Structural variation in the sequencing era

SS Ho, AE Urban, RE Mills - Nature Reviews Genetics, 2020 - nature.com
Identifying structural variation (SV) is essential for genome interpretation but has been
historically difficult due to limitations inherent to available genome technologies. Detection …

Fibroblast growth factor receptors as treatment targets in clinical oncology

M Katoh - Nature reviews Clinical oncology, 2019 - nature.com
FGFRs are receptor tyrosine kinases with a role in several biological processes, such as the
regulation of development and tissue repair. However, alterations in FGFRs 1–4, such as …

Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing

SR Viswanathan, G Ha, AM Hoff, JA Wala… - Cell, 2018 - cell.com
Nearly all prostate cancer deaths are from metastatic castration-resistant prostate cancer
(mCRPC), but there have been few whole-genome sequencing (WGS) studies of this …

Resolving the full spectrum of human genome variation using Linked-Reads

P Marks, S Garcia, AM Barrio, K Belhocine… - Genome …, 2019 - genome.cshlp.org
Large-scale population analyses coupled with advances in technology have demonstrated
that the human genome is more diverse than originally thought. To date, this diversity has …

A new era of long-read sequencing for cancer genomics

Y Sakamoto, S Sereewattanawoot… - Journal of human genetics, 2020 - nature.com
Cancer is a disease largely caused by genomic aberrations. Utilizing many rapidly emerging
sequencing technologies, researchers have studied cancer genomes to understand the …

What is speciation genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species

CR Campbell, JW Poelstra… - Biological Journal of the …, 2018 - academic.oup.com
As is true of virtually every realm of the biological sciences, our understanding of speciation
is increasingly informed by the genomic revolution of the past decade. Investigators can ask …

Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer

CY Wu, BT Lau, HS Kim, A Sathe, SM Grimes… - Nature …, 2021 - nature.com
Cancer progression is driven by both somatic copy number aberrations (CNAs) and
chromatin remodeling, yet little is known about the interplay between these two classes of …

Circulating tumor DNA enables sensitive detection of actionable gene fusions and rearrangements across cancer types

PM Kasi, JK Lee, LW Pasquina, B Decker… - Clinical Cancer …, 2024 - AACR
Purpose: Genomic rearrangements can generate potent oncogenic drivers or disrupt tumor
suppressor genes. This study examines the landscape of fusions and rearrangements …

Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562

B Zhou, SS Ho, SU Greer, X Zhu, JM Bell… - Genome …, 2019 - genome.cshlp.org
K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE
and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional …

Structural variation detection and analysis using Bionano optical mapping

S Chan, E Lam, M Saghbini, S Bocklandt… - Copy number variants …, 2018 - Springer
The need to accurately identify the complete structural variation profile of genomes is
becoming increasingly evident. In contrast to reference-based methods like sequencing or …