Journal: Genome Biology

Article Title: Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample

doi: 10.1186/s13059-021-02592-9

Figure Lengend Snippet: Performance comparisons on the library preparation and FFPE data sets. a , b F1-score (%) comparison for different somatic mutation callers across different library kits and DNA amounts. Results of different callers for the same library preparation kit and DNA amount are connected for better illustration. c F1-score (%) comparison for different somatic mutation callers on 16 FFPE WGS replicates with FFPE or fresh matched normal. d SNV F1-score (%) comparison for different somatic mutation callers on 14 FFPE WES replicates with FFPE or fresh matched normal. Here, the SEQC-WGS-GT50-SpikeWGS10 trained models were used for NeuSomatic and NeuSomatic-S

Article Snippet: The selected samples included a WGS sample sequenced by a NovaSeq instrument, a WES sample, a sample prepared with a Nextera Flex library-prep kit with 1ng DNA, a 30x WGS sample with 50% tumor purity, a 100x WGS sample with 10% tumor purity, and two WGS and two WES FFPE samples each treated with formalin for 24h and matched with fresh/FFPE normal samples.

Techniques: Comparison, Mutagenesis

Journal: Frontiers in Microbiology

Article Title: Birds Kept in the German Zoo “Tierpark Berlin” Are a Common Source for Polyvalent Yersinia pseudotuberculosis Phages

doi: 10.3389/fmicb.2021.634289

Figure Lengend Snippet: The PYps23T genome contains long terminal direct repeats. (A) MbiI and NdeI restriction patterns of the phage DNA obtained by agarose gel electrophoresis and by in silico analysis. Fragments that were present only in the gel or in the in silico analysis are boxed. In silico restriction pattern predictions of PYps23T were obtained using NEBcutter v2.0 . Shown are patterns of the PYps23T genome without and with terminal repeats of 2.3 kb. M, Lambda Eco32I marker (fragment sizes are given). (B) . Determination of the start and end of the direct repeat. PED, PCR End Determination primer; DS, Direct Sequencing primer. See the text for details.

Article Snippet: The phage DNA was used for the preparation of DNA sequencing libraries using the Illumina DNA Flex Library Preparation kit (Illumina, CA, United States).

Techniques: Agarose Gel Electrophoresis, In Silico, Marker, Sequencing