Genomics in the long-read sequencing era
EL van Dijk, D Naquin, K Gorrichon, Y Jaszczyszyn… - Trends in Genetics, 2023 - cell.com
Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …
explore genomes. While in the early years these methods suffered technical limitations, they …
Most large structural variants in cancer genomes can be detected without long reads
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many
structural variants (SVs), particularly large chromosomal alterations. To characterize missing …
structural variants (SVs), particularly large chromosomal alterations. To characterize missing …
Extrachromosomal DNA: Biogenesis and Functions in Cancer
In cancer, oncogenes can untether themselves from chromosomes onto circular,
extrachromosomal DNA (ecDNA) particles. ecDNA are common in many of the most …
extrachromosomal DNA (ecDNA) particles. ecDNA are common in many of the most …
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes
Summary The Long-Read Personalized OncoGenomics (POG) dataset comprises a cohort
of 189 patient tumors and 41 matched normal samples sequenced using the Oxford …
of 189 patient tumors and 41 matched normal samples sequenced using the Oxford …
[HTML][HTML] HPV16 genome structure analysis in oropharyngeal cancer PDXs identifies tumors with integrated and episomal genomes
CD James, RO Otoa, AH Youssef, CT Fontan… - Tumour Virus …, 2024 - Elsevier
HPV+ oropharyngeal squamous cell carcinoma (OPC) incidence recently surpassed
cervical cancer and is the most common HPV-related cancer in the developed world. HPV16 …
cervical cancer and is the most common HPV-related cancer in the developed world. HPV16 …
[HTML][HTML] Targeting PARP for the optimal immunotherapy efficiency in gynecologic malignancies
T Li, X Wang, S Qin, B Chen, M Yi, J Zhou - Biomedicine & …, 2023 - Elsevier
Gynecologic cancer, which includes ovarian, cervical, endometrial, vulvar, and vaginal
cancer, is a major health concern for women all over the world. Despite the availability of …
cancer, is a major health concern for women all over the world. Despite the availability of …
Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing
I Rodriguez, NM Rossi, AG Keskus, Y **e… - The American Journal of …, 2024 - cell.com
Cervical cancer is caused by human papillomavirus (HPV) infection, has few approved
targeted therapeutics, and is the most common cause of cancer death in low-resource …
targeted therapeutics, and is the most common cause of cancer death in low-resource …
Impact and characterization of serial structural variations across humans and great apes
Modern sequencing technology enables the systematic detection of complex structural
variation (SV) across genomes. However, extensive DNA rearrangements arising through a …
variation (SV) across genomes. However, extensive DNA rearrangements arising through a …
Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer
N Sasa, T Kishikawa, M Mori, R Ito, Y Mizoro… - Nature …, 2025 - nature.com
Integration of human papillomavirus (HPV) into the host genome drives HPV-positive head
and neck squamous cell carcinoma (HPV+ HNSCC). Whole-genome sequencing of 51 …
and neck squamous cell carcinoma (HPV+ HNSCC). Whole-genome sequencing of 51 …
Genome Instability Precedes Viral Integration in Human Papillomavirus–Transformed Tonsillar Keratinocytes
K Chan, C Tseng, E Milarachi, D Goldrich… - Molecular Cancer …, 2025 - aacrjournals.org
Approximately 70% of oropharyngeal squamous carcinomas (OPSCC) are associated with
human papillomavirus (HPV). Although patients with HPV-positive (HPV+) tumors generally …
human papillomavirus (HPV). Although patients with HPV-positive (HPV+) tumors generally …