Genomic DNA Extraction and STR Genotyping

Ten milliliters of venous blood were collected in EDTA as a source of peripheral blood leukocytes. Genomic DNA was extracted and purified according to established protocols^{35 (link),44 (link)} by using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). Five of the eight candidate STRs (TAAA-ACTG2, GAAA-GRHL2, TTTTG-TRIB1, TG-PCA3, CAAAA-MXI1, GAAA-PTGIS, and TTTTTG-PRUNE2) were genotyped in 40 individuals using the Applied Biosystems 3500 Genetic Analyser. Briefly, 40 cycles of PCR were carried out using the Multiplex PCR kit (QIAGEN) and fluorescently labelled primers (Supplementary Table S6) according to the manufacturer’s instructions. STR allele sizes were determined using GeneMapper v.5.0 (Life Technologies). Homozygous PCR products were sequenced (AGRF) and used as positive controls for the GeneMapper Software analysis. Similarly, the prostate cancer patient and control cohorts were genotyped for the PCA3 dinucleotide repeat using the Applied Biosystems 3500 Genetic Analyser.

Free full text: Click here

Lai J., Moya L., An J., Hoffman A., Srinivasan S., Panchadsaram J., Walpole C., Perry-Keene J.L., Chambers S., Lehman M.L., Nelson C.C., Clements J.A, & Batra J. (2017). A microsatellite repeat in PCA3 long non-coding RNA is associated with prostate cancer risk and aggressiveness. Scientific Reports, 7, 16862.

Publication 2017

QIAamp DNA Mini Kit 3500 Genetic Analyser Multiplex PCR kit GeneMapper v.5.0

Allele Biosystems Dinucleotide repeat Edta Genomic Homozygous Multiplex pcr Mxi1 Patient Pca3 Peripheral blood leukocytes Primers Prostate cancer Ptgis Venous blood

Corresponding Organization :

Other organizations : Translational Research Institute, Queensland Health, Griffith University, Queensland University of Technology, Sullivan Nicolaides Pathology

Top 5 similar protocols

Variable analysis

independent variables

Volume of venous blood collected (10 milliliters)
Source of peripheral blood leukocytes (venous blood)

dependent variables

Genomic DNA extraction and purification
Genotyping of candidate STRs (TAAA-ACTG2, GAAA-GRHL2, TTTTG-TRIB1, TG-PCA3, CAAAA-MXI1, GAAA-PTGIS, and TTTTTG-PRUNE2) in 40 individuals
Genotyping of the PCA3 dinucleotide repeat in prostate cancer patient and control cohorts

control variables

EDTA as the anticoagulant for blood collection
Established protocols for genomic DNA extraction and purification (references 35 and 44)
Use of the QIAamp DNA Mini Kit for DNA extraction
Homozygous PCR products as positive controls for GeneMapper Software analysis
Applied Biosystems 3500 Genetic Analyser for STR genotyping

controls

Homozygous PCR products as positive controls for GeneMapper Software analysis

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!