Proteogenomic data and resources for pan-cancer analysis

Y Li, Y Dou, FDV Leprevost, Y Geffen, AP Calinawan… - Cancer cell, 2023 - cell.com
Summary The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium
(CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics …

Variant calling and benchmarking in an era of complete human genome sequences

ND Olson, J Wagner, N Dwarshuis, KH Miga… - Nature Reviews …, 2023 - nature.com
Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …

Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients

M Menzel, S Ossowski, S Kral, P Metzger… - NPJ Precision …, 2023 - nature.com
A growing number of druggable targets and national initiatives for precision oncology
necessitate broad genomic profiling for many cancer patients. Whole exome sequencing …

Control-independent mosaic single nucleotide variant detection with DeepMosaic

X Yang, X Xu, MW Breuss, D Antaki, LL Ball… - Nature …, 2023 - nature.com
Mosaic variants (MVs) reflect mutagenic processes during embryonic development and
environmental exposure, accumulate with aging and underlie diseases such as cancer and …

Comprehensive benchmarking and guidelines of mosaic variant calling strategies

YJ Ha, S Kang, J Kim, J Kim, SY Jo, S Kim - Nature Methods, 2023 - nature.com
Rapid advances in sequencing and analysis technologies have enabled the accurate
detection of diverse forms of genomic variants represented as heterozygous, homozygous …

TMBserval: a statistical explainable learning model reveals weighted tumor mutation burden better categorizing therapeutic benefits

Y Wang, J Wang, W Fang, X Xiao, Q Wang… - Frontiers in …, 2023 - frontiersin.org
A high tumor mutation burden (TMB) is known to drive the response to immune checkpoint
inhibitors (ICI) and is associated with favorable prognoses. However, because it is a one …

Performance evaluation of six popular short-read simulators

M Milhaven, SP Pfeifer - Heredity, 2023 - nature.com
High-throughput sequencing data enables the comprehensive study of genomes and the
variation therein. Essential for the interpretation of this genomic data is a thorough …

De novo identification of expressed cancer somatic mutations from single-cell RNA sequencing data

T Zhang, H Jia, T Song, L Lv, DC Gulhan, H Wang… - Genome Medicine, 2023 - Springer
Identifying expressed somatic mutations from single-cell RNA sequencing data de novo is
challenging but highly valuable. We propose RESA–Recurrently Expressed SNV Analysis, a …

Evidence of site-specific and male-biased germline mutation rate in a wild songbird

H Zhang, M Lundberg, M Tarka… - Genome Biology and …, 2023 - academic.oup.com
Germline mutations are the ultimate source of genetic variation and the raw material for
organismal evolution. Despite their significance, the frequency and genomic locations of …

[HTML][HTML] Recommendations for the use of in silico approaches for next-generation sequencing bioinformatic pipeline validation: a joint report of the Association for …

EJ Duncavage, JF Coleman, ME de Baca… - The Journal of Molecular …, 2023 - Elsevier
In silico approaches for next-generation sequencing (NGS) data modeling have utility in the
clinical laboratory as a tool for clinical assay validation. In silico NGS data can take a variety …