Beyond assembly: the increasing flexibility of single-molecule sequencing technology

PW Hook, W Timp - Nature Reviews Genetics, 2023 - nature.com
The maturation of high-throughput short-read sequencing technology over the past two
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …

Copy number variation: methods and clinical applications

O Pös, J Radvanszky, J Styk, Z Pös, G Buglyó… - Applied Sciences, 2021 - mdpi.com
Gains and losses of large segments of genomic DNA, known as copy number variants
(CNVs) gained considerable interest in clinical diagnostics lately, as particular forms may …

Resolving complex structural variants via nanopore sequencing

S Romagnoli, N Bartalucci, AM Vannucchi - Frontiers in Genetics, 2023 - frontiersin.org
The recent development of high-throughput sequencing platforms provided impressive
insights into the field of human genetics and contributed to considering structural variants …

Nanopore sequencing from liquid biopsy: analysis of copy number variations from cell-free DNA of lung cancer patients

F Martignano, U Munagala, S Crucitta, A Mingrino… - Molecular cancer, 2021 - Springer
In the “precision oncology” era the characterization of tumor genetic features is a pivotal step
in cancer patients' management. Liquid biopsy approaches, such as analysis of cell-free …

Evaluation of germline structural variant calling methods for nanopore sequencing data

D Bolognini, A Magi - Frontiers in Genetics, 2021 - frontiersin.org
Structural variants (SVs) are genomic rearrangements that involve at least 50 nucleotides
and are known to have a serious impact on human health. While prior short-read …

Comprehensive identification of pathogenic variants in retinoblastoma by long-and short-read sequencing

J Zheng, T Li, H Ye, Z Jiang, W Jiang, H Yang, Z Wu… - Cancer Letters, 2024 - Elsevier
Retinoblastoma (RB) is the most common intraocular malignancy in childhood. The causal
variants in RB are mostly characterized by previously used short-read sequencing (SRS) …

Probability distribution of copy number alterations along the genome: an algorithm to distinguish different tumour profiles

L Esteves, F Caramelo, IP Ribeiro, IM Carreira… - Scientific Reports, 2020 - nature.com
Copy number alterations (CNAs) comprise deletions or amplifications of fragments of
genomic material that are particularly common in cancer and play a major contribution in its …

Barcode aware adaptive sampling for GridION and PromethION Oxford Nanopore sequencers

A Payne, R Munro, N Holmes, C Moore, M Carlile… - BioRXiv, 2021 - biorxiv.org
Adaptive sampling enables selection of individual DNA molecules from sequencing
libraries, a unique property of nanopore sequencing. Here we develop our adaptive …

A blood drop through the pore: nanopore sequencing in hematology

N Bartalucci, S Romagnoli, AM Vannucchi - Trends in Genetics, 2022 - cell.com
The development of new sequencing platforms, technologies, and bioinformatics tools in the
past decade fostered key discoveries in human genomics. Among the most recent …

GASOLINE: detecting germline and somatic structural variants from long-reads data

A Magi, G Mattei, A Mingrino, C Caprioli, C Ronchini… - Scientific Reports, 2023 - nature.com
Long-read sequencing allows analyses of single nucleic-acid molecules and produces
sequences in the order of tens to hundreds kilobases. Its application to whole-genome …