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
linked-read WGS on 23 mCRPC biopsy specimens and analyzed cell-free DNA sequencing
… In addition to frequent rearrangements affecting known prostate cancer genes, we observed …

Identifying phased mutations and complex rearrangements in human prostate cancer cell lines through linked-read whole-genome sequencing

MT Pham, A Gupta, H Gupta, A Vaghasia… - Molecular Cancer …, 2022 - AACR
prostate cancer research, but their genomes remain incompletely characterized. Here, we
utilized whole-genome linked-read sequencing for … lines in prostate cancer research including …

Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines

MT Pham, H Gupta, A Gupta, A Vaghasia, AM Skaist… - Cancer Research, 2021 - AACR
sequencing with allelic phasing of genomic alterations has not been … whole genome
linked-read sequencing of high molecular weight DNA (>60Kbp) from eight common prostate cancer

Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing

E Heitzer, P Ulz, J Belic, S Gutschi, F Quehenberger… - Genome medicine, 2013 - Springer
reads (range, 1.1 (CSPC4) to 5.2 (CRPC5) million reads) for the plasma samples from patients
with prostate cancer … and men with prostate cancer we first calculated the genome-wide z-…

Whole-genome sequence of the metastatic PC3 and LNCaP human prostate cancer cell lines

I Seim, PL Jeffery, PB Thomas… - … : Genes, Genomes …, 2017 - academic.oup.com
prostate cancer cell lines are widely studied, having been described in thousands of
publications over the last four decades. Here, we report short-read whole-genome sequencing (…

Phased Mutations and Complex Rearrangements in Human Prostate Cancer Cell Lines through Linked-Read Whole Genome Sequencing

MT Pham, H Gupta, A Gupta, A Vaghasia, A Skaist… - bioRxiv, 2021 - biorxiv.org
Linked-read sequencing of human PCa cell lines We performed linked read sequencing of
high molecular weight DNA from … prostatic epithelial cell line RWPE-1 (Fig. 1A; Table S1). The …

Integrated analyses highlight interactions between the three-dimensional genome and DNA, RNA and epigenomic alterations in metastatic prostate cancer

SG Zhao, M Bootsma, S Zhou, R Shrestha… - Nature Genetics, 2024 - nature.com
… the effects of regulatory regions linked through 3D DNA structure to the promoters of genes,
we integrated our Hi-C data with linear prostate cancer histone modification ChIP–seq data …

Exploring the tumor genomic landscape of aggressive prostate cancer by whole‐genome sequencing of tissue or liquid biopsies

S Weiss, P Lamy, M Rusan, M Nørgaard… - … Journal of Cancer, 2024 - Wiley Online Library
… age-related signatures SBS1 and SBS5. In addition, they detected the DNA repair-related
, supporting our finding that DNA repair-related signatures were more frequently observed in …

Prostate cancer genomics by high-throughput technologies: genome-wide association study and sequencing analysis

H Nakagawa - Endocrine-related cancer, 2013 - erc.bioscientifica.com
… in high-throughput genomic technologies enable us to analyze prostate cancer genomics
more … Next-generation sequencing (NGS) can analyze whole genomes (3 Gb) and the whole …

Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer

C Wu, AW Wyatt, AV Lapuk, A McPherson… - The Journal of …, 2012 - Wiley Online Library
… a novel and highly aggressive case of prostate cancer with unique biological features and, …
of genome, exome and transcriptome sequences for basic tumour biology, sequence‐based …