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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.  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
8.  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
9.  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
10.  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
11.  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
12.  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
13.  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
14.  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
15.  A universal pre-analytic solution for concurrent stabilization of salivary proteins, RNA and DNA at ambient temperature 
Archives of oral biology  2008;54(3):268-273.
Objective
Saliva is a biofluid that can be obtained from individuals without supervision by health care providers. To maximize this clinical advantage, it is highly desirable to have a global salivary analyte stabilizer for proteins, RNA and DNA at ambient temperature.
Design
Whole saliva, saliva supernatant and saliva filtrate (5.0 μm) were treated with RPS at room temperature (RT) for up to 6 days and then subjected to SDS-PAGE. Immunoblotting of β-actin and cystatin C were used to evaluate protein stability. For salivary DNA/RNA, whole saliva was incubated with RPS at RT for up to 10 weeks. After extracting total DNA/RNA in samples at week 0, 2, 6 and 10, DNA stability was assayed by chromosome 18 DNA qPCR and RNA stability by β-actin mRNA RT-qPCR.
Results
β-actin completely degraded in all types of saliva samples after 6-day incubation at RT. However, 24.0%, 91.4% and 89.3% of β-actin remained intact with RPS for whole saliva, saliva supernatant and filtrate, respectively. Similarly, 70.3% of cystatin C in supernatant remained intact in the presence of RPS. For salivary DNA/RNA, the cycle threshold (Ct) values showed no significant change for chromosome 18 DNA and β-actin mRNA in RPS-incubated saliva during the 10-week time course while significant increase in Ct values were observed in controls without RPS for both β-actin mRNA and DNA.
Conclusions
RPS provided effective concurrent stabilization to salivary DNA/RNA in whole saliva for up to 10 weeks and proteins in saliva filtrate for 6 days at RT. We also achieved separation of saliva supernatant from cellular elements by a simple filtration step (bypassing the need for centrifugation).
doi:10.1016/j.archoralbio.2008.10.004
PMCID: PMC2674508  PMID: 19047016
Saliva diagnostics; Saliva stabilizer; Salivary biomarkers; Proteins; DNA; RNA
16.  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
17.  Aggregation and Adherence of Streptococcus sanguis: Role of Human Salivary Immunoglobulin A 
Infection and Immunity  1979;26(3):1104-1110.
Fourteen freshly isolated strains of Streptococcus sanguis were obtained from the dental plaque of five healthy adults. Whole saliva was collected concomitant with the plaque isolates from the five subjects, and a second whole saliva sample was collected 10 weeks later. All possible combinations of the first five saliva samples, the second five saliva samples, and 14 strains of bacteria were tested for aggregation. Of the 140 combinations examined, 108 of 140 (77%) of the strains aggregated with the first saliva samples and 95 of 140 (68%) aggregated with the second saliva samples. Overall, 72% of the strains aggregated with both the first and second saliva samples. Removal of immunoglobulin A (IgA) from these same salivas resulted in 38 of 108 (35%) of the aggregates decreasing in intensity with the first saliva samples and 27 of 95 (29%) of the aggregates decreasing in intensity with the second saliva samples. No aggregates increased in intensity with saliva samples when IgA had been removed. Removal of IgA from saliva also resulted in a mean decrease of 46% in adherence of S. sanguis to hydroxyapatite coated with the IgA-deficient saliva. Several strains of S. sanguis were shown to aggregate strongly with human salivary and colostral IgA. In addition, S. sanguis strain S7 showed a 31% stimulation of adherence to hydroxyapatite precoated with human salivary IgA over the uncoated controls. Stepwise removal of IgA from saliva resulted in a decrease in aggregation intensity from strong (4+) to weak (1+ to 2+). Similarly, the adherence of S. sanguis to hydroxyapatite coated with these saliva samples decreased linearly as the salivary IgA was depleted. Alternatively, the addition of a small quantity of salivary IgA (20 μg/ml) to progressively diluted saliva maintained a high level of adherence and strong aggregation until the saliva dilutions reached between 1:8 in the adherence experiments and 1:32 for the aggregations. These data indicate that salivary IgA may play an important role in the microbial ecology of human dental plaque formation.
PMCID: PMC414734  PMID: 528050
18.  Common Data Elements for Pediatric Traumatic Brain Injury: Recommendations from the Biospecimens and Biomarkers Workgroup 
Journal of Neurotrauma  2012;29(4):672-677.
Abstract
Biospecimens represent a critically important resource in pediatric brain injury research. Data from these specimens can be used to identify and classify injury, understand the molecular mechanisms underlying different types of brain injury, and ultimately identify therapeutic targets to tailor treatments for individual patient needs. To realize the full potential of biospecimens in pediatric traumatic brain injury (TBI), standardization and adoption of best practice guidelines are needed to ensure the quality and consistency of specimens. Multiple groups, including the National Cancer Institute (NCI), the International Society for Biological and Environmental Repositories (ISBER), and the Organisation for Economic Co-operation and Development (OECD), have previously published best practice guidelines for biospecimen resources. Recommendations have also been provided by the Biospecimens and Biomarkers Workgroup of the interagency TBI Common Data Elements (CDE) initiative. The recommendations from all of these sources, however, focus exclusively on adult biospecimen collection. There are no published pediatric-specific biospecimen collection guidelines. An additional workgroup was formed to specifically address this gap. The aim of the Pediatric TBI CDE Biospecimens and Biomarkers Workgroup was to provide recommendations for best practice guidelines to standardize the quality and accessibility of biospecimens for pediatric brain injury research in general, and for pediatric TBI research in particular. Consensus recommendations were developed by review of previously published adult-specific recommendations, including the recommendations of the original TBI Common Data Elements Biospecimens and Biomarkers Workgroup, and by participation in the interagency workshop “Common Data Elements for TBI Research: Pediatric Considerations,” held in Houston, Texas in March of 2010. These recommendations represent expert opinion on this subject. The authors of this article were members of the Biospecimens Workgroup. We hope that with adoption of these best practices, future investigators will be able to obtain biospecimens in a consistent way that meets the needs of pediatric patients, and helps to accelerate acquisition of pediatric-specific biomarker data.
doi:10.1089/neu.2011.1861
PMCID: PMC3289842  PMID: 22106839
best practices; biomarkers; common data elements; pediatrics; standardization; traumatic brain injury
19.  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
20.  Designing prospective cohort studies for assessing reproductive and developmental toxicity during sensitive windows of human reproduction and development – the LIFE Study 
Summary
Buck Louis GM, Schisterman EF, Sweeney AM, Wilcosky TC, Gore-Langton RE, Lynch CD, Boyd Barr D, Schrader SM, Kim S, Chen Z, Sundaram R, on behalf of the LIFE Study. Designing prospective cohort studies for assessing reproductive and developmental toxicity during sensitive windows of human reproduction and development – the LIFE Study. Paediatric and Perinatal Epidemiology 2011; 25: 413–424.
The relationship between the environment and human fecundity and fertility remains virtually unstudied from a couple-based perspective in which longitudinal exposure data and biospecimens are captured across sensitive windows. In response, we completed the LIFE Study with methodology that intended to empirically evaluate a priori purported methodological challenges: implementation of population-based sampling frameworks suitable for recruiting couples planning pregnancy;obtaining environmental data across sensitive windows of reproduction and development;home-based biospecimen collection; anddevelopment of a data management system for hierarchical exposome data.
We used two sampling frameworks (i.e. fish/wildlife licence registry and a direct marketing database) for 16 targeted counties with presumed environmental exposures to persistent organochlorine chemicals to recruit 501 couples planning pregnancies for prospective longitudinal follow-up while trying to conceive and throughout pregnancy. Enrolment rates varied from <1% of the targeted population (n = 424 423) to 42% of eligible couples who were successfully screened; 84% of the targeted population could not be reached, while 36% refused screening. Among enrolled couples, ~85% completed daily journals while trying; 82% of pregnant women completed daily early pregnancy journals, and 80% completed monthly pregnancy journals. All couples provided baseline blood/urine samples; 94% of men provided one or more semen samples and 98% of women provided one or more saliva samples. Women successfully used urinary fertility monitors for identifying ovulation and home pregnancy test kits.
Couples can be recruited for preconception cohorts and will comply with intensive data collection across sensitive windows. However, appropriately sized sampling frameworks are critical, given the small percentage of couples contacted found eligible and reportedly planning pregnancy at any point in time.
doi:10.1111/j.1365-3016.2011.01205.x
PMCID: PMC4118054  PMID: 21819423
cohort; environment; fecundity; fertility; LIFE Study; preconception; pregnancy; study design; enrolment
21.  Monitoring HIV vaccine trial participants for primary infection: studies in the SIV/macaque model 
AIDS (London, England)  2009;23(12):1453-1460.
Objectives
The ability to detect and quantify acute HIV-1 infection prior to seroconversion would be an important tool for use in HIV vaccine clinical efficacy trials. We have utilized the SIV/rhesus monkey model to evaluate whether samples more easily obtained than peripheral blood might be used for intensive monitoring of vaccine trial participants.
Methods
We have evaluated viral loads in peripheral blood, saliva, feces, and urine of five rhesus monkeys during primary SIVmac251 infection by quantitative real-time PCR. As an alternative to the direct monitoring of frozen samples, we have also developed a fully quantitative viral load assay utilizing dried blood spots.
Results
Although all compartments were found to harbor viral RNA during primary infection, viral RNA could be detected in the peripheral compartments only when levels of plasma viremia exceed a threshold value of 104 RNA copies/ml. We found no direct correlation between viral burden in plasma and saliva, feces, or urine viral loads. Importantly, both dried saliva and whole blood spots can be used for viral detection. Quantitative whole blood or plasma spotting correlated well with viral burden in plasma during both the acute and set point phase of infection.
Conclusion
Dried blood spots are amenable to rapid quantitative viral load testing. Whole blood spotting has a significant logistical benefit as it requires low blood volumes and no blood processing. Saliva or dried saliva spots or both are potential candidates for acute phase diagnostic screening. These studies indicate the feasibility of intensive monitoring of HIV-1 vaccine trial participants for virus acquisition in resource-limited settings.
doi:10.1097/QAD.0b013e32832b43d9
PMCID: PMC2776694  PMID: 19550289
acute HIV infection; HIV-1 infection monitoring; simian immunodeficiency virus
22.  Quantitative detection of PfHRP2 in saliva of malaria patients in the Philippines 
Malaria Journal  2012;11:175.
Background
Malaria is a global health priority with a heavy burden of fatality and morbidity. Improvements in field diagnostics are needed to support the agenda for malaria elimination. Saliva has shown significant potential for use in non-invasive diagnostics, but the development of off-the-shelf saliva diagnostic kits requires best practices for sample preparation and quantitative insight on the availability of biomarkers and the dynamics of immunoassay in saliva. This pilot study measured the levels of the PfHRP2 in patient saliva to inform the development of salivary diagnostic tests for malaria.
Methods
Matched samples of blood and saliva were collected between January and May, 2011 from eight patients at Palawan Baptist Hospital in Roxas, Palawan, Philippines. Parasite density was determined from thick-film blood smears. Concentrations of PfHRP2 in saliva of malaria-positive patients were measured using a custom chemiluminescent ELISA in microtitre plates. Sixteen negative-control patients were enrolled at UCLA. A substantive difference between this protocol and previous related studies was that saliva samples were stabilized with protease inhibitors.
Results
Of the eight patients with microscopically confirmed P. falciparum malaria, seven tested positive for PfHRP2 in the blood using rapid diagnostic test kits, and all tested positive for PfHRP2 in saliva. All negative-control samples tested negative for salivary PfHRP2. On a binary-decision basis, the ELISA agreed with microscopy with 100 % sensitivity and 100 % specificity. Salivary levels of PfHRP2 ranged from 17 to 1,167 pg/mL in the malaria-positive group.
Conclusion
Saliva is a promising diagnostic fluid for malaria when protein degradation and matrix effects are mitigated. Systematic quantitation of other malaria biomarkers in saliva would identify those with the best clinical relevance and suitability for off-the-shelf diagnostic kits.
doi:10.1186/1475-2875-11-175
PMCID: PMC3422183  PMID: 22631858
23.  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
24.  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
25.  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

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