Journal: Genome Medicine

Article Title: Nanopore sequencing with unique molecular identifiers enables accurate mutation analysis and haplotyping in the complex lipoprotein(a) KIV-2 VNTR

doi: 10.1186/s13073-024-01391-8

Figure Lengend Snippet: Performance measures compared to ultra-deep NGS sequencing of 15 human DNA samples (SAPHIR) for the V14 chemistry (HAC and SUP basecalling). A Performance of UMI-ONT-Seq for the 15 human DNA samples. Black points are median values. Colored points are the single samples. We observed high agreement between the ultra-deep NGS sequencing and UMI-ONT-Seq for most samples, leading to median performance values above 95% and slightly higher performance values for SUP basecalling. B Performance values for duplex basecalling (SUPDUP). Black points and lines are median values and interquartile range. Gray points are the single samples. Despite increased raw read quality, there was a significant drop in sensitivity when using SUPDUP basecalling (see “ ” for explanation). C Performance values for ONT-Seq (without UMIs) for different chemistries (R9, V14) and basecalling algorithms (HAC, SUP, SUPDUP) (black points and lines are median values and interquartile ranges; colored points are the single samples). Sensitivity increased with increasing raw read quality up to median values of 95% for SUPDUP basecalling, but precision and F1 score were consistently low due to by high number of false positives. D Correlation of variant levels for each mutation of all 15 DNA samples (black points) of UMI-ONT-Seq for V14 HAC and SUP basecalling compared to ultra-deep NGS sequencing. We observed nearly 100% correlation ( r and R . 2 > 0.977) for both conditions, with no bias across the variant level range ( E )

Article Snippet: Fig. 4 Performance measures compared to ultra-deep NGS sequencing of 15 human DNA samples (SAPHIR) for the V14 chemistry (HAC and SUP basecalling).

Techniques: Sequencing, Variant Assay, Mutagenesis