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Supplemental Methods. Library preparation and semiconductor sequencing. For screening of the three PMBL cell lines we employed a multiplex PCR based Ion Torrent AmpliSeqTM cancer panel (Life Technologies) covering approx. 2,800 COSMIC annotated mutations in 50 key cancer genes (Supplemental Table 1). Amplicon library preparation was performed using ~10ng of DNA as advised by the manufacturer. B...
Direct sequencing remains the most widely used method for the detection of epidermal growth factor receptor (EGFR) mutations in lung cancer; however, its relatively low sensitivity limits its clinical use. The objective of this study was to investigate the sensitivity of detecting an epidermal growth factor receptor (EGFR) mutation from peptide nucleic acid-locked nucleic acid polymerase chain ...
The study of rotary steering drilling technology is currently one of the hot topics in the drilling engineering field. It requires accurate well trajectory control instructions when rotary steerable tools are applied to achieve the well trajectory control goal. A drilling trajectory prediction model will benefit this progress. According to the continuous beam theory, a mechanical model of push-...
The objective of this study was to design and validate a next-generation sequencing assay (NGS) to detect BRCA1 and BRCA2 mutations. We developed an assay using random shearing of genomic DNA followed by RNA bait tile hybridization and NGS sequencing on both the Illumina MiSeq and Ion Personal Gene Machine (PGM). We determined that the MiSeq Reporter software supplied with the instrument could ...
The fully annotated genome sequence of the European strain, 26695 was first published in 1997 and, in 1999, it was directly compared to the USA isolate J99, promoting two standard laboratory isolates for Helicobacter pylori (H. pylori) research. With the genomic scaffolds available from these important genomes and the advent of benchtop high-throughput sequencing technology, a bacterial genome ...
BACKGROUND AND AIM Next generation sequencing (NGS) has quickly the tool of choice for genome and exome data generation. The multitude of sequencing platforms as well as the variabilities within each platform need to be assessed. In this paper we used two platforms (ION TORRENT AND ILLUMINA) to assess single nucleotides variants in colorectal cancer (CRC) specimens. METHODS CRC specimens (n =...
We study the problem of Robust Least Squares Regression (RLSR) where several response variables can be adversarially corrupted. More specifically, for a data matrix X ∈ Rp×n and an underlying model w∗, the response vector is generated as y = XTw∗+b where b ∈ R is the corruption vector supported over at most C ·n coordinates. Existing exact recovery results for RLSR focus solely on L1-penalty ba...
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