Circumscribed sebaceous neoplasms: a morphological, immunohistochemical and molecular analysis.

Sebaceous neoplasms encompass a range of lesions, including benign entities such as sebaceous adenoma and sebaceoma, as well as sebaceous carcinoma. The distinction of sebaceous carcinoma from benign lesions relies on histological identification of architectural or cytological features of malignancy. In this study we have assessed the diagnostic discriminatory ability of mitotic rate and immunohistochemical markers (p53, bcl-2 and p16) in a selected group of well circumscribed sebaceous neoplasms, incorporating examples of sebaceous adenoma, sebaceoma and sebaceous carcinoma.

Mutational Analysis of BRAF Inhibitor-Associated Squamoproliferative Lesions.

In recent years, there has been increasing use of BRAF-inhibiting drugs for the treatment of various malignancies, including melanoma. However, these agents are associated with the development of other nonmelanoma skin lesions, in particular squamoproliferative lesions such as keratoacanthomas (KAs), squamous cell carcinomas, and BRAF inhibitor-associated verrucous keratoses. The molecular pathogenesis of these lesions is of interest, not only for therapeutic reasons, but also for the insight it might provide into the development of similar lesions in a sporadic setting.

Somatic mutations in glioblastoma are associated with methylguanine-DNA methyltransferase methylation.

The high level of methylguanine-DNA methyltransferase (MGMT) in glioblastoma is responsible for resistance to alkylating agents, such as temozolomide (TMZ). In glioblastomas with a methylated promoter, MGMT deficiency is presumed, resulting in an enhanced effect of TMZ. The aim of the present study was to investigate whether genomic alterations work synergistically with methylation status and contribute to the response to treatment and overall prognosis in glioblastoma.

Multigene profiling to identify alternative treatment options for glioblastoma: a pilot study.

Unlabelled: Glioblastoma (GBM) is a highly aggressive malignancy and the most effective treatment regime has a high relapse rate. Increasingly, the development of therapies involves defining drug-diagnostic combinations where the presence of a molecular target or marker identifies patients who are most likely to respond to a specific therapy. Trials in other solid cancers have demonstrated clear utility in the incorporation of biomarkers to stratify patients to targeted treatment, however, there are no mutations that are currently used to inform treatment options for GBM.

High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples.

Ureaplasma sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human Ureaplasma spp.

Developments in the immunophenotypic analysis of haematological malignancies.

Immunophenotyping is the method by which antibodies are used to detect cellular antigens in clinical samples. Although the major role is in the diagnosis and classification of haematological malignancies, applications have expanded over the past decade. Immunophenotyping is now used extensively for disease staging and monitoring, to detect surrogate markers of genetic aberrations, to identify potential immuno-therapeutic targets and to aid prognostic prediction.

Prevalence of human papillomavirus genotypes in women with cervical cancer in Papua New Guinea.

Objective: Prophylactic human papillomavirus (HPV) vaccines are currently not available in Papua New Guinea. Prior to introducing these vaccines, knowledge about the HPV genotypes present in cervical cancer in this region is necessary to determine whether the types covered by the 2 commercially licensed vaccines are the same as those in other regions of the world.

Methods: Fresh, frozen cervical biopsies from 70 women with cervical cancer in Papua New Guinea were collected over a 3-year period from 2006-2009.

Temperature switch PCR (TSP): Robust assay design for reliable amplification and genotyping of SNPs.

Background: Many research and diagnostic applications rely upon the assay of individual single nucleotide polymorphisms (SNPs). Thus, methods to improve the speed and efficiency for single-marker SNP genotyping are highly desirable. Here, we describe the method of temperature-switch PCR (TSP), a biphasic four-primer PCR system with a universal primer design that permits amplification of the target locus in the first phase of thermal cycling before switching to the detection of the alleles.

Mismatch oxidation assay: detection of DNA mutations using a standard UV/Vis microplate reader.

Simple, low-cost mutation detection assays that are suitable for low-throughput analysis are essential for diagnostic applications where the causative mutation may be different in every family. The mismatch oxidation assay is a simple optical absorbance assay to detect nucleotide substitutions, insertions, and deletions in heteroduplex DNA. The method relies on detecting the oxidative modification products of mismatched thymine and cytosine bases by potassium permanganate as it is reduced to manganese dioxide.

The chemical cleavage of mismatch for the detection of mutations in long DNA fragments.

Methods to rapidly scan large regions of DNA that are not dependent on highly specific melting temperatures or suitable only for large-scale discovery are important to reduce the amount of sequencing required for DNA samples that appear to contain a mutation. This protocol describes the chemical cleavage of mismatch method to assess if a region of DNA contains a mutation and accurately localize the position of the mutation in the same reaction. To detect mutations, PCR heteroduplexes are incubated with two mismatch-specific reagents.

Abnormal nuclear pore formation triggers apoptosis in the intestinal epithelium of elys-deficient zebrafish.

Background & Aims: Zebrafish mutants generated by ethylnitrosourea-mutagenesis provide a powerful tool for dissecting the genetic regulation of developmental processes, including organogenesis. One zebrafish mutant, "flotte lotte" (flo), displays striking defects in intestinal, liver, pancreas, and eye formation at 78 hours postfertilization (hpf). In this study, we sought to identify the underlying mutated gene in flo and link the genetic lesion to its phenotype.

The R229Q mutation in NPHS2 may predispose to proteinuria in thin-basement-membrane nephropathy.

Thin-basement-membrane nephropathy (TBMN) is characterized by persistent dysmorphic hematuria, and the presence of proteinuria is a risk factor for renal impairment. TBMN is often due to mutations in the COL4A3 and COL4A4 genes, and this study determined whether additional mutations in genes encoding other structures in the glomerular filtration barrier contributed to the development of proteinuria. Fifty-six unrelated individuals with TBMN including 18 (32%) with proteinuria > or = 300 mg/L and ten (18%) with proteinuria > or = 500 mg/L were studied.

Mutations, structural variations, and genome-wide resequencing: where to from here in our understanding of disease and evolution?

The 9th International Symposium on Mutations in the Genome, Mutation Detection 2007, was held on 23-27 September 2007 in Xiamen, China. Meeting participants reported on a broad range of advances in mutation detection technologies and their applications, including developments in SNP genotyping systems applicable to point-of-care diagnostic testing; and emerging views on structural variation, high-throughput sequencing and the importance of bioinformatic tools to support the growing amounts of genome variation data. This meeting report summaries the major themes presented at the meeting.

Chemical cleavage of mismatch (CCM) to locate base mismatches in heteroduplex DNA.

This protocol describes the use of the chemical cleavage of mismatch (CCM) method to assess whether a region of DNA contains mutations and to localize them. Compared with other mutation-detection techniques (such as single strand-conformation polymorphism (SSCP) analysis, denaturing high-performance liquid chromatography (DHPLC) and denaturing gradient gel electrophoresis (DGGE)) that detect mutations in short DNA fragments and require highly specific melting temperatures, CCM has a higher diagnostic sensitivity suited to the detection of mutations in tumor genes, and can analyze amplicons < or = 2 kb in length. To detect mutations, PCR heteroduplexes are incubated with two mismatch-specific reagents.

Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning.

We report the development of a simple and inexpensive assay for the detection of DNA polymorphisms and mutations that is based on the modification of mismatched bases by potassium permanganate. Unlike the chemical cleavage of mismatch assay, which also exploits the reactivity of potassium permanganate to detect genomic variants, the assay we describe here does not require a cleavage manipulation and therefore does not require expensive or toxic chemicals or a separation step, as mismatches are detected using direct optical methods in a microplate format. Studies with individual deoxynucleotides demonstrated that the reactivity with potassium permanganate resulted in a specific colour change.

The 2004 Human Genome Variation Society scientific meeting.

The Human Genome Variation Society annual scientific meeting was held on 26 October 2004 in Toronto, Canada, and attracted 85 registrants. Meeting participants from 14 countries reported on the recent advances and progress made toward the detection, analysis, and documentation of genetic variation. Reports were made on improvements to software that can enable curators to create mutation databases that are uniform and are therefore more widely used and easy to distribute.