Spectral Prediction Features as a Solution for the Search Space Size Problem in Proteogenomics.

Proteogenomics approaches often struggle with the distinction between true and false peptide-to-spectrum matches as the database size enlarges. However, features extracted from tandem mass spectrometry intensity predictors can enhance the peptide identification rate and can provide extra confidence for peptide-to-spectrum matching in a proteogenomics context. To that end, features from the spectral intensity pattern predictors MSPIP and Prosit were combined with the canonical scores from MaxQuant in the Percolator postprocessing tool for protein sequence databases constructed out of ribosome profiling and nanopore RNA-Seq analyses.

Epigenetic markers in circulating cell-free DNA as prognostic markers for survival of castration-resistant prostate cancer patients.

Background: Noninvasive biomarkers to guide personalized treatment for castration-resistant prostate cancer (CRPC) are needed. In this study, we analyzed hypermethylation patterns of two genes (GSTP1 and APC) in plasma cell-free DNA (cfDNA) of CRPC patients. The aim of this study was to analyze the cfDNA concentrations and levels of the epigenetic markers and to assess the value of these biomarkers for prognosis.

Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform.

Background: Hereditary hearing loss (HL) can originate from mutations in one of many genes involved in the complex process of hearing. Identification of the genetic defects in patients is currently labor intensive and expensive. While screening with Sanger sequencing for GJB2 mutations is common, this is not the case for the other known deafness genes (> 60).

Applying massive parallel sequencing to molecular diagnosis of Marfan and Loeys-Dietz syndromes.

The Marfan (MFS) and Loeys-Dietz (LDS) syndromes are caused by mutations in the fibrillin-1 (FBN1) and Transforming Growth Factor Beta Receptor 1 and 2 (TGFBR1 and TGFBR2) genes, respectively. With the current conventional mutation screening technologies, analysis of this set of genes is time consuming and expensive. We have tailored a cost-effective and reliable mutation discovery strategy using multiplex PCR followed by Next Generation Sequencing (NGS).