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
Og 500
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.
Lab products found in correlation
9 protocols using og 500
Salivary DNA Extraction and SNP Genotyping
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
Saliva DNA extraction and genotyping
Genotyping of Infantile Nystagmus Patients
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.
Whole Exome Sequencing Variant Identification
Genotyping E756del Mutation
Waterpipe Smoking Effects on Oral Cells
Biospecimen Collection Kit Protocols
MC1R Genetic Variation Analysis
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).
MC1R Genetic Variation Analysis
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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