Journal: Frontiers in Molecular Biosciences

Article Title: A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

doi: 10.3389/fmolb.2023.1141534

Figure Lengend Snippet: Schematic representation of mechanistic strategies of barcoding. (A–C) Barcodes can be introduced to a template using adaptors through direct ligation (A) , using RT- or PCR primers at the reverse transcription or PCR amplification step (B) , and using hybridizing molecular inversion probes (C) . (D) Schematic representation of the difference between “barcodes” and “sample indexes”. Barcodes aim to correct sequencing errors. For example, a misreading nucleotide, guanosine (G) can be corrected in final consensus sequences for a pool of Sample 1 (top panel). Sample indexes are used to multiplex different sequencing amplicons generated from different pools of samples (Sample 1, 2, and 3) (bottom panel). Panel (A) is modified based on in and panel (C) is modified based on in .

Article Snippet: Primer-associated approach , Sequence-based barcodes , SQK-RBK004: transposase carrying barcodes to the site of the cleavage , - , - , Whole genome , Oxford Nanopore Rapid Barcoding kit (SQK-RBK004) , SARS-CoV-2 patient samples (nasopharyngeal swab) , Oxford Nanopore , Guppy version 3.6.0; ARTIC Network bioinformatics protocol , Multiplex samples , Propose a method to sequence the whole genome of SARS-CoV-2 in a rapid and cost-efficient manner , .

Techniques: Ligation, Reverse Transcription, Amplification, Sequencing, Multiplex Assay, Generated, Modification

Journal: Frontiers in Molecular Biosciences

Article Title: A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level

doi: 10.3389/fmolb.2023.1141534

Figure Lengend Snippet: Systematic comparison of barcoding strategies used in the category of molecular barcodes.

Article Snippet: Primer-associated approach , Sequence-based barcodes , SQK-RBK004: transposase carrying barcodes to the site of the cleavage , - , - , Whole genome , Oxford Nanopore Rapid Barcoding kit (SQK-RBK004) , SARS-CoV-2 patient samples (nasopharyngeal swab) , Oxford Nanopore , Guppy version 3.6.0; ARTIC Network bioinformatics protocol , Multiplex samples , Propose a method to sequence the whole genome of SARS-CoV-2 in a rapid and cost-efficient manner , .

Techniques: Comparison, Software, Sequencing, Multiplex Assay, CRISPR, Plasmid Preparation, Microarray, Binding Assay, Amplification, Extraction, Ligation, DNA Sequencing, Multiplexing, Generated, Reverse Transcription, Staining, Flow Cytometry, High Throughput Screening Assay, Inhibition, Blocking Assay, Conjugation Assay, RNA Sequencing Assay, Transmission Assay, Incubation, Diagnostic Assay, Next-Generation Sequencing, Infection

Journal: bioRxiv

Article Title: FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies

doi: 10.1101/2023.03.02.530819

Figure Lengend Snippet: A . Overall percentage of CG:TA transitions in sequencing reads after library amplification using Q5 (left), Q5U® (center) and Taq DNA polymerase (right), with (DNA repair (orange), UDG (brown)) and without (blue) DNA repair treatment of the lung tumor FFPE sample. Experiments were done in duplicate and error bars are reflecting the variability between replicates. B . Profiles of C to T transitions on read 1 (R1, left) and read 2 (R2, right) as a function of read position (in bp). Libraries were amplified using Q5 (top), Q5U® (middle) and Taq DNA polymerase (bottom). Experiments were done in duplicate. Fraction of C to T is a global count of the of C (on the reference genome) to T (on the mapped reads) normalized to the total number of C to C matches. C . Schema representing the fate of the deaminated strand (gray) and the un-damaged strand (purple) after end repair (red) and amplification with Q5 (left) and Taq or Q5U (right).

Article Snippet: The DNA repair step commonly used in this manuscript corresponds to the NEBNext FFPE DNA Repair v2 Module and contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow including UDG, Endonuclease IV, Fpg, Endonuclease VIII, T4 PDG, Taq DNA ligase and Bst DNA polymerase.

Techniques: Sequencing, Amplification

Journal: bioRxiv

Article Title: FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies

doi: 10.1101/2023.03.02.530819

Figure Lengend Snippet: A . Overall percentage of CG:TA transitions in sequencing reads for lung (left) and pancreatic (right) tumor FFPE samples. Samples were either left untreated (orange) or treated with DNA repair mix before (red) and after (blue) end repair. B . Breakdown of the fraction of C:T transitions according to Read types, Read 1 (R1, top) and Read 2 (R2, bottom) and position on the read starting from the 5’ end. Two FFPE samples have been used for these experiments : Lung tumor FFPE sample (Blue) and pancreatic tumor FFPE sample (red) treated with DNA repair after end repair (left), before end repair (right) and no treatment (middle). Fraction of C to T is a global count of the of C (on the reference genome) to T (on the mapped reads) normalized to the total number of C to C matches. Red arrows indicate positions of increased C to T transition rate.

Article Snippet: The DNA repair step commonly used in this manuscript corresponds to the NEBNext FFPE DNA Repair v2 Module and contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow including UDG, Endonuclease IV, Fpg, Endonuclease VIII, T4 PDG, Taq DNA ligase and Bst DNA polymerase.

Techniques: Sequencing

Journal: bioRxiv

Article Title: FFPE DNA shows two major error profiles derived from deamination of cytosine and methylcytosine that can be mitigated using distinct repair strategies

doi: 10.1101/2023.03.02.530819

Figure Lengend Snippet: Substitution profiles for low (less than 1% A ) and high (more than 10% B ) allelic frequency substitution. Barplot representing the number of genomic positions per megabases (mb). The barplots are color coded according to the substitution types and organized by contexts (XpA, XpT, XpC and XpG with X= A, C, T or G) and reads (read1, top and read2, bottom). Sequencing depth has been downsample to 300-fold coverage for comparison, thus the variant read number for high (>10%) allelic frequency is above 30 reads supporting the presence of a variant and low (<1%) allelic frequency is below 3 reads supporting the presence of a variant. The equivalent result for medium (1 to 10%) allelic frequency substitution is plotted on and . All reads substitution have a Phred Quality Scores Q>30. CpA context has no high allelic frequency substitution in Read 2 in the DNA repair sample. The excess of G to T can be attributed to oxidative damage.

Article Snippet: The DNA repair step commonly used in this manuscript corresponds to the NEBNext FFPE DNA Repair v2 Module and contains enzymes and buffers that are optimized to repair FFPE DNA in next generation sequencing workflow including UDG, Endonuclease IV, Fpg, Endonuclease VIII, T4 PDG, Taq DNA ligase and Bst DNA polymerase.

Techniques: Sequencing, Variant Assay