Journal: medRxiv

Article Title: Combination of BRCA deep targeted sequencing and shallow whole genome sequencing to detect homologous recombination deficiency in ovarian cancer

doi: 10.1101/2024.09.10.24313378

Figure Lengend Snippet: Sensitivity of the HRD INSIGHT assay to detect (A) germline and somatic SNV and small Indel mutations, (B) germline large genomic rearrangements (LGRs) of BRCA1/2 genes in reference standards. (C) Concordance of the HRD INSIGHT assay to determine the genomic instability score and status of the reference standards. (D) Positive-, negative- and overall-percent agreement (NPA, PPA, Overall) of the HRD INSIGHT assay with the HRD Focus Panel (AmoyDx), TruSight Oncology TSO 500 HRD (Illumina) and SOPHiA DDM HRD Solutions (Sophia Genetics) to determine HRD status of clinical FFPE ovarian samples. For 4 conflicting samples, the results of individual assays were shown.

Article Snippet: While the PPA and NPA among all assays were mostly above 90%, the HRD INSI assay shared the lowest PPA with the AmoyDx kit (94.7%) and the lowest NPA with the Illumina TSO kit (81.3%).

Techniques:

Journal: medRxiv

Article Title: Combination of BRCA deep targeted sequencing and shallow whole genome sequencing to detect homologous recombination deficiency in ovarian cancer

doi: 10.1101/2024.09.10.24313378

Figure Lengend Snippet: (A) The successful rate of each assay to determine HRD status of clinical samples. (B) Distribution of noise index and DNA integrity number among samples that failed AmoyDx test. (C) Noise reduction algorithm improved the correlation of wGI score with TSO genomic instability (GIS) score. (D) Tumor fraction (TF) was determined in-silico and compared with AmoyDx and TSO kits. (E) In-silico simulation of TF serial dilution at different levels showed stable wGI scores at a minimum TF of 30%. (F) wGI score measurement was robust and reproducible among different runs across different sequencing platforms.

Article Snippet: While the PPA and NPA among all assays were mostly above 90%, the HRD INSI assay shared the lowest PPA with the AmoyDx kit (94.7%) and the lowest NPA with the Illumina TSO kit (81.3%).

Techniques: In Silico, Serial Dilution, Sequencing

Journal: mBio

Article Title: Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment

doi: 10.1128/mBio.01150-21

Figure Lengend Snippet: (Top) 18 O labeling of 16S rRNA genes from Thalassospira OTU_6 after 6 and 18 months of incubation with 18 O-labeled water from the 3-mbsf sediment . OTU_6 was one of >30 OTUs that were identified as 18 O labeled and actively growing in the incubations . (Middle) Oxygen concentration over time in the 18-month slurry from the 3-mbsf incubation (filled circles) and slurries containing labeled water and autoclaved sediment (killed control). The O 2 consumption rate was 0.04 μmol O 2 liter −1 day −1 . (Bottom) Cultivation of colony-forming bacteria on solid medium after the 18-month incubation of sediment slurries in sterile 18 O-labeled artificial seawater. No bacterial colonies formed on petri dishes that were inoculated with the killed-control slurries. A total of 21 colonies were picked for genome sequencing, all of which were affiliated with the genus Thalassospira .

Article Snippet: Sequencing libraries for the MinION system were prepared using the ligation sequencing kit (Oxford Nanopore Technologies) according to the manufacturer’s instructions.

Techniques: Labeling, Incubation, Concentration Assay, Bacteria, Sterility, Sequencing

Journal: mBio

Article Title: Genome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment

doi: 10.1128/mBio.01150-21

Figure Lengend Snippet: Recombination in the conserved core genome is limited in subseafloor Thalassospira populations. The maximum likelihood (PhyML) phylogenetic tree is based on a concatenated alignment of 1,809 genes conserved across all Thalassospira genomes (“core genes”). Black circles on nodes represent bootstrap values of >95%. The positions of recombination events in the core genome are represented by dark-blue dots. Positions of low nucleotide diversity and no recombination events in the core genome are shown in light blue. Nucleotide diversity at specific sites in the core genome is illustrated with a color gradient (white, less diversity; orange, more diversity). Histograms on the right display the total number of recombination events (imports) in each genome sequence and ancestral-state reconstructions (internal nodes), as detected by ClonalFrameML.

Article Snippet: Sequencing libraries for the MinION system were prepared using the ligation sequencing kit (Oxford Nanopore Technologies) according to the manufacturer’s instructions.

Techniques: Sequencing