Variant calling and benchmarking in an era of complete human genome sequences
Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …
[HTML][HTML] A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
C Xu - Computational and structural biotechnology journal, 2018 - Elsevier
Detection of somatic mutations holds great potential in cancer treatment and has been a
very active research field in the past few years, especially since the breakthrough of the next …
very active research field in the past few years, especially since the breakthrough of the next …
Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer
Abstract The Zero Childhood Cancer Program is a precision medicine program to benefit
children with poor-outcome, rare, relapsed or refractory cancer. Using tumor and germline …
children with poor-outcome, rare, relapsed or refractory cancer. Using tumor and germline …
Pan-cancer whole-genome analyses of metastatic solid tumours
Metastatic cancer is a major cause of death and is associated with poor treatment efficacy. A
better understanding of the characteristics of late-stage cancer is required to help adapt …
better understanding of the characteristics of late-stage cancer is required to help adapt …
Reference standards for next-generation sequencing
Next-generation sequencing (NGS) provides a broad investigation of the genome, and it is
being readily applied for the diagnosis of disease-associated genetic features. However, the …
being readily applied for the diagnosis of disease-associated genetic features. However, the …
Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors
INTRODUCTION Gene fusions are often disease-defining events in cancer. The mutational
processes that give rise to fusions, their timing relative to initial diagnosis, and whether they …
processes that give rise to fusions, their timing relative to initial diagnosis, and whether they …
Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv
Y Shiraishi, J Koya, K Chiba, A Okada… - Nucleic acids …, 2023 - academic.oup.com
We present our novel software, nanomonsv, for detecting somatic structural variations (SVs)
using tumor and matched control long-read sequencing data with a single-base resolution …
using tumor and matched control long-read sequencing data with a single-base resolution …
SJPedPanel: a pan-cancer gene panel for childhood malignancies to enhance cancer monitoring and early detection
P Kolekar, V Balagopal, L Dong, Y Liu… - Clinical Cancer …, 2024 - aacrjournals.org
Purpose: The purpose of the study was to design a pan-cancer gene panel for childhood
malignancies and validate it using clinically characterized patient samples. Experimental …
malignancies and validate it using clinically characterized patient samples. Experimental …
Unscrambling cancer genomes via integrated analysis of structural variation and copy number
Complex somatic genomic rearrangements and copy number alterations are hallmarks of
nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural …
nearly all cancers. We have developed an algorithm, LINX, to aid interpretation of structural …
Single-cell sequencing of genomic DNA resolves sub-clonal heterogeneity in a melanoma cell line
EI Velazquez-Villarreal, S Maheshwari… - Communications …, 2020 - nature.com
We performed shallow single-cell sequencing of genomic DNA across 1475 cells from a cell-
line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has …
line, COLO829, to resolve overall complexity and clonality. This melanoma tumor-line has …