Towards accurate and reliable resolution of structural variants for clinical diagnosis

Z Liu, R Roberts, TR Mercer, J Xu, FJ Sedlazeck… - Genome biology, 2022 - Springer
Structural variants (SVs) are a major source of human genetic diversity and have been
associated with different diseases and phenotypes. The detection of SVs is difficult, and a …

Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing

LT Fang, B Zhu, Y Zhao, W Chen, Z Yang… - Nature …, 2021 - nature.com
The lack of samples for generating standardized DNA datasets for setting up a sequencing
pipeline or benchmarking the performance of different algorithms limits the implementation …

From samples to germline and somatic sequence variation: a focus on next-generation sequencing in melanoma research

A Muñoz-Barrera, LA Rubio-Rodríguez… - Life, 2022 - mdpi.com
Next-generation sequencing (NGS) applications have flourished in the last decade,
permitting the identification of cancer driver genes and profoundly expanding the …

Haplotype-resolved assemblies and variant benchmark of a Chinese Quartet

P Jia, L Dong, X Yang, B Wang, SJ Bush, T Wang, J Lin… - Genome Biology, 2023 - Springer
Background Recent state-of-the-art sequencing technologies enable the investigation of
challenging regions in the human genome and expand the scope of variant benchmarking …

Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome

D Masood, L Ren, C Nguyen, FG Brundu, L Zheng… - Genome Biology, 2024 - Springer
Background Copy number variation (CNV) is a key genetic characteristic for cancer
diagnostics and can be used as a biomarker for the selection of therapeutic treatments …

A multiomic characterization of the leukemia cell line REH using short-and long-read sequencing

ML Wiklander, G Arvidsson, I Bunikis… - Life Science …, 2024 - life-science-alliance.org
The B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t (12; 21) ETV6::
RUNX1 translocation, is known to have a complex karyotype defined by a series of large …

The Application of Long-Read Sequencing to Cancer

L Ermini, P Driguez - Cancers, 2024 - mdpi.com
Simple Summary Cancer is a complex disease caused by a slew of genetic mutations
discovered through advances in sequencing technologies such as next-generation …

Effects of Food Concentration and Light Intensity on the Growth of a Model Coral

TY Fan, YL Huang, A Mayfield - Oceans, 2024 - mdpi.com
Since reef-building corals rely on both heterotrophy and endosymbiotic dinoflagellate
autotrophy to meet their metabolic needs, it is necessary to consider both food supply and …

A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data

X Chen, LT Fang, Z Chen, W Chen, B Zhu, H Wu… - bioRxiv, 2024 - biorxiv.org
Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful tool for cancer
research, enabling in-depth characterization of tumor heterogeneity at the single-cell level …

Epigenomic, transcriptomic and proteomic characterizations of reference samples

C Nepal, W Chen, Z Chen, JA Wrobel, L Xie, W Liao… - bioRxiv, 2024 - biorxiv.org
A variety of newly developed next-generation sequencing technologies are making their
way rapidly into the research and clinical applications, for which accuracy and cross-lab …