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This Week in Nucleic Acids Research: Sep 27, 2017

A team led by investigators at the Iowa State University and Data2Bio present a genotyping-by-sequencing method designed to pick up heterozygous SNPs and other genotyping information that may be missed by typical genotyping-by-sequencing methods. The genome reduction-based approach, known as tGBS, relies on double-digestion with two restriction enzymes and replaces double-stranded adaptor molecules with single-stranded oligonucleotides, the researchers explain. The tGBS strategy "simplifies the preparation of high-quality [genotyping-by-sequencing] libraries," the authors say, leading to SNP calling accuracy exceeding 97 percent. "tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci."

University of Dundee researchers introduce the Encyclopedia of Proteome Dynamics (EPD), a resource for visualizing and analyzing large quantities of mass spectrometry-based protein and peptide data. The EPD contains information on more than 30,000 proteins from published datasets, the team reports, combining a proteomic database with an online application to interact with the data. "The EPD offers a flexible and scalable ecosystem to integrate proteomics data with genomics information, RNA expression, and other related, large-scale datasets," the authors write.

Finally, a team from the US and Korea describes the "Tissue-specific Gene Database in Cancer," or TissGDB, which encompasses gene expression information for nearly 2,500 tissue-specific genes. The researchers focused on 22 tissues that coincided with cancer types in the Cancer Genome Atlas, bringing together tissue-specific gene expression cues from the Human Protein Atlas, GTEx, and the Tissue-specific Gene Expression and Regulation (TiGER) databases. With the help of TissGDB, they profiled TCGA data, considering everything from gene expression to mutations and prognostic markers in 28 cancer types. "Our analyses identified hundreds of [tissue-specific genes], including genes that universally kept or lost tissue-specific gene expression," the authors say, noting that the analysis also highlighted the expression of cancer type-specific isoforms, oncogene-related fusions, and more.