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We performed integrated genomic, transcriptomic, and proteomic profiling of 150 pancreatic ductal adenocarcinoma (PDAC) specimens, including samples with characteristic low neoplastic cellularity. Deep whole-exome sequencing revealed recurrent somatic mutations in KRAS, TP53, CDKN2A, SMAD4, RNF43, ARID1A, TGFβR2, GNAS, RREB1, and PBRM1. KRAS wild-type tumors harbored alterations in other oncogenic...
Paired-end sequencing yields a read from each end of a DNA fragment, typically leaving a gap of unsequenced nucleotides in the middle. Closing this gap using information from other reads in the same sequencing experiment offers the potential to generate longer “pseudo-reads” using short read sequencing platforms. Such long reads may benefit downstream applications such as de novo sequence assembly,...
This past decade, genome sciences have benefitted from rapid advances in DNA sequencing technologies, and development of efficient algorithms for processing short nucleotide sequences played a key role in enabling their uptake in the field. In particular, reassembly of human genomes (de novo or reference-guided) from short DNA sequence reads had a substantial impact on health research. De novo assembly...
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