Notes: These authors generated a set of probes that could be used in fluorescence in situ hybridization (FISH) analyses for karyotyping studies on maize chromosomes. Specific target regions composed of genes or gene clusters and free from repetetive elements were identified for each chromosome. Target regions were amplified by PCR, gel purified using the Wizard^® SV Gel and PCR Clean-Up System, and tested in a FISH assay. Probes showing low background were selected, subcloned into the pGEM^® -T Vector and sequenced to confirm identity. (3627)

Notes: Saliva samples from a total of 142 dogs (36 different pure breeds and several cross breeds) were collected on cotton swabs. Genomic DNA was isolated using the ReadyAmp™ Genomic DNA Purification System. Single amplifications of six canine STR loci were performed using 1–5µl of saliva DNA extract. (3424)

Notes: In this study, genomic DNA was extracted from 99 frozen thymic epithelial tumor samples using the Wizard^® SV Genomic DNA Purification System. Purified DNA was used in TaqMan SNP genotyping assays for 13 epidermal growth factor receptor (EGFR) gene mutations. (3585)

Notes: The expression level of the seven-transmembrane Epstein-Barr virus-induced receptor 2 (EBI2) was measured in peripheral blood mononuclear cells. Total RNA was isolated from T-lymphocytes, B-lymphocytes, monocytes and NK cells, and reverse transcribed using the ImProm-II™ Reverse Transcription System. The resulting cDNA was quantitated using real-time PCR. (3449)

Notes: To examine the flowering time for three new Arabidopsis thaliana recombinant inbred lines (RIL), genomic DNA was isolated from leaves of 92 Arabidopsis accessions and from flower buds of the three RILs using the Wizard^® Magnetic 96 DNA Plant System. The purified DNA was used for single sequence length polymorphisms (SSLPs) genotyping. (3417)

Notes: To study sarcolemmal ATP-sensitive K+ (KATP) channels, transgenic mice were generated that express SUR2A, the proposed regulatory protein of the complex. Genomic DNA was extracted from mouse ears using the Wizard^® SV Genomic DNA Purification System and used for genotyping transgenic animals.
(3584)

Notes: The authors evaluated a 96-channel microfabricated capillary array electrophoresis (µCAE) device for forensic STR typing using the PowerPlex^® 16 System and the AmpFlSTR^® Profiler Plus^® kit. DNA was isolated from one semen (sperm and nonsperm fractions), nine saliva, four blood and two mixed blood stains using either organic extraction or the DNA IQ™ System, then .5–1.0 ng was amplified using the PowerPlex^® 16 System and the AmpFlSTR^® Profiler Plus^® kit according to the manufacturer's instructions. Amplified products were analyzed initially using an ABI PRISM^® 310 or Hitachi FMBIO^® II instrument, then using the µCAE device. All 48 samples, as well as all minor alleles in 3:1 mixture samples, were accurately typed using the µCAE device. (3772)

Notes: The authors developed a new set of miniplex primers for DNA typing of degraded DNA from human skeletal remains. The miniplex primers produced smaller amplicons (50–280 base pairs) than standard STR systems. The DNA-typing results obtained with the miniplex primers were compared to results obtained with the PowerPlex^® 16 System. The authors determined that larger loci failed to amplify when using degraded DNA and that the degradation cut-off length of template fragments occurred predominantly at 200bp and is not kit-dependent. (3808)

Notes: The authors generated Y-STR haplotype frequency data for several ethnic populations in Poland using the PowerPlex^® Y System. DNA was isolated using Chelex^® resin and a proteinase K protocol and amplified, and amplification products were detected using an ABI PRISM^® 310 Genetic Analyzer. (3869)

Notes: The authors conducted a classical twin study to define the genetic contribution to cytokine production and regulation of T cell-specific transcription factors. Twins were classified as monozygotic and dizygotic by typing 15 short tandem repeat loci using the PowerPlex^® 16 System. (3807)

Notes: On November 20, 2002, an explosion in a munitions facility left 7 people dead, 100 injured and 5 missing. The authors used DNA typing to identify 2 tissue samples and 19 bone samples. These samples, as well as reference samples from relatives of the missing persons, were analyzed using the PowerPlex^® 16 System. DNA was extracted using phenol:chloroform:isoamyl alcohol extraction and concentrated, then amplified using 28–30 cycles. For bone samples, the cycle number was increased to 35. The success rate was 90% (19 of 21 samples identified; 2 of 21 samples had a high degree of contamination and could not be identified). (3819)

Notes: To rapidly characterize somatic mutations in the EGF receptor in lung cancer tissues, genomic DNA was extracted from lung biopsies using the Wizard^® SV Genomic DNA Purification System. The extracted DNA was used in a LightCycler SNP genotyping assay to determine the genotype of common loci associated with improved patient response to the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor. (3588)

Notes: GoTaq^® DNA Polymerase was used in PCR genotyping of Giardia intestinalis. Primers were designed around a 177 bp sequence of the glutamete dehydrogenase gene (gdh). Typing was based on previously reported assemblages of gdh from cats, dogs, cows and monkeys. PCR was performed in a total reaction volume of 25μl using 1.25 units of GoTaq^® DNA Polymerase.
(3364)

Notes: These authors used DNA typing to identify human skeletal remains found in mass graves. DNA was isolated using standard phenol/chloroform extraction, the DNA IQ™ System or other methods. A modified DNA IQ™ System protocol was developed using 2g of pulverized bone. DNA was quantitated using the AluQuant^® Human DNA Quantitation System or Quanti-Blot™ Human DNA quantitation kit. DNA typing was performed using several STR amplification kits, including the PowerPlex^® 16 System. In some cases mitochondrial DNA testing was necessary due to the degree of nuclear DNA degradation. Of the 481 samples, 385 were amplified successfully and 109 sets of remains were identified. (3640)

Notes: These authors used a new DNA purification method that combines cetyltrimethylammonium bromide (CTAB) and isoamyl alcohol/chloroform extraction to isolate DNA from bones soaked in water, burned bones, or bones that had been buried for a long time. Following the CTAB and isoamyl alcohol/chloroform extraction, PCR inhibitors were removed using the DNA IQ™ System or the QIAquick PCR Purification Kit. The authors preferred the DNA IQ™ System because of its speed and ease-of-use. (3642)

Notes: This paper discusses automated DNA purification from a variety of forensic casework samples using the DNA IQ™ System on a Beckman BioMek® 2000 Laboratory Automated Workstation.  DNA was purified from various forensic casework samples including vaginal swabs, blood stains, tissue and samples.  The researchers also tested diluted and contaminated samples and the ability of the DNA IQ™ System on the Beckman BioMek® 2000 to purify DNA from these samples.  The PowerPlex® 1.1 System was used as a representative forensic laboratory typing system to test the contaminant level in all of the DNA IQ™ purified DNA samples.  (3052)

Notes: These authors assessed the risk of transmitting genetic defects to children after intracytoplasmic sperm injection (ICSI) for treatment of male factor infertility. Genomic DNA was isolated from blood of both parents and children using the Wizard® Genomic DNA Purification Kit. Multiplex amplification of 22 sequence tagged sites on the Y chromosome was then performed on 123 samples using the Y Chromosome Deletion Detection System, Version 1.1 and a prototype Multiplex E from Promega. (3117)

Notes: GoTaq^® DNA Polymerase was used in a multiplexed genotyping reaction with three primers to differentiate wild-type, heterozygous, and mutant transgenic mouse alleles simultaneously. The wild-type target was 670bp and the mutant or knockout target was 1,030bp. Various other amplimers (1.4kb, 471bp, & 311bp) were subcloned with the aid of the pGEM^®-T Easy Vector System. (3360)

Notes: The authors evaluated the ability of the PowerPlex^® 16 System to amplify degraded DNA samples and compared the results with those obtained using the AmpFlSTR^® SGM Plus^® kit. They amplified DNA from six whole blood samples that had been stored at 4°C or room temperature for 20 days, DNA isolated from six pairs of archived whole blood samples, and from corresponding plasma samples that had been stored below –20°C for 1–3 years and were assumed to be degraded. Amplifications were assembled and performed using protocols optimized in their laboratory. For the whole blood and plasma samples stored below –20°C, the PowerPlex® 16 System gave eight full profiles and the SGM Plus^® kit gave six full profiles. No differences were observed between the two kits with DNA extracts stored at 4°C or room temperature. As expected, the frequency of allele dropout increased as the amplified fragment length increased. (3876)

Notes: The Wizard^® Genomic DNA Purification System was used to isolate genomic DNA from clinically isolated Haemophilus influenzae samples.  The genomic DNA was then digested with EcoRI and used in Southern blots to identify the presence of various Haemophilus influenzae adhesin genes. (3102)

Notes: Terminal Deoxynucleotidyl Transferase was used to biotin end-label PCR products generated from adaptor-ligated genomic DNA fragment templates. The labeled probes were then hybridized to microarrays spotted with SNP alleles. The Terminal Deoxynucleotidyl Transferase reaction was performed for 4 hours at 37°C using 15-20 units TdT, TdT reaction buffer and 18μM biotin-ddATP. (2758)

Notes: The PolyATtract^® System 1000 was used to isolate mRNA from mouse spleen. The researchers used 3μg of the isolated poly(A)+ RNA in reverse transcriptase reactions to make cDNAs. The cDNAs were ultimately used as templates in in vitro transcription reactions to produce biotin labeled cRNAs that were used as targets in microarray analysis experiments.  (2743)

Notes: Genomic DNA was isolated from Madurella mycetomatis samples.  A modified  Wizard^® Genomic DNA Purification Kit protocol was used for the isolations.  Mycelia were sonicated and ground in liquid nitrogen before the addition of Nuclei Lysis Solution. The purified DNA was used in PCR.  (3049)

Notes: The authors generated population data from 508 unrelated Japanese individuals using the PowerPlex^® 16 System. DNA was collected as buccal swabs and isolated using Chelex^® resin followed by phenol:chloroform extraction and ethanol precipitation. For each PowerPlex^® 16 reaction, 2ng of DNA was amplified using a GeneAmp^® PCR System 9700, and amplified products were detected using the ABI PRISM^® 377 DNA Sequencer. (3843)

Notes: In this paper, researchers from both Promega and state crime laboratories provide an evaluation of the Powerplex^® 16 System loci (CODIS, Penta D, Penta E, and amelogenin). Data from several laboratories using a variety of thermal cyclers and the ABI PRISM^® 310 Genetic Analyzer or ABI PRISM^® 377 DNA Sequencer are presented. The Powerplex^® 16 System was able to consistently genotype samples from as little as 0.0625-2ng of genomic DNA template. Other factors such as reaction volume, annealing temperature, titration of AmpliTaq Gold^® DNA Polymerase, magnesium, or primer pairs, and 1ng DNA mixtures were analyzed using the Powerplex^® 16 System.  The researchers also present data on stutter analysis and cross reactivity of primer sets on primate DNA templates for each loci. (2675)