DNA extraction from fresh and frozen plasma: an alternative for real-time PCR genotyping in pharmacogenetics.
DNA extraction
Pharmacogenetics
Plasma
Polymorphisms
Real time PCR
Journal
Molecular biology reports
ISSN: 1573-4978
Titre abrégé: Mol Biol Rep
Pays: Netherlands
ID NLM: 0403234
Informations de publication
Date de publication:
Aug 2020
Aug 2020
Historique:
received:
29
04
2020
accepted:
11
07
2020
pubmed:
25
7
2020
medline:
27
5
2021
entrez:
25
7
2020
Statut:
ppublish
Résumé
Genomic DNA, extracted from whole blood samples, is a key element for all genotyping workflows. When stored serum or plasma is the only source of DNA available, the main problem to overcome is the low quantity and poor quality of the DNA obtained, irrespective of the isolation procedure applied. The prevalence of artifacts, such as unbalanced amplification of alleles at specific sites (allelic dropout), is typically associated with PCR amplification of low quality/quantity DNA template, which is known to promote genotyping errors. The aim of this study was to determine whether the quality of genomic DNA from plasma samples may affect genotyping results. The ABCB1 c.3435C>T polymorphism was determined with two different real-time PCR assays, LightSNiP and TaqMan assays. We observed higher signal fluorescence values with DNA isolated from whole blood samples than with those from fresh and frozen plasma samples, due to reduced DNA concentration in the second ones. Despite the signal strength, a 100% concordance of genotyping data was however obtained in both assay types, regardless of the method of extraction. Our results show that, regardless of the lower DNA yield, extraction from plasma samples can still represent a valid alternative for real-time PCR genotyping application.
Identifiants
pubmed: 32705507
doi: 10.1007/s11033-020-05664-4
pii: 10.1007/s11033-020-05664-4
doi:
Substances chimiques
ABCB1 protein, human
0
ATP Binding Cassette Transporter, Subfamily B
0
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6451-6455Subventions
Organisme : Ministero della Salute
ID : RF-2016-02363761
Références
Carpi FM, Di Pietro F, Vincenzetti S, Mignini F, Napolioni V (2011) Human DNA extraction methods: patents and applications. Recent Pat DNA Gene Seq Rev. https://doi.org/10.2174/187221511794839264
doi: 10.2174/187221511794839264
Hanks E, Todd H, Palarea-Albaladejo J, McNeilly TN, Britton C, Ballingall KT (2020) A novel technique for retrospective genetic analysis of the response to vaccination or infection using cell-free DNA from archived sheep serum and plasma. Vet Res. https://doi.org/10.1186/s13567-020-0737-9
doi: 10.1186/s13567-020-0737-9
pubmed: 32024546
pmcid: 7003321
Clendenen TV, Rendleman J, Ge W, Koenig KL, Wirgin I, Currie D, Shore RE, Kirchhoff T, Zeleniuch-Jacquotte A (2015) Genotyping of single nucleotide polymorphisms in DNA isolated from serum using sequenom MassARRAY technology. PLoS ONE. https://doi.org/10.1371/journal.pone.0135943
doi: 10.1371/journal.pone.0135943
pubmed: 26488576
pmcid: 4619526
Catsburg A, van der Zwet WC, Morré SA, Ouburg S, Vandenbroucke-Grauls CM, Savelkoul PH (2007) Analysis of multiple single nucleotide polymorphisms (SNP) on DNA traces from plasma and dried blood samples. J Immunol Methods. https://doi.org/10.1016/j.jim.2007.01.015
doi: 10.1016/j.jim.2007.01.015
pubmed: 17321541
Chacon-Cortes D, Griffiths LR (2014) Methods for extracting genomic DNA from whole blood samples: current perspectives. J Biorepository Sci Appl Med. https://doi.org/10.1007/s10592-006-9194-x
doi: 10.1007/s10592-006-9194-x
Fleischhacker M, Schmidt B, Weickmann S, Fersching DM, Leszinski GS, Siegele B, Stötzer OJ, Nagel D, Holdenrieder S (2011) Methods for isolation of cell-free plasma DNA strongly affect DNA yield. Clin Chim Acta. https://doi.org/10.1016/j.cca.2011.07.011
doi: 10.1016/j.cca.2011.07.011
pubmed: 21861994
Soulsbury CD, Iossa G, Edwards KJ, Baker PJ, Harris S (2007) Allelic dropout from a high-quality DNA source. Conserv Genet. https://doi.org/10.1007/s10592-006-9194-x
doi: 10.1007/s10592-006-9194-x
Hodges LM, Markova SM, Chinn LW, Gow JM, Kroetz DL, Klein TE, Altmana RB (2012) Very important pharmacogene summary: ABCB1 (MDR1, P-glycoprotein). Pharmacogenet Genomics. https://doi.org/10.1097/FPC.0b013e3283385a1c
Croft DT Jr, Jordan RM, Patney HL, Shriver CD, Vernalis MN, Orchard TJ, Ellsworth DL (2008) Performance of whole-genome amplified DNA isolated from serum and plasma on high-density single nucleotide polymorphism arrays. J Mol Diagn. https://doi.org/10.2353/jmoldx.2008.070155
doi: 10.2353/jmoldx.2008.070155
pubmed: 18403606
pmcid: 2329790
Hoque A, Goodman P, Ambrosone CB, Figg WD, Price DK, Kopp W, Wu X, Conroy J, Lehman TA, Santella RM (2008) Extraction of DNA from serum for high-throughput genotyping: findings from pilot studies within the Prostate Cancer Prevention Trial. Urology 71(5):967–970. https://doi.org/10.1016/j.urology.2007.11.042
doi: 10.1016/j.urology.2007.11.042
pubmed: 18267333
pmcid: 2387066