BRAF mutation testing in solid tumors: a methodological comparison.

Solid tumor genotyping has become standard of care for the characterization of proto-oncogene mutational status, which has traditionally been accomplished with Sanger sequencing. However, companion diagnostic assays and comparable laboratory-developed tests are becoming increasingly popular, such as the cobas 4800 BRAF V600 Mutation Test and the INFINITI KRAS-BRAF assay, respectively. This study evaluates and validates the analytical performance of the INFINITI KRAS-BRAF assay and compares concordance of BRAF status with two reference assays, the cobas test and Sanger sequencing.

MTHFR (C677T) polymorphisms and stage III colon cancer: response to therapy.

Background: Leucovorin and 5-fluorouracil (5-FU) chemotherapeutics are often used as coinhibitors of the thymidylate synthase pathway to thwart the growth of cancer cells in certain types of neoplasms. The metabolism of leucovorin is mediated through the enzyme methylenetetrahydrofolate reductase (MTHFR). A common polymorphism in the MTHFR gene has been reported to be responsible for as much as a 70% reduction in activity of this enzyme when present in the homozygous form.

Simultaneous polymerase chain reaction restriction fragment length polymorphism identification of the factor V Leiden allele and the prothrombin 20210A mutation.

A novel mutation in the 3' untranslated region of the prothrombin gene, prothrombin 20210A, recently has been identified. This mutation is associated with increased serum prothrombin levels and an increased risk for venous thromboembolism. Patients who carry a mutation in the factor V gene (factor V Leiden) have also been demonstrated to be at increased risk for venous thromboembolism, and previous studies have identified a population prevalence of approximately 5% to 10% for the factor V Leiden allele.

The role of preoperative factor V Leiden screening in different geographic populations.

Patients harboring a specific mutation in the coagulation factor V gene have been identified as being at significantly increased risk for venous thrombosis. A simple genetic test that identifies carriers of this mutation (the factor V Leiden allele) is available and may have utility in various clinical settings, including preoperative risk assessment for thromboembolic complications. In this regard, it is generally agreed that prospective studies addressing the role of preoperative factor V Leiden mutational analysis are needed to clearly define the clinical prognostic/diagnostic significance of the presence of this mutation in surgical patients.

Cleavage of cottontail rabbit papillomavirus E7 RNA with an anti-E7 ribozyme.

We have designed and constructed a plasmid (pE7RZ-1) that contains a gene for a hammerhead ribozyme that specifically cleaves cottontail rabbit papillomavirus (CRPV) E7 RNA sequences in vitro. The in vitro produced transcripts of pE7RZ-1 cleave CRPV E7 target sequences in trans at 37 degrees C. Pretreatment of pE7RZ-1 RNA with poly-L-lysine (PLL) increases the stability of the RNA to greater than 2 hours in the presence of a crude papilloma cell extract and the pE7RZ-1 RNA/PLL mixture retains catalytic activity in this system.

Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus and proposal for creation of a new genus, Alicyclobacillus gen. nov.

Comparative 16S rRNA (rDNA) sequence analyses performed on the thermophilic Bacillus species Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cycloheptanicus revealed that these organisms are sufficiently different from the traditional Bacillus species to warrant reclassification in a new genus, Alicyclobacillus gen. nov. An analysis of 16S rRNA sequences established that these three thermoacidophiles cluster in a group that differs markedly from both the obligately thermophilic organisms Bacillus stearothermophilus and the facultatively thermophilic organism Bacillus coagulans, as well as many other common mesophilic and thermophilic Bacillus species.

How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity.

16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical.

Phylogenetic diversity in the genus Bacillus as seen by 16S rRNA sequencing studies.

Comparative sequence analysis of 16S ribosomal (r)RNAs or DNAs of Bacillus alvei, B. laterosporus, B. macerans, B.

PCR amplification of 16S rDNA from lyophilized cell cultures facilitates studies in molecular systematics.

The sequence of the major portion of a Bacillus cycloheptanicus strain SCH(T) 16S rRNA gene is reported. This sequence suggests that B. cycloheptanicus is genetically quite distinct from traditional Bacillus strains (e.