Computational immunogenomic approaches to predict response to cancer immunotherapies

V Addala, F Newell, JV Pearson, A Redwood… - Nature Reviews …, 2024 - nature.com
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The
establishment of large-scale genomic collaborative efforts along with the development of …

[HTML][HTML] The evolution of lung cancer and impact of subclonal selection in TRACERx

AM Frankell, M Dietzen, M Al Bakir, EL Lim, T Karasaki… - Nature, 2023 - nature.com
Lung cancer is the leading cause of cancer-associated mortality worldwide. Here we
analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 …

Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer

C Herberts, M Annala, J Sipola, SWS Ng, XE Chen… - Nature, 2022 - nature.com
Circulating tumour DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer
genoty** and longitudinal disease monitoring. However, owing to past emphasis on …

CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction

K Grigoriadis, A Huebner, A Bunkum, E Colliver… - Nature …, 2024 - nature.com
Intratumor heterogeneity provides the fuel for the evolution and selection of subclonal tumor
cell populations. However, accurate inference of tumor subclonal architecture and …

Haplotype-aware analysis of somatic copy number variations from single-cell transcriptomes

T Gao, R Soldatov, H Sarkar, A Kurkiewicz… - Nature …, 2023 - nature.com
Genome instability and aberrant alterations of transcriptional programs both play important
roles in cancer. Single-cell RNA sequencing (scRNA-seq) has the potential to investigate …

Characterizing allele-and haplotype-specific copy numbers in single cells with CHISEL

S Zaccaria, BJ Raphael - Nature biotechnology, 2021 - nature.com
Single-cell barcoding technologies enable genome sequencing of thousands of individual
cells in parallel, but with extremely low sequencing coverage (< 0.05×) per cell. While the …

Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidates for targeted treatment

H Sun, S Cao, RJ Mashl, CK Mo, S Zaccaria… - Nature …, 2021 - nature.com
Abstract Development of candidate cancer treatments is a resource-intensive process, with
the research community continuing to investigate options beyond static genomic …

Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective

R Mathur, Q Wang, PG Schupp, A Nikolic, S Hilz… - Cell, 2024 - cell.com
Treatment failure for the lethal brain tumor glioblastoma (GBM) is attributed to intratumoral
heterogeneity and tumor evolution. We utilized 3D neuronavigation during surgical resection …

[HTML][HTML] Deterministic evolution and stringent selection during preneoplasia

K Karlsson, MJ Przybilla, E Kotler, A Khan, H Xu… - Nature, 2023 - nature.com
The earliest events during human tumour initiation, although poorly characterized, may hold
clues to malignancy detection and prevention. Here we model occult preneoplasia by …

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

S Aganezov, S Goodwin, RM Sherman… - Genome …, 2020 - genome.cshlp.org
Improved identification of structural variants (SVs) in cancer can lead to more targeted and
effective treatment options as well as advance our basic understanding of the disease and …