Nanopore adaptive sampling accurately detects nucleotide variants and improves the characterization of large-scale rearrangement for the diagnosis of cancer predisposition.

Background: Molecular diagnosis has become highly significant for patient management in oncology.

Methods: Here, 30 well-characterized clinical germline samples were studied with adaptive sampling to enrich the full sequence of 152 cancer predisposition genes. Sequencing was performed on Oxford Nanopore (ONT) R10.

Genomic analysis of adult thrombotic microangiopathies in less than 3 days: from rapid to fast genomics to treatment.

Using nanopore sequencing, we showed the feasibility and impact of rapid genomic screening for managing thrombotic microangiopathies in 18 prospective cases, achieving diagnoses in <3 days. We compared the results with standard exome sequencing, cost efficiency, and complement blockade initiation.

dipwmsearch: a Python package for searching di-PWM motifs.

Motivation: Seeking probabilistic motifs in a sequence is a common task to annotate putative transcription factor binding sites or other RNA/DNA binding sites. Useful motif representations include position weight matrices (PWMs), dinucleotide PWMs (di-PWMs), and hidden Markov models (HMMs). Dinucleotide PWMs not only combine the simplicity of PWMs-a matrix form and a cumulative scoring function-but also incorporate dependency between adjacent positions in the motif (unlike PWMs which disregard any dependency).