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Og 500

Manufactured by DNA Genotek
Sourced in Canada

The OG-500 is a laboratory collection device designed to collect and preserve DNA samples. It provides a reliable and convenient method for collecting high-quality DNA samples from individuals.

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9 protocols using og 500

1

Salivary DNA Extraction and SNP Genotyping

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Genomic DNA was isolated from salivary samples by means of OG-500 (DNA Genotek, Stittsville, ON, Canada) Oragene using the protocol recommended by the manufacturer.
Genotyping of the selected single-nucleotide variations was conducted through the application of restriction length polymorphism analysis [23 (link),24 (link)]; the methods are summarized in Table 1.
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2

Saliva DNA extraction and genotyping

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DNA was extracted from Oragene OG-500 (adults) and OG-575 (babies) saliva kits using Oragene prepIT (PT-L2P-5) extraction kit (supplied by DNA Genotek). DNA yield was measured by Qubit (ThermoFisher). Samples were genotyped on a panel of Taqman single nucleotide polymorphisms (SNPs) using the QuantStudio12K Flex and analysed using
QuantStudio v1.2.2 software. Samples from mothers were genotyped using autosomal SNPs
rs6427699,
rs4751955,
rs11083515,
rs7588807,
rs10938367 &
rs10869955. Samples from babies were run on the same six autosomal SNPs and an additional three SNPs from the Y-chromosome to determine sex (
rs2032598,
rs768983 &
rs3913290). An aliquot of DNA was normalised in plates for future analysis. DNA samples were transferred for storage and used as part of the Edinburgh Reproductive Tissues Biobank (REC reference 09/S0704/3).
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3

Genotyping of Infantile Nystagmus Patients

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As part of a large-scale genotyping project, patients with IN (n = 511) were recruited at one centre in the UK (University Hospitals of Leicester) and two centres in Korea (Yonsei University College of Medicine and University of Ulsan College of Medicine) over a period of 5 years (2014–2019). Informed consent was obtained from all participants involved. The study was approved with a local ethics committee and all aspects of the study were conducted in accordance with the Tenets of the Declaration of Helsinki.
The details of our pilot genotyping project have been previously described (14 (link),15 (link)). Briefly, this included extraction of genomic DNA from saliva samples (DNA Genotek OG-500 and OG-575 Oragene saliva kits (Ottawa, Ontario, Canada)) or peripheral blood and subsequently performing targeted NGS using our nystagmus gene capture panels or whole exome sequencing. Our nystagmus gene panels included all known nystagmus genes described in the literature (14 (link),15 (link)). Our initial panels were revised to also include the recently identified nystagmus gene, AHR, mutations of which we have described to be causative of IN and FH (33 (link)). Our aim was to identify the prevalence of SLC38A8 mutations in our cohorts and describe the phenotypical characteristics.
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4

Whole Exome Sequencing Variant Identification

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Genomic DNA was extracted with the use of kits that were designed to obtain saliva samples (OG-500, DNA Genotek) or peripheral blood (QIAamp DNA Blood Mini Kit, Qiagen, Hilden, Germany), according to the manufacturer’s instructions. WES was performed in the CCHMC Genetic Variation and Gene Discovery Core, the Oklahoma Medical Research Foundation (OMRF) Genomics facility, Perkin Elmer, and Broad Institute. Libraries were prepared using the Illumina TruSeq capture kit and sequenced on an Illumina HiSeq2000 or HiSeq4000 to generate 100–150-base, paired-end reads. Sequencing reads were aligned using Burrows–Wheeler Aligner (BWA) and GRCh37 human reference genome, and variant calls were made simultaneously following the Genome Analysis Toolkit (GATK) Best Practices by using the GATK Unified Genotyper43 (link)–45 .
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5

Genotyping E756del Mutation

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At the end of the study visit, saliva samples were collected with a DNA collection kit (OG-500, DNA Genotek, Canada). Genomic DNA was isolated according to the manufacturer’s instructions (prepIT-L2P, DNA Genotek, Canada). The E756 locus was amplified with the primers described in Ma et al. (26 (link)), and the amplicon was sequenced (Microsynth AG, Switzerland) to distinguish E756del carriers from noncarriers.
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6

Waterpipe Smoking Effects on Oral Cells

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Participants: Waterpipe smokers (N=150; > 5 uses/month for at least 3 year; no other tobacco products lifetime) and never-tobacco users (N=150; age- and sex-matched) were recruited through advertisements distributed via university employee e-mail directory (about 5000 employee) as well as print and online media such as WhatsApp. In addition, waterpipe smokers were directly recruited from waterpipe cafes and restaurants. Most of the participants (90%) were from Middle (Capital) and Northern (Irbid, Jarash and Ajloun) regions of Jordan. Exclusion criteria included chronic or acute illness and any prescription medication use. To achieve good distribution of age and gender, the sample included in the study (150 waterpipe smokers and 150 controls) was selected from about 480 subjects who met the inclusion criteria. Written, informed consent was obtained from all participants according to Institutional Review Boards of Jordan University of Science and Technology and Virginia Commonwealth University.
Collection of samples: Oral epithelial cells were collected by using Oragene DNA collection kit from saliva as described by the manufacturer (OG-500, DNA Genotek Inc., Ontario, Canada). Blood samples (~5 ml) were obtained via venipuncture in sterile vacutainer EDTA tubes. Samples were stored at −80° C until used (Zavodnik et al., 1998).
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7

Biospecimen Collection Kit Protocols

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Biospecimen collection kits containing all necessary materials were assembled and placed in a quart-sized Ziploc bag, with illustrated and written instructions for participants for each type of biospecimen. For hair collection for HCC, we included an envelope with client ID label, rubber band, gloves, notecard and adhesive to indicate location of the roots from the hair provided. For saliva collection for TL, we included an Oragene saliva kit (DNA Genotek OG-500) and a small Ziploc bag labeled with the client ID number. Lastly, for self-collection of saliva samples for CAR, we included color-coded and numbered tubes in a storage box, color-coded straw-like aides to transfer saliva to tubes, and a log to record time of collection and notes regarding any unusual activity.
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8

MC1R Genetic Variation Analysis

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Genomic DNA was isolated from peripheral blood lymphocytes or from epithelial cells in saliva samples.
Genomic DNA from the Spanish cohort blood samples was isolated using the CMG-715 Chemagic TM DNA blood kit with the automated method Chemagic TM MSM1 (Chemagen, Baesweiler, Germany), or using an Autopure LS (Qiagen, Hilden, Germany) workflow from the Marseille cohort samples. Saliva was collected in OG-500 or OG-575 Oragene® saliva collection kits, depending on the age of the patient, and DNA was extracted using the prepIT®-L2P reagents (DNAGenotek, Ontario, Canada). Polymerase chain reaction (PCR) was used to amplify two overlapping fragments of the MC1R coding region using the following primers: NT-F, 5'-TGTAAAACGACGGCCAGTGCAGCACCATGAACTAAGCA-3' together with TM-R, 5'-CAGGAAACAGCTATGACCTTTAAGGCCAAAGCCCTGGT-3'; and CT-R, 5'-CAGGAAACAGCTATGACCCAGGGTCACACAGGAACCA-3' together with TM-F, 5'-TGTAAAACGACGGCCAGTAACCTGCACTCACCCATGTA-3'. The thermal cycling conditions were as follows: 1 cycle of denaturation at 95ºC for 5 min, 35 amplification cycles (94ºC for 1 min, 55ºC for 1 min, and 72ºC for 3 min), and a final extension at 72ºC for 10 min. The entire MC1R coding region was sequenced using universal M13 primers by GENEWIZ (Takeley, UK). Sequences were analyzed using SeqPilot 4.0.1 software (JSI Medical Systems, Ettenheim, Germany).
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9

MC1R Genetic Variation Analysis

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Genomic DNA was isolated from peripheral blood lymphocytes or from epithelial cells in saliva samples.
Genomic DNA from the Spanish cohort blood samples was isolated using the CMG-715 Chemagic TM DNA blood kit with the automated method Chemagic TM MSM1 (Chemagen, Baesweiler, Germany), or using an Autopure LS (Qiagen, Hilden, Germany) workflow from the Marseille cohort samples. Saliva was collected in OG-500 or OG-575 Oragene® saliva collection kits, depending on the age of the patient, and DNA was extracted using the prepIT®-L2P reagents (DNAGenotek, Ontario, Canada). Polymerase chain reaction (PCR) was used to amplify two overlapping fragments of the MC1R coding region using the following primers: NT-F, 5'-TGTAAAACGACGGCCAGTGCAGCACCATGAACTAAGCA-3' together with TM-R, 5'-CAGGAAACAGCTATGACCTTTAAGGCCAAAGCCCTGGT-3'; and CT-R, 5'-CAGGAAACAGCTATGACCCAGGGTCACACAGGAACCA-3' together with TM-F, 5'-TGTAAAACGACGGCCAGTAACCTGCACTCACCCATGTA-3'. The thermal cycling conditions were as follows: 1 cycle of denaturation at 95ºC for 5 min, 35 amplification cycles (94ºC for 1 min, 55ºC for 1 min, and 72ºC for 3 min), and a final extension at 72ºC for 10 min. The entire MC1R coding region was sequenced using universal M13 primers by GENEWIZ (Takeley, UK). Sequences were analyzed using SeqPilot 4.0.1 software (JSI Medical Systems, Ettenheim, Germany).
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