Abstract
BackgroundMicroarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology. This new technique uses pooled DNA, thereby reducing costs associated with the typing of DNA from numerous individuals. Moreover, use of an oligonucleotide gene chip reduces costs related to processing various DNA segments (e.g., primers, reagents). Thus, the technique provides an overall cost-effective solution for large-scale genomic/genetic research. However, few publicly shared tools are available to systematically analyze the rapidly accumulating volume of whole-genome pooled DNA data.ResultsWe propose a generalized concept of pooled DNA and present a user-friendly tool named Microarray Pooled DNA Analyzer (MPDA) that we developed to analyze hybridization intensity data from microarray-based pooled DNA experiments. MPDA enables whole-genome DNA preferential amplification/hybridization analysis, allele frequency estimation, association mapping, allelic imbalance detection, and permits integration with shared data resources online. Graphic and numerical outputs from MPDA support global and detailed inspection of large amounts of genomic data. Four whole-genome data analyses are used to illustrate the major functionalities of MPDA. The first analysis shows that MPDA can characterize genomic patterns of preferential amplification/hybridization and provide calibration information for pooled DNA data analysis. The second analysis demonstrates that MPDA can accurately estimate allele frequencies. The third analysis indicates that MPDA is cost-effective and reliable for association mapping. The final analysis shows that MPDA can identify regions of chromosomal aberration in cancer without paired-normal tissue.ConclusionMPDA, the software that integrates pooled DNA association analysis and allelic imbalance analysis, provides a convenient analysis system for extensive whole-genome pooled DNA data analysis. The software, user manual and illustrated examples are freely available online at the MPDA website listed in the Availability and requirements section.
Highlights
Microarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology
Whole-genome CPA analysis Preferential amplification/hybridization, which is quantified by CPA, is a major factor interfering with the estimation of AF in pooled DNA studies
Subjects who were heterozygous with respect to single nucleotide polymorphisms (SNPs) from the 367 subjects were selected, and the hybridization peak intensities for both alleles from these individuals were extracted to estimate the pairs of composite RAS (CRAS) and estimate three CPAs of SNPs across the human genome
Summary
Microarray-based pooled DNA experiments that combine the merits of DNA pooling and gene chip technology constitute a pivotal advance in biotechnology This new technique uses pooled DNA, thereby reducing costs associated with the typing of DNA from numerous individuals. The millennium revolution of the pooled DNA technique was its integration with microarrays [12], and the performance of which has been examined broadly [13,14,15,16,17,18,19,20,21,22,23] This newgeneration biotechnique significantly decreases the cost of large-scale genomic/genetic studies; for example, costs due to typing numerous DNA samples are reduced by pooling genomic DNA, and expenses related to primers and assay kits are reduced by using microarray genotyping.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
