The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma

Renal cell carcinoma(RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival

Multiplexed detection of infectious diseases by SERRS

Surface enhanced resonance Raman scattering (SERRS) is an analytical technique with several advantages over competitive techniques in terms of improved sensitivity and multiplexing. However, the lack of quantitative data relating to real examples has prevented more widespread adoption of the technique. Here we show multiplexed detection of two infectious diseases using a SERRS based DNA assay. SERRS active DNA probes were used in conjunction with PCR to allow simultaneous detection of Chlamydia and Gonorrhoea from urine. Silver nanoparticles were used to provide the enhancement and an assay compatible with existing instrumentation was created. Two assays have been studied and the data can be obtained in a single tube format and offers the flexibility to add further targets as desired. The technique is more sensitive than corresponding fluorescence detection and quantitative data has been obtained. This study demonstrates how SERRS can be a useful tool for meaningful analysis in molecular diagnostics

Bead-based dna diagnostic assay for chlamydia using nanoparticle-mediated surface-enhanced resonance raman scattering detection within a lab-on-a-chip format

There is a continued interest in the development of new on-chip protocols for the determination of the causes of infectious disease. In this paper, we demonstrate the use of surface-enhanced resonance Raman scattering (SERRS) for detecting the clinically relevant nucleic acid sequences of Chlamydia trachomatis in a bead-based lab-on-a-chip format, incorporating a solid-phase sample clean-up on-chip. The assay uses streptavidinated polymer microspheres to capture a biotinylated PCR product of the oligonucleotide sequence, which was subsequently hybridized against a complementary rhodamine-labeled, Raman active probe. Central to the assay is an in-channel integrated microfilter, which was used to retain the microspheres, enabling the bound target to be separated from the rest of the sample as part of a solid-phase clean-up (thereby removing any contributions from the background). After washing, the bound Rhodamine labeled detection probe was released thermally from the microspheres by heating and was subsequently mixed on-chip with a stream of silver nanoparticles. The signal was detected downstream using a Raman spectrometer to collect the SERRS response. The assay offers several advantages over traditional laboratory methods, including: the speed of the assay on-chip, the potential for sample clean-up; and the low volume of sample required