Development and validation of the high-quality 'rapid method for swab' to genotype the HTTLPR serotonin transporter (SLC6A4) promoter DOlvmorDhism

Bryan Maloney, Balmiki Ray, Elizabeth R. Hayden, John Nurnberger, Debomoy Lahiri

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Background The importance of genetic variation to the etiology of neuropsychiatric disorders is well established and is currently being examined for diagnosis and treatment. The most popular method of obtaining material for genotype analysis, high-yielding DNA extraction from blood, has several limitations, including invasiveness, need for skilled individuals to collect material, and requirement for cold storage. Saliva sampling is noninvasive and trained personnel are less necessary, but it still requires a relatively high level of subject compliance. Buccal mucosa cells sampling is almost completely noninvasive, reducing compliance issues significantly. Samples collected have been shown to produce usable DNA after shipment through conventional mail. The DNA produced by rapid elution of these swabs in chaotropic buffers is, however, of limited quality and low purity. Objective Our aim was to develop a rapid, economical, and environmentally safe method for extraction of high-quality genomic DNA, which can be used to determine clinically important genotypes from trace quantity samples and which has sufficient yield for multiple assays. Methods We developed a method of extracting high-quality genomic DNA from buccal swab, which we termed the 'rapid method for swab' (RMS). We compared RMS with two established procedures, specifically the original rapid method and the commercially available Buccal Amp method. We assessed the generated genomic DNAs by their (i) quality, (ii) quantity, (iii) restriction enzyme digestibility, and (iv) PCR-based genotyping in addition to time, cost, and environmental impact of the procedures. Main results DNA generated by RMS was of higher purity than that by Buccal Amp. RMS is nonenzymatic and does not use strong chaotropic salts or extreme pH. We also showed the suitability of RMS-DNA for L A/LG genotyping as generated by PCR using 7-deaza-dGTP. Conclusion The RMS procedure is novel, efficient, safe, and yields sufficient material for multiple genotyping analyses. The RMS produces DNA of high quality from a single human buccal swab. RMS is a noninvasive technique and particularly suitable for children and older individuals and in field collection settings.

Original languageEnglish
Pages (from-to)72-82
Number of pages11
JournalPsychiatric Genetics
Volume19
Issue number2
DOIs
StatePublished - Apr 2009

Fingerprint

Serotonin Plasma Membrane Transport Proteins
Genotype
DNA
Cheek
Polymerase Chain Reaction
Mouth Mucosa
Postal Service

Keywords

  • Buccal mucosa
  • DNA
  • DNA purification
  • Genomic DNA
  • Genotyping
  • HTTLPR
  • Large sample size
  • Nucleic acid
  • Serotonin transporter gene
  • Swab

ASJC Scopus subject areas

  • Genetics(clinical)
  • Psychiatry and Mental health
  • Genetics
  • Biological Psychiatry

Cite this

Development and validation of the high-quality 'rapid method for swab' to genotype the HTTLPR serotonin transporter (SLC6A4) promoter DOlvmorDhism. / Maloney, Bryan; Ray, Balmiki; Hayden, Elizabeth R.; Nurnberger, John; Lahiri, Debomoy.

In: Psychiatric Genetics, Vol. 19, No. 2, 04.2009, p. 72-82.

Research output: Contribution to journalArticle

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abstract = "Background The importance of genetic variation to the etiology of neuropsychiatric disorders is well established and is currently being examined for diagnosis and treatment. The most popular method of obtaining material for genotype analysis, high-yielding DNA extraction from blood, has several limitations, including invasiveness, need for skilled individuals to collect material, and requirement for cold storage. Saliva sampling is noninvasive and trained personnel are less necessary, but it still requires a relatively high level of subject compliance. Buccal mucosa cells sampling is almost completely noninvasive, reducing compliance issues significantly. Samples collected have been shown to produce usable DNA after shipment through conventional mail. The DNA produced by rapid elution of these swabs in chaotropic buffers is, however, of limited quality and low purity. Objective Our aim was to develop a rapid, economical, and environmentally safe method for extraction of high-quality genomic DNA, which can be used to determine clinically important genotypes from trace quantity samples and which has sufficient yield for multiple assays. Methods We developed a method of extracting high-quality genomic DNA from buccal swab, which we termed the 'rapid method for swab' (RMS). We compared RMS with two established procedures, specifically the original rapid method and the commercially available Buccal Amp method. We assessed the generated genomic DNAs by their (i) quality, (ii) quantity, (iii) restriction enzyme digestibility, and (iv) PCR-based genotyping in addition to time, cost, and environmental impact of the procedures. Main results DNA generated by RMS was of higher purity than that by Buccal Amp. RMS is nonenzymatic and does not use strong chaotropic salts or extreme pH. We also showed the suitability of RMS-DNA for L A/LG genotyping as generated by PCR using 7-deaza-dGTP. Conclusion The RMS procedure is novel, efficient, safe, and yields sufficient material for multiple genotyping analyses. The RMS produces DNA of high quality from a single human buccal swab. RMS is a noninvasive technique and particularly suitable for children and older individuals and in field collection settings.",
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AB - Background The importance of genetic variation to the etiology of neuropsychiatric disorders is well established and is currently being examined for diagnosis and treatment. The most popular method of obtaining material for genotype analysis, high-yielding DNA extraction from blood, has several limitations, including invasiveness, need for skilled individuals to collect material, and requirement for cold storage. Saliva sampling is noninvasive and trained personnel are less necessary, but it still requires a relatively high level of subject compliance. Buccal mucosa cells sampling is almost completely noninvasive, reducing compliance issues significantly. Samples collected have been shown to produce usable DNA after shipment through conventional mail. The DNA produced by rapid elution of these swabs in chaotropic buffers is, however, of limited quality and low purity. Objective Our aim was to develop a rapid, economical, and environmentally safe method for extraction of high-quality genomic DNA, which can be used to determine clinically important genotypes from trace quantity samples and which has sufficient yield for multiple assays. Methods We developed a method of extracting high-quality genomic DNA from buccal swab, which we termed the 'rapid method for swab' (RMS). We compared RMS with two established procedures, specifically the original rapid method and the commercially available Buccal Amp method. We assessed the generated genomic DNAs by their (i) quality, (ii) quantity, (iii) restriction enzyme digestibility, and (iv) PCR-based genotyping in addition to time, cost, and environmental impact of the procedures. Main results DNA generated by RMS was of higher purity than that by Buccal Amp. RMS is nonenzymatic and does not use strong chaotropic salts or extreme pH. We also showed the suitability of RMS-DNA for L A/LG genotyping as generated by PCR using 7-deaza-dGTP. Conclusion The RMS procedure is novel, efficient, safe, and yields sufficient material for multiple genotyping analyses. The RMS produces DNA of high quality from a single human buccal swab. RMS is a noninvasive technique and particularly suitable for children and older individuals and in field collection settings.

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