were approximately equivalent: 33.5% (941/2806) and 37.5% (1020/2723), respectively. However, the percentage of samples with high HSV-1 genome copy numbers was greater in saliva than in tears, which may have been a result of the sample volume collected. Shedding frequency in tears was nearly the same in men (347/1003; 34.6%) and women (594/1705; 34.8%); in saliva, men had a higher frequency of shedding (457/1009; 45.3% vs. 563/1703; 33.1%, men versus women). Overall, 49 (98%) of 50 subjects shed HSV-1 DNA at least once during the course of the 30-day study.
Conclusions
The percentage of asymptomatic subjects who intermittently shed HSV-1 DNA in tears or saliva was higher than the percentage of subjects with positive ELISA or neutralization antibodies to HSV. Because most HSV transmission occurs during asymptomatic shedding, further knowledge of the prevalence of HSV-1 DNA in tears and saliva is warranted to control its spread. Shedding is simple to study, and its suppression may be an efficient way to evaluate new antivirals in humans.
doi:10.1167/iovs.04-0614
PMCID: PMC1200985  PMID: 15623779
9.  High resolution of microRNA signatures in human whole saliva 
Archives of oral biology  2011;56(12):1506-1513.
Objective
Identifying discriminatory human salivary RNA biomarkers reflective of disease in a low-cost non-invasive screening assay is crucial to salivary diagnostics. Recent studies have reported both mRNA and microRNA (miRNA) in saliva, but little information has been documented on the quality and yield of RNA collected. Therefore, the aim of the present study was to develop an improved RNA isolation method from saliva and to identify major miRNA species in human whole saliva.
Design
RNA samples were isolated from normal human saliva using a combined protocol based on the Oragene®•RNA collection kit and the mirVana™ miRNA isolation kit in tandem. RNA samples were analyzed for quality and subjected to miRNA array analysis.
Results
RNA samples isolated from twenty healthy donors ranged from 2.59–29.4 μg/ml saliva and with 1.92–2.16 OD260/280nm ratios. RNA yield and concentration of saliva samples were observed to be stable over 48 hours at room temperature. Analysis of total salivary RNA isolated from these twenty donors showed no statistical significance between sexes; however, the presence of high-, medium-, and low-yield salivary RNA producers were detected. MiRNA array analysis of salivary RNA detected five abundantly expressed miRNAs, miR-223, miR-191, miR-16, miR-203, and miR-24, that were similarly described in other published reports. Additionally, many previously undetected miRNAs were also identified.
Conclusion
High quality miRNAs can be isolated from saliva using available commercial kits, and in future studies, the availability of this isolation protocol may allow specific changes in their levels to be measured accurately in various relevant diseases.
doi:10.1016/j.archoralbio.2011.05.015
PMCID: PMC3189266  PMID: 21704302
biomarkers; gene expression; salivary RNA
10.  Saliva and Plasma Quantitative Polymerase Chain Reaction–Based Detection and Surveillance of Human Papillomavirus–Related Head and Neck Cancer 
IMPORTANCE
Human papillomavirus type 16 (HPV-16) is a major causative factor in oropharyngeal squamous cell carcinoma (OPSCC). The detection of primary OPSCC is often delayed owing to the challenging anatomy of the oropharynx.
OBJECTIVE
To investigate the feasibility of HPV-16 DNA detection in pretreatment and posttreatment plasma and saliva and its potential role as a marker of prognosis.
DESIGN, SETTING, AND PARTICIPANTS
This is a retrospective analysis of a prospectively collected cohort. Among a cohort of patients with oropharyngeal and unknown primary squamous cell carcinoma with known HPV-16 tumor status from the Johns Hopkins Medical Institutions and Greater Baltimore Medical Center (from 1999 through 2010), 93 patients were identified with a complete set of pretreatment and posttreatment plasma or saliva samples, of which 81 patients had HPV-16–positive tumors and 12 patients had HPV-16–negative tumors. Real-time quantitative polymerase chain reaction was used to detect HPV-16 E6 and E7 DNA in saliva and plasma samples.
MAIN OUTCOMES AND MEASURES
Main outcomes included sensitivity, specificity, negative predictive value of combined saliva and plasma pretreatment HPV-16 DNA status for detecting tumor HPV-16 status, as well as the association of posttreatment HPV DNA status with clinical outcomes, including recurrence-free survival and overall survival.
RESULTS
The median follow-up time was 49 months (range, 0.9–181.0 months). The sensitivity, specificity, negative predictive value, and positive predictive value of combined saliva and plasma pretreatment HPV-16 DNA status for detecting tumor HPV-16 status were 76%, 100%, 42%, and 100%, respectively. The sensitivities of pretreatment saliva or plasma alone were 52.8%and 67.3%, respectively. In a multivariable analysis, positive posttreatment saliva HPV status was associated with higher risk of recurrence (hazard ratio [HR], 10.7; 95% CI, 2.36–48.50) (P = .002). Overall survival was reduced among those with posttreatment HPV-positive status in saliva (HR, 25.9; 95% CI, 3.23–208.00) (P = .002) and those with HPV-positive status in either saliva or plasma but not among patients with HPV-positive status in plasma alone. The combined saliva and plasma posttreatment HPV-16 DNA status was 90.7%specific and 69.5%sensitive in predicting recurrence within 3 years.
CONCLUSIONS AND RELEVANCE
Using a combination of pretreatment plasma and saliva can increase the sensitivity of pretreatment HPV-16 status as a tool for screening patients with HPV-16–positive OPSCC. In addition, analysis of HPV-16 DNA in saliva and plasma after primary treatment may allow for early detection of recurrence in patients with HPV-16–positive OPSCC.
doi:10.1001/jamaoto.2014.1338
PMCID: PMC4313904  PMID: 25078109
11.  Effects of saliva collection using cotton swabs on melatonin enzyme immunoassay 
Background
Although various acceptable and easy-to-use devices have been used for saliva collection, cotton swabs are among the most common ones. Previous studies reported that cotton swabs yield a lower level of melatonin detection. However, this statistical method is not adequate for detecting an agreement between cotton saliva collection and passive saliva collection, and a test for bias is needed. Furthermore, the effects of cotton swabs have not been examined at lower melatonin level, a level at which melatonin is used for assessment of circadian rhythms, namely dim light melatonin onset (DLMO). In the present study, we estimated the effect of cotton swabs on the results of salivary melatonin assay using the Bland-Altman plot at lower level.
Methods
Nine healthy males were recruited and each provided four saliva samples on a single day to yield a total of 36 samples. Saliva samples were directly collected in plastic tubes using plastic straws, and subsequently pipetted onto cotton swabs (cotton saliva collection) and into clear sterile tubes (passive saliva collection). The melatonin levels were analyzed in duplicate using commercially available ELISA kits.
Results
The mean melatonin concentration in cotton saliva collection samples was significantly lower than that in passive saliva collection samples at higher melatonin level (>6 pg/mL). The Bland-Altman plot indicated that cotton swabs causes relative and proportional biases in the assay results. For lower melatonin level (<6 pg/mL), although the BA plots didn't show proportional and relative biases, there was no significant correlation between passive and cotton saliva collection samples.
Conclusion
Our findings indicate an interference effect of cotton swabs on the assay result of salivary melatonin at lower melatonin level. Cotton-based collection devices might, thus, not be suitable for assessment of DLMO.
doi:10.1186/1740-3391-9-1
PMCID: PMC3024305  PMID: 21219623
12.  Effects of DNA mass on multiple displacement whole genome amplification and genotyping performance 
BMC Biotechnology  2005;5:24.
Background
Whole genome amplification (WGA) promises to eliminate practical molecular genetic analysis limitations associated with genomic DNA (gDNA) quantity. We evaluated the performance of multiple displacement amplification (MDA) WGA using gDNA extracted from lymphoblastoid cell lines (N = 27) with a range of starting gDNA input of 1–200 ng into the WGA reaction. Yield and composition analysis of whole genome amplified DNA (wgaDNA) was performed using three DNA quantification methods (OD, PicoGreen® and RT-PCR). Two panels of N = 15 STR (using the AmpFlSTR® Identifiler® panel) and N = 49 SNP (TaqMan®) genotyping assays were performed on each gDNA and wgaDNA sample in duplicate. gDNA and wgaDNA masses of 1, 4 and 20 ng were used in the SNP assays to evaluate the effects of DNA mass on SNP genotyping assay performance. A total of N = 6,880 STR and N = 56,448 SNP genotype attempts provided adequate power to detect differences in STR and SNP genotyping performance between gDNA and wgaDNA, and among wgaDNA produced from a range of gDNA templates inputs.
Results
The proportion of double-stranded wgaDNA and human-specific PCR amplifiable wgaDNA increased with increased gDNA input into the WGA reaction. Increased amounts of gDNA input into the WGA reaction improved wgaDNA genotyping performance. Genotype completion or genotype concordance rates of wgaDNA produced from all gDNA input levels were observed to be reduced compared to gDNA, although the reduction was not always statistically significant. Reduced wgaDNA genotyping performance was primarily due to the increased variance of allelic amplification, resulting in loss of heterozygosity or increased undetermined genotypes. MDA WGA produces wgaDNA from no template control samples; such samples exhibited substantial false-positive genotyping rates.
Conclusion
The amount of gDNA input into the MDA WGA reaction is a critical determinant of genotyping performance of wgaDNA. At least 10 ng of lymphoblastoid gDNA input into MDA WGA is required to obtain wgaDNA TaqMan® SNP assay genotyping performance equivalent to that of gDNA. Over 100 ng of lymphoblastoid gDNA input into MDA WGA is required to obtain optimal STR genotyping performance using the AmpFlSTR® Identifiler® panel from wgaDNA equivalent to that of gDNA.
doi:10.1186/1472-6750-5-24
PMCID: PMC1249558  PMID: 16168060
13.  New Saliva DNA Collection Method Compared to Buccal Cell Collection Techniques for Epidemiological Studies 
Epidemiological studies may require noninvasive methods for off-site DNA collection. We compared the DNA yield and quality obtained using a whole-saliva collection device (Oragene™ DNA collection kit) to those from three established noninvasive methods (cytobrush, foam swab, and oral rinse). Each method was tested on 17 adult volunteers from our center, using a random crossover collection design and analyzed using repeated-measures statistics. DNA yield and quality were assessed via gel electrophoresis, spectophotometry, and polymerase chain reaction (PCR) amplification rate. The whole-saliva method provided a significantly greater DNA yield (mean ± SD = 154.9 ± 103.05 μg, median = 181.88) than the other methods (oral rinse = 54.74 ± 41.72 μg, 36.56; swab = 11.44 ± 7.39 μg, 10.72; cytobrush = 12.66 ± 6.19, 13.22 μg) (all pairwise P < 0.05). Oral-rinse and whole-saliva samples provided the best DNA quality, whereas cytobrush and swab samples provided poorer quality DNA, as shown by lower OD260/OD280 and OD260/OD230 ratios. We conclude that both a 10-ml oral-rinse sample and 2-ml whole-saliva sample provide sufficient DNA quantity and better quality DNA for genetic epidemiological studies than do the commonly used buccal swab and brush techniques.
doi:10.1002/ajhb.20586
PMCID: PMC2797479  PMID: 17421001
14.  Genotyping Performance between Saliva and Blood-Derived Genomic DNAs on the DMET Array: A Comparison 
PLoS ONE  2012;7(3):e33968.
The Affymetrix Drug Metabolism Enzymes and Transporters (DMET) microarray is the first assay to offer a large representation of SNPs conferring genetic diversity across known pharmacokinetic markers. As a convenient and painless alternative to blood, saliva samples have been reported to work well for genotyping on the high density SNP arrays, but no reports to date have examined this application for saliva-derived DNA on the DMET platform. Genomic DNA extractions from saliva samples produced an ample quantity of genomic DNA for DMET arrays, however when human amplifiable DNA was measured, it was determined that a large percentage of this DNA was from bacteria or fungi. A mean of 37.3% human amplifiable DNA was determined for saliva-derived DNAs, which results in a significant decrease in the genotyping call rate (88.8%) when compared with blood-derived DNAs (99.1%). More interestingly, the percentage of human amplifiable DNA correlated with a higher genotyping call rate, and almost all samples with more than 31.3% human DNA produced a genotyping call rate of at least 96%. SNP genotyping results for saliva derived DNA (n = 39) illustrated a 98.7% concordance when compared with blood DNA. In conclusion, when compared with blood DNA and tested on the DMET array, saliva-derived DNA provided adequate genotyping quality with a significant lower number of SNP calls. Saliva-derived DNA does perform very well if it contains greater than 31.3% human amplifiable DNA.
doi:10.1371/journal.pone.0033968
PMCID: PMC3309006  PMID: 22448283
15.  Patients’ Willingness to Participate in a Breast Cancer Biobank at Screening Mammogram 
Purpose
To characterize patients’ willingness to donate a biospecimen for future research as part of a breast cancer-related biobank involving a general screening population.
Materials and Methods
We performed a prospective cross-sectional study of 4,217 women aged 21 to 89 years presenting to our facilities for screening mammogram between December 2010 and October 2011. This HIPAA-compliant study was approved by our institutional review board. We collected data on patients’ interest in and actual donation of a biospecimen, motivators and barriers to donating, demographic information, and personal breast cancer risk factors. A multivariate logistic regression analysis was performed to identify patient-level characteristics associated with an increased likelihood to donate.
Results
Mean patient age was 57.8 years (SD 11.1 years). While 66.0% (2785/4217) of patients were willing to donate blood or saliva during their visit, only 56.4% (2378/4217) actually donated. Women with a college education (OR=1.27, p=0.003), older age (OR=1.02, p<0.001), previous breast biopsy (OR=1.23, p=0.012), family history of breast cancer (OR=1.23, p=0.004), or a comorbidity (OR=1.22, p=0.014) were more likely to donate. Asian-American women were significantly less likely to donate (OR=0.74, p=0.005). The major reason for donating was to help all future patients (42.3%) and the major reason for declining donation was privacy concerns (22.3%).
Conclusion
A large proportion of women participating in a breast cancer screening registry are willing to donate blood or saliva to a biobank. Among minority participants, Asian-American women are less likely to donate and further qualitative research is required to identify novel active recruitment strategies to ensure their involvement.
doi:10.1007/s10549-012-2324-x
PMCID: PMC3676182  PMID: 23129174
biospecimen; biobank; breast cancer; screening; patient willingness
16.  The role of polymorphisms associated with early tooth eruption in dental and occlusal traits in East Asian populations 
Korean Journal of Orthodontics  2014;44(2):96-102.
Objective
A recent study suggested that rs6504340, a polymorphism within the homeobox B (HOXB) gene cluster, is associated with the susceptibility for malocclusions in Europeans. The resulting malocclusions require orthodontic treatment. The aim of this study was to investigate the association of rs6504340 and other dentition-implicated polymorphisms with dental and occlusal traits in Korean and Japanese populations.
Methods
The study participants included 223 unrelated Koreans from the Busan area and 256 unrelated Japanese individuals from the Tokyo metropolitan area. DNA samples were extracted from saliva specimens. Genotyping for rs6504340 and four single nucleotide polymorphisms (SNPs) that have been shown to be associated with the timing of first tooth eruption and the number of teeth at 1 year of age (rs10506525, rs1956529, rs9674544, and rs8079702) was performed using TaqMan assays. The Index of Orthodontic Treatment Need (IOTN), overjet, overbite, arch length discrepancy, crown sizes, and length and width of the dental arches were measured. Spearman's correlation coefficients were calculated to evaluate relationships between rs6504340 and these dental/occlusal traits.
Results
We evaluated the aesthetic components and dental health components of the IOTN in the Korean and Japanese populations and found that neither rs6504340 nor the other four SNPs showed any association with dental and occlusal traits in these East Asian populations.
Conclusions
These negative results suggest that further research is needed to identify the genetic determinants of malocclusions in order to reach a consensus.
doi:10.4041/kjod.2014.44.2.96
PMCID: PMC3971131  PMID: 24696826
Genetics; Tooth size; Orthodontic index
17.  The Congenital Heart Disease Genetic Network Study 
Circulation research  2013;112(4):698-706.
Congenital heart defects (CHD) are the leading cause of infant mortality among birth defects, and later morbidities and premature mortality remain problematic. Although genetic factors contribute significantly to cause CHD, specific genetic lesions are unknown for most patients. The National Heart, Lung, and Blood Institute-funded Pediatric Cardiac Genomics Consortium established the Congenital Heart Disease Genetic Network Study to investigate relationships between genetic factors, clinical features, and outcomes in CHD. The Pediatric Cardiac Genomics Consortium comprises 6 main and 4 satellite sites at which subjects are recruited, and medical data and biospecimens (blood, saliva, cardiovascular tissue) are collected. Core infrastructure includes an administrative/data-coordinating center, biorepository, data hub, and core laboratories (genotyping, whole-exome sequencing, candidate gene evaluation, and variant confirmation). Eligibility includes all forms of CHD. Annual follow-up is obtained for probands <1-year-old. Parents are enrolled whenever available. Enrollment from December 2010 to June 2012 comprised 3772 probands. One or both parents were enrolled for 72% of probands. Proband median age is 5.5 years. The one third enrolled at age <1 year are contacted annually for follow-up information. The distribution of CHD favors more complex lesions. Approximately, 11% of probands have a genetic diagnosis. Adequate DNA is available from 97% and 91% of blood and saliva samples, respectively. Genomic analyses of probands with heterotaxy, atrial septal defects, conotruncal, and left ventricular outflow tract obstructive lesions are underway. The scientific community’s use of Pediatric Cardiac Genomics Consortium resources is welcome.
doi:10.1161/CIRCRESAHA.111.300297
PMCID: PMC3679175  PMID: 23410879
congenital cardiac defects; congenital heart disease; genome-wide analysis; genomic study; human genetics
18.  Plasma Pharmacokinetic Characteristics of Risperidone and Their Relationship to Saliva Concentrations in Children with Psychiatric or Neurodevelopmental Disorders 
Clinical therapeutics  2007;29(7):1476-1486.
Background
Risperidone is a second-generation antipsychotic agent widely used in the treatment of schizophrenia and other psychotic disorders in adults. Risperidone is probably the most frequently used atypical antipsychotic in the pediatric population.
Objectives
The goals of this study were to estimate the pharmacokinetic parameters of risperidone and its enantiomers in a pediatric population and explore relationships between saliva and plasma concentrations.
Methods
Eligible patients, between 4 and 15 years of age, included those taking a stable dose of oral risperidone ranging from 0.01 to 0.07 mg/kg BID for ≥4 weeks to treat psychiatric or neurodevelopmental conditions. A trough blood level and predose saliva sample were collected at study initiation; the regular risperidone dose was administered; and paired samples of blood and saliva were collected at 1, 2, 4, and 7 hours postdose. Plasma/saliva concentrations of risperidone and enantiomers of its principal active metabolite, 9-hydroxyrisperidone (9-OH-risperidone), were measured using a chiral liquid chromatography–tandem mass spectrometry assay. Standard pharmacokinetic parameters were calculated. Cytochrome P450 2D6 genotypes of *3,*4,*5 deletion and duplication were determined.
Results
The study included 19 patients (age range, 4 years 2 months to 15 years 11 months). Mean (SD) values for Cmax, t1/2, and AUC 0 to 12 hours for risperidone in plasma were 15.9 (22.2) ng/mL, 3.0 (2.3) h, and 92.1 (200.6) ng · h/mL, respectively. Corresponding values in saliva were 12.0 (21.0) ng/mL, 3.4 (3.2) h, and 27.8 (38.7) ng · h/mL, respectively. Mean (SD) plasma enantiomer values for Cmax and AUC calculated up to the last observation were: (+)-9-OH-risperidone, 13.6 (10.0) ng/mL and 73.6 (52.3) ng · h/mL; (−)-9-OH-risperidone, 4.9 (3.1) ng/mL and 29.3 (19.1) ng · h/mL. Corresponding enantiomer values in saliva were: (+)-9-OH-risperidone, 5.2 (8.8) ng/mL and 15.6 (8.9) ng · h/mL; (−)-9-OH-risperidone, 5.0 (7.9) ng/mL and 15.6 (9.1) ng · h/mL, respectively. Large interindividual variability in risperidone and enantiomer concentrations was noted. A highly significant relationship between predose plasma and predose saliva risperidone concentrations was observed. The logarithmic regression model indicated that the log risperidone saliva concentration = −0.100 + 0.594 · log plasma concentration (R2 = 0.93 [Spearman]).
Conclusions
In this preliminary pharmacokinetic study of parameters for risperidone and the enantiomers of 9-OH-risperidone in a pediatric population, mean C max and t1/2 of risperidone were generally similar to those previously described in adults. The highly significant relationship between predose plasma and predose saliva risperidone concentrations suggests that saliva measurements may be a viable alternative to plasma sampling in children.
doi:10.1016/j.clinthera.2007.07.026
PMCID: PMC3740764  PMID: 17825699
risperidone; children; pharmacokinetics; saliva; plasma; 9-hydroxyrisperidone enantiomers
19.  Glucagon-Like Peptide-1 Receptor Gene Polymorphism (Leu260Phe) Is Associated With Morning Cortisol in Preschoolers 
Glucagon like peptide-1 (GLP-1) has been shown to be a potent stress-regulating neuropeptide in animal models, but little is known about whether genetic polymorphisms that influence this peptide influence stress responses in humans. We therefore explored whether a missense mutation (rs1042044) in the GLP-1 receptor was associated with morning and evening salivary cortisol levels in preschool aged children. Morning and evening saliva samples and individual buccal swabs for DNA extraction were collected from seventy-seven preschool aged children. Salivary cortisol was assayed using a time-resolved fluorescence immunoassay with fluorometric end-point detection (DELFIA), and the rs1042044 single nucleotide polymorphism (SNP) was genotyped using allele specific TaqMan probes. Children homozygous for the phenylalanine (C) substitution in GLP-1R gene had significantly higher morning salivary cortisol levels than children with other GLP-1R genotypes (p = 0.029). Additionally, children with one or two copies of the phenylalanine (C) allele had significantly higher morning cortisol levels compared to children homozygous for the leucine (A) allele (p = 0.008). Our results identify associations between a novel genetic variant of GLP-1R and hypothalamus-pituitary-adrenal (HPA) axis regulation. This polymorphism may have functional significance in stress-related psychiatric disorders.
doi:10.1016/j.pnpbp.2010.05.007
PMCID: PMC2910171  PMID: 20483198
cortisol; GLP-1R; HPA axis; polymorphism; rs104204; stress
20.  Identification of the main malaria vectors in the Anopheles gambiae species complex using a TaqMan real-time PCR assay 
Malaria Journal  2007;6:155.
Background
The Anopheles gambiae sensu lato species complex comprises seven sibling species of mosquitoes that are morphologically indistinguishable. Rapid identification of the two main species which vector malaria, Anopheles arabiensis and An. gambiae sensu stricto, from the non-vector species Anopheles quadriannulatus is often required as part of vector control programmes. Currently the most widely used method for species identification is a multiplex PCR protocol that targets species specific differences in ribosomal DNA sequences. While this assay has proved to be reasonably robust in many studies, additional steps are required post-PCR making it time consuming. Recently, a high-throughput assay based on TaqMan single nucleotide polymorphism genotyping that detects and discriminates An. gambiae s.s and An. arabiensis has been reported.
Methods
A new TaqMan assay was developed that distinguishes between the main malaria vectors (An. arabiensis and An. gambiae s.s.) and the non-vector An. quadriannulatus after it was found that the existing TaqMan assay incorrectly identified An. quadriannulatus, An. merus and An. melas as An. gambiae s.s. The performance of this new TaqMan assay was compared against the existing TaqMan assay and the standard PCR method in a blind species identification trial of over 450 samples using field collected specimens from a total of 13 countries in Sub-Saharan Africa.
Results
The standard PCR method was found to be specific with a low number of incorrect scores (<1%), however when compared to the TaqMan assays it showed a significantly higher number of failed reactions (15%). Both the new vector-specific TaqMan assay and the exisiting TaqMan showed a very low number of incorrectly identified samples (0 and 0.54%) and failed reactions (1.25% and 2.96%). In tests of analytical sensitivity the new TaqMan assay showed a very low detection threshold and can consequently be used on a single leg from a fresh or silica-dried mosquito without the need to first extract DNA.
Conclusion
This study describes a rapid and sensitive assay that very effectively identifies the two main malaria vectors of the An. gambiae species complex from the non-vector sibling species. The method is based on TaqMan SNP genotyping and can be used to screen single legs from dried specimens. In regions where An. merus/melas/bwambae, vectors with restricted distributions, are not present it can be used alone to discriminate vector from non-vector or in combination with the Walker TaqMan assay to distinguish An. arabiensis and An. gambiae s.s.
doi:10.1186/1475-2875-6-155
PMCID: PMC2213665  PMID: 18034887
21.  A Simple Saliva-Based Test for Detecting Antibodies to Human Immunodeficiency Virus* 
This study was performed to determine the feasibility of using saliva as a diagnostic medium for the detection of antibodies to human immunodeficiency virus type 1 (HIV-1) and HIV-2 under nonlaboratory conditions and to evaluate the performance characteristics of such a test. We developed for this purpose a self-contained kit (Saliva · Strip [ST]), which combines the collection and processing, as well as the analysis, of the specimen. The kit’s performance was evaluated in a blinded study. Saliva collection was facilitated with a specially designed device that contains a sample adequacy indicator, and immunochromatography test strips were used for the analysis. A total of 1,336 matched serum and saliva specimens (684 reactive and 652 nonreactive specimens) were tested. We tested sera using an enzyme immunoassay (EIA) and a rapid strip test. Sera reactive in one of the assays were also analyzed by Western blotting. Sensitivity and specificity were 99.4 and 99.4%, respectively, for ST, 100 and 99.1%, respectively, for EIA, and 99.7 and 100%, respectively, for the serum strip test. The saliva test performed well when HIV-2-positive sera or a low-titer performance panel (HIV-1) of serum or plasma specimens were diluted (1:2,000) in nonreactive saliva. Because the methodology we present here uses a noninvasively obtained medium, the methodology may be suitable for use in the field where laboratory support and personnel are limited, such as community outreach programs, doctors’ offices, surveillance studies, and community hospitals.
PMCID: PMC95731  PMID: 10391866
22.  Disparities in knowledge and willingness to donate research biospecimens: a mixed-methods study in an underserved urban community 
Journal of Community Genetics  2014;5(4):329-336.
Although research involving biospecimens is essential in advancing cancer research, minorities, especially African-Americans, are underrepresented in such research. We conducted a mixed-method (qualitative focus groups among African-Americans and quantitative cross-sectional surveys) study on factors associated with biospecimen knowledge and donation intent in the medically underserved urban communities in Southeast and Southwest Washington, DC. Focus groups were conducted among 41 African-Americans and survey data was available from 302 community residents of different races/ethnicities using convenience sampling. We used logistic regression to model the association between biospecimen knowledge and donation intent with selected sociodemographic variables using survey data. Only 47 % of the participants had knowledge of the different types of biospecimens. In multivariate logistic regression models, male gender, African-American race, and low education levels were significantly associated with lower knowledge about biospecimens. Compared to Whites (79 %), fewer African-Americans (39 %) and Hispanics (57 %) had knowledge of biospecimens but the difference was significant for African-Americans only. Positive intent to donate biospecimens for research was observed among 36 % of the survey respondents. After multivariate adjustment, only biospecimen knowledge was associated with donation intent (odds ratio = 1.91, 95 % confidence interval 1.12, 3.27). Contrary to popular opinion, “mistrust of the medical community” was not the most commonly reported barrier for biospecimen donation among African-Americans. “Not knowing how biospecimens will be used” and “lack of knowledge of biospecimens” were the most common barriers. Our study highlights the importance of education on biospecimens among community residents to increase minority participation in biospecimen research.
Electronic supplementary material
The online version of this article (doi:10.1007/s12687-014-0187-z) contains supplementary material, which is available to authorized users.
doi:10.1007/s12687-014-0187-z
PMCID: PMC4159473  PMID: 24771039
Biospecimen; Knowledge; African-American; Disparities
23.  Is pepsin detected in the saliva of patients who experience pharyngeal reflux? 
Hippokratia  2007;11(3):145-149.
Objectives: To investigate if pepsin is detected, with an activity assay, in the saliva of patients with a clinical diagnosis of laryngopharyngeal reflux (LPR) and can therefore be used as a diagnostic marker of laryngopharyngeal reflux.
Study design: Pilot, prospective study.
Methods: Adult participants with a clinical diagnosis of LPR collected whole saliva samples on regular intervals for a day, and upon experiencing symptoms attributed to LPR. Patients were selected on the basis of presence of severe symptoms and laryngoscopic findings of laryngopharyngeal reflux and symptoms of gastroesopharyngeal reflux. They reported voice disorders, dysphagia, throat clearing, excessive secretions, breathing difficulties, cough, globus sensation and throat pain. Control participants reported the absence of pharyngeal and laryngeal symptoms and of symptoms of gastroesophageal reflux. Saliva samples were assayed with fibrinogen on an agarose gel plate. The detection of pepsin was based on the presence of peptic activity which was qualitatively evaluated.
Results: The control participants had negative assays. No saliva samples from the LPR patients, collected at regular sampling, tested positive for pepsin. All the samples collected at the presence of symptoms and following regurgitation episodes tested negative for pepsin. Saliva samples pH ranged from 7 to 8.
Conclusions: Pepsin was not detected, with an activity assay, in the saliva of patients with a clinical diagnosis of LPR. A concentration method might be more sensitive although saliva and swallowing physiology renders the detection of pepsin in the saliva difficult.
PMCID: PMC2658799  PMID: 19582210
laryngopharyngeal reflux; pepsin; saliva; diagnosis; gastroesophageal reflux; laryngitis
24.  Feasibility of pharmacy-initiated pharmacogenetic screening for CYP2D6 and CYP2C19 
Purpose
Our purpose was to investigate the feasibility of pharmacy-initiated pharmacogenetic (PGt) screening in primary care with respect to patient willingness to participate, quality of DNA collection with saliva kits, genotyping, and dispensing data retrieved from the pharmacy.
Methods
Polypharmacy patients aged >60 years who used at least one drug with Anatomical Therapeutic Chemical (ATC) code N06AA01–N06AX19 (antidepressants), A02BC01–A02BC05 (proton-pump inhibitors), N05AA01–N05AH04 (antipsychotics), or C07AB02 (metoprolol) in the preceding 2 years were randomly selected. DNA was collected with saliva kits and genotyped for CYP2D6 and CYP2C19 with the AmpliChip. Pharmacy dispensing records were retrieved and screened for drugs interacting with the patient’s CYP2D6 and CYP2C19 genotype by using the evidence-based PGt guidelines from the Dutch Pharmacogenetics Working Group.
Results
Out of the 93 invited patients, 54 (58.1%) provided informed consent. Nine saliva samples (16.7%) contained too little DNA. Call rates for CYP2D6 and CYP2C19 were 93.3% and 100%, respectively. Frequencies of genotype-predicted phenotype were 2.4%, 38.1%, 54.8%, and 4.8% for CYP2D6 poor metabolizers (PM), intermediate metabolizers (IM), extensive metabolizers (EM), and ultrarapid metabolizers (UM) respectively. For CYP2C19 genotype-predicted phenotype, frequencies were 2.2%, 15.6%, and 82.2% for PM, IM, and EM, respectively.
Conclusions
This study shows that pharmacy-initiated PGt screening is feasible for a primary care setting.
doi:10.1007/s00228-011-1130-4
PMCID: PMC3303061  PMID: 21984116
Pharmacogenetics; Cytochrome P-450 CYP2D6; Cytochrome P-450 CYP2C19; Primary health care
25.  Randomised trial investigating the relationship of response rate for blood sample donation to site of biospecimen collection, fasting status and reminder letter: The 45 and Up Study 
Background
Various options exist for collecting biospecimens and biomarkers from cohort study participants, and these have important logistic, resource and scientific implications. Evidence on how different collection methods affect participation and data quality is lacking. This parallel-design randomised trial, the Link-Up Study, involved blood sample donation and other data collection among participants in an existing cohort study, The 45 and Up Study. It aimed to investigate the relation of fasting status, reminder letters and data collection site to response rates, data quality and biospecimen yield.
Methods
Individuals aged 45 and over participating in The 45 and Up Study and living ≤20 km from central Wagga Wagga, NSW (regional area) or ≤10 km from central Parramatta, NSW (urban area) (n = 2340) were randomised, stratified by area of residence, to be invited to give a blood sample and additional data by attending either a clinic established specifically for the trial, with an appointment time (“dedicated clinic”, n = 1336) or an existing local commercial pathology centre (n = 1004). Within dedicated clinic groups, participants were randomised into fasting (n = 668) or non-fasting (n = 668) and, at the Parramatta pathology centre site, reminder letter after two weeks (n = 336) or no reminder (n = 334).
Results
Overall, 33% (762/2340) of invitees took part in the Link-Up Study; 41% (410/1002) among regional and 26% (352/1338) among urban-area residents (p < 0.0001). At the dedicated clinics, response rates were 38% (257/668) not fasting and 38% fasting (257/668) (participation rate ratio (RR) = 1.00, 95%CI 0.91-1.08, p = 0.98). The response rate was 22% among individuals randomised to attend the Parramatta pathology centre without a reminder and 23% among those sent a reminder letter (RR = 1.01, 0.93-1.09, p = 0.74). In total, the response rate was 38% (514/1336) at the dedicated clinics and 25% (248/1004) at the pathology centres (RR = 0.67, 0.56-0.78, p < 0.01); measures of height, weight and systolic and diastolic blood pressure did not vary materially between these groups, nor did the median number of aliquots of plasma, buffy coat and red cells collected.
Conclusions
Among cohort study participants, response rates for an additional study involving biospecimen collection, but not data quality or average biospecimen yield, were considerably higher at dedicated clinics than at existing commercial pathology sites.
doi:10.1186/1471-2288-12-147
PMCID: PMC3532153  PMID: 23006657
Biobank; Response rate; Fasting status; Reminder; Biospecimens

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