Tag Archives: TCGA

Contamination of reagents and cross contamination across samples is a long-recognized issue in molecular biology laboratories. While often innocuous, contamination can lead to inaccurate results. Cantalupo et al., for example, found HeLa...

Identifying genetic biomarkers of patient survival remains a major goal of large-scale cancer profiling studies. Using gene expression data to predict the...

University of Kentucky researchers have developed SeqOthello, an ultra-fast and memory-efficient indexing structure to support arbitrary sequence query against large collections of RNA-seq...

Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional...

RNA sequencing (RNA-Seq) and microarray are two of the most commonly used high-throughput technologies for transcriptome profiling; however, they both have their own inherent strengths and limitations. Researchers from Fudan University aimed to analyze the correlation between microarrays and RNA-Seq detection of ...

The Cancer Genome Atlas (TCGA) has generated comprehensive molecular profiles. Researchers at the National Institute of Environmental Health Sciences aimed to identify a set of genes whose expression patterns can distinguish diverse tumor types. Those features may serve as biomarkers ...

Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of ...

A multi-institution research group jointly led by Professor Jan Prins and UNC CS alumna Professor Jinze Liu at the University of Kentucky is developing algorithms and software to analyze RNA using high-throughput sequencers. The software is in use in multiple ...

MicroRNAs (miRNAs) play important roles in cellular functions and developmental processes. They are also implicated in oncogenesis mechanisms and could serve as potential cancer biomarkers. Using high-throughput miRNA sequencing information, expression of both the 5p-arm and 3p-arm mature miRNAs were ...

by JM Kocarnik at FHCRC Alternative splicing of specific genes can contribute to cancer initiation, progression, and metastasis.  With the advent of cancer genome sequencing, it was discovered that many tumor types contain high frequencies of somatic mutations affecting components ...