Springer protocols feed by Genetics/Genomics 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.Analysis of 3 Biallelic INDEL Markers Using the Investigator DIPplex & reg; Kit
Insertion/deletion polymorphisms (INDELs) are a relatively new class of a DNA marker to be used in forensic casework; used most commonly as a supplementary method to STR-based typing. INDELs, like SNPs, are particularly useful for the analysis of highly degraded DNA as the amplicon sizes are typically below 160 bp; they can also be valuable as an additional tool to help resolve kinship cases, with the advantage over STRs that they do not have high mutation rates. INDELs have an advantage over SNPs in that they are length polymorphisms and so can be analyzed by simply measuring the length of the allele(s). The Qiagen Invest...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
A Practical Guide to the HIrisPlex System: Simultaneous Prediction of Eye and Hair Color from DNA
The HIrisPlex system, which consists of two parts, allows the simultaneous prediction of eye and hair color from DNA, e.g., samples extracted from crime scene evidence. The first part is a highly sensitive multiplex genotyping assay consisting of 24 DNA markers using SNaPshot™ chemistry, for analysis on all Capillary Electrophoresis machines. The second part consists of statistical models that respectively establish eye and hair color prediction probabilities from complete and incomplete genotype profiles using parameters generated from large genotype and phenotype databases. This combined prediction tool constitutes...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Analysis of Rapidly Mutating Y Chromosome Short Tandem Repeats (RM Y-STRs)
Rapidly mutating (RM) Y-STRs were recently identified and can help to differentiate between paternally related males in paternity and forensic casework. Normal Y-STRs are often used in casework due to their paternal inheritance, which can help to resolve kinship cases, and identify male components in male/female mixtures; however, more discriminating profiles are obtained if rapidly mutating Y-STRs are used. Previously two or three multiplex PCRs have been used to amplify 13 RM Y-STRs; here, an assay amplifying these 13 markers in a single multiplex PCR is described. Commercially available male control DNA samples have bee...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Enhanced DNA Profiling of the Semen Donor in Late Reported Sexual Assaults: Use of Y-Chromosome-Targeted Pre-amplification and Next Generation Y-STR Amplification Systems
In some cases of sexual assault the victim may not report the assault for several days after the incident due to various factors. The ability to obtain an autosomal STR profile of the semen donor from a living victim rapidly diminishes as the post-coital interval is extended due to the presence of only a small amount of male DNA amidst an overwhelming amount of female DNA. Previously, we have utilized various technological tools to overcome the limitations of male DNA profiling in extended interval post-coital samples including the use of Y-chromosome STR profiling, cervical sample, and post-PCR purification permitting the...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
In-Solution Hybridization for the Targeted Enrichment of the Whole Mitochondrial Genome
A detailed protocol is presented for the targeted enrichment of whole mitochondrial genomes based on an in-solution hybridization strategy. Bait is produced in-house by sonication of two long-range PCR amplicons and ligation of biotinylated double-stranded adapters. Indexed target DNA is hybridized with the bait in a multiplex enrichment reaction and pulled down using magnetic streptavidin beads followed by subsequent post-enrichment PCR and sequencing on an Illumina MiSeq. This strategy removes the need for expensive commercial bait probes while allowing enrichment of multiple samples in a single hybridization reaction. T...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Whole Human Mitochondrial DNA Sequencing
Mitochondrial DNA (mtDNA) can help in the identification of biological evidence recovered from crime scenes and human remains. Typically the hypervariable regions are targeted for sequencing; however, more discriminating profiles are obtained if the whole genome is sequenced. Different approaches exist as to how best amplify and sequence whole mtDNA from forensic specimens. Here, we describe a method based on two-round PCR, combining multiplex and simplex PCRs. This method has been used in the analysis of mitochondrial genomes from archival saliva samples applied to FTA® cards after 10 years of transportation and prese...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Analysis of Mitochondrial Control Region Using Sanger Sequencing
The analysis of mitochondrial DNA (mtDNA) is an established forensic tool and has been used extensively to aid with both the identification of human remains and evidence recovered from scenes of crime. The biology of mtDNA confers both advantages and disadvantages when using it as a tool for identification. It benefits from a high copy number, which facilitates analysis from samples with highly degraded DNA or trace amounts of DNA, but the maternal mode of inheritance restricts its power of discrimination. With Next Generation Sequencing being used in research and some forensic casework laboratories the scope of mtDNA anal...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Analysis of 3 Biallelic INDEL Markers Using the Investigator DIPplex® Kit
Insertion/deletion polymorphisms (INDELs) are a relatively new class of a DNA marker to be used in forensic casework; used most commonly as a supplementary method to STR-based typing. INDELs, like SNPs, are particularly useful for the analysis of highly degraded DNA as the amplicon sizes are typically below 160 bp; they can also be valuable as an additional tool to help resolve kinship cases, with the advantage over STRs that they do not have high mutation rates. INDELs have an advantage over SNPs in that they are length polymorphisms and so can be analyzed by simply measuring the length of the allele(s). The Qiagen Invest...
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Purification of PCR Products to Improve STR Profiles
Forensic laboratories routinely perform STR analyses using commercially available STR kits. Very low levels of DNA are extracted from many forensic samples. In these samples, the amount of DNA that can be placed in a PCR is below the optimal DNA range for the commercial kits, leading to weak profiles and allelic dropout. STR profiles generated from poor quality samples can be improved by purification of the PCR product prior to capillary electrophoresis. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - December 31, 2015 Category: Genetics & Stem Cells Source Type: news
Single Nucleotide Polymorphisms as Genomic Markers for High-Throughput Pharmacogenomic Studies
Genetic variations in patients have strong impact on their drug therapies and responses because the variations may contribute to the efficacy and/or produce undesirable side effects for any given drug. The Drug Metabolizing Enzymes and Transporters (DMET) assay is a high-throughput technology by Affymetrix that is able to simultaneously genotype variants in multiple genes involved in absorption, distribution, metabolism, and excretion of drugs for subsequent clinical applications, i.e., the assay allows for a precise genetic map that can guide therapeutic interventions and avoid side effects. (Source: Springer protocols fe...
Source: Springer protocols feed by Genetics/Genomics - December 1, 2015 Category: Genetics & Stem Cells Source Type: news
High-Throughput DNA Array for SNP Detection of KRAS Gene Using a Centrifugal Microfluidic Device
Here, we describe detection of single nucleotide polymorphism (SNP) in genomic DNA samples using a NanoBioArray (NBA) chip. Fast DNA hybridization is achieved in the chip when target DNAs are introduced to the surface-arrayed probes using centrifugal force. Gold nanoparticles (AuNPs) are used to assist SNP detection at room temperature. The parallel setting of sample introduction in the spiral channels of the NBA chip enables multiple analyses on many samples, resulting in a technique appropriate for high-throughput SNP detection. The experimental procedure, including chip fabrication, probe array printing, DNA amplificati...
Source: Springer protocols feed by Genetics/Genomics - December 1, 2015 Category: Genetics & Stem Cells Source Type: news
Probe Design Strategies for Oligonucleotide Microarrays
Oligonucleotide microarrays have been widely used for gene detection and/or quantification of gene expression in various samples ranging from a single organism to a complex microbial assemblage. The success of a microarray experiment, however, strongly relies on the quality of designed probes. Consequently, probe design is of critical importance and therefore multiple parameters should be considered for each probe in order to ensure high specificity, sensitivity, and uniformity as well as potentially quantitative power. Moreover, to assess the complete gene repertoire of complex biological samples such as those studied in ...
Source: Springer protocols feed by Genetics/Genomics - December 1, 2015 Category: Genetics & Stem Cells Source Type: news
Detection and Quantification of MicroRNAs by Ligase-Assisted Sandwich Hybridization on a Microarray
Extracellular microRNAs (miRNAs) in body fluids have been identified as promising biomarkers for different human diseases. The high-throughput, multiplexed detection and quantification of these miRNAs are highly beneficial for the rapid and accurate diagnosis of diseases. Here, we developed a simple and convenient microarray-based technique, named ligase-assisted sandwich hybridization (LASH), for the detection and quantification of miRNAs. The LASH assay involves the hybridization of capture and detection probe pairs with the target miRNA to form a double-stranded structure which is then nick-sealed by T4 DNA ligase. Usin...
Source: Springer protocols feed by Genetics/Genomics - December 1, 2015 Category: Genetics & Stem Cells Source Type: news
Microarray Developed on Plastic Substrates
There is a huge potential interest to use synthetic polymers as versatile solid supports for analytical microarraying. Chemical modification of polycarbonate (PC) for covalent immobilization of probes, micro-printing of protein or nucleic acid probes, development of indirect immunoassay, and development of hybridization protocols are described and discussed. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - December 1, 2015 Category: Genetics & Stem Cells Source Type: news
The “Clickable” Method for Oligonucleotide Immobilization Onto Azide-Functionalized Microarrays
The DNA microarray technique was supposed to help identifying and analyzing the expression level of tens of thousands of genes in the whole genome. But there is a serious problem concerning fabrication of the microarrays by chemical synthesis, such as specific and efficient linking of probes to a solid support. Therefore, we reckon that applying “click” chemistry to covalently anchor oligonucleotides on chemically modified supports may help construct microarrays in applications such as gene identification. Silanization of the glass support with organofunctional silane makes it possible to link azide groups on g...
Source: Springer protocols feed by Genetics/Genomics - December 1, 2015 Category: Genetics & Stem Cells Source Type: news
