Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Resolving genetic heterogeneity in cancer

S Turajlic, A Sottoriva, T Graham… - Nature Reviews Genetics, 2019 - nature.com
To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones
mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the …

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

K Grosselin, A Durand, J Marsolier, A Poitou… - Nature …, 2019 - nature.com
Modulation of chromatin structure via histone modification is a major epigenetic mechanism
and regulator of gene expression. However, the contribution of chromatin features to tumor …

Clonal heterogeneity and tumor evolution: past, present, and the future

N McGranahan, C Swanton - Cell, 2017 - cell.com
Intratumor heterogeneity, which fosters tumor evolution, is a key challenge in cancer
medicine. Here, we review data and technologies that have revealed intra-tumor …

Machine learning approaches to drug response prediction: challenges and recent progress

G Adam, L Rampášek, Z Safikhani, P Smirnov… - NPJ precision …, 2020 - nature.com
Cancer is a leading cause of death worldwide. Identifying the best treatment using
computational models to personalize drug response prediction holds great promise to …

Unravelling biology and shifting paradigms in cancer with single-cell sequencing

T Baslan, J Hicks - Nature Reviews Cancer, 2017 - nature.com
The fundamental operative unit of a cancer is the genetically and epigenetically innovative
single cell. Whether proliferating or quiescent, in the primary tumour mass or disseminated …

Tumor evolution: Linear, branching, neutral or punctuated?

A Davis, R Gao, N Navin - Biochimica et Biophysica Acta (BBA)-Reviews …, 2017 - Elsevier
Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of
how this genetic diversity emerges over time remains limited. A central challenge in studying …

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

MJ McConnell, JV Moran, A Abyzov, S Akbarian, T Bae… - Science, 2017 - science.org
BACKGROUND Elucidating the genetic architecture of neuropsychiatric disorders remains a
major scientific and medical challenge. Emerging genomic technologies now permit the …

Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer

A McPherson, A Roth, E Laks, T Masud, A Bashashati… - Nature …, 2016 - nature.com
We performed phylogenetic analysis of high-grade serous ovarian cancers (68 samples
from seven patients), identifying constituent clones and quantifying their relative …

Understanding tumour cell heterogeneity and its implication for immunotherapy in liver cancer using single-cell analysis

S Heinrich, AJ Craig, L Ma, B Heinrich, TF Greten… - Journal of …, 2021 - Elsevier
Over the last decade, precision medicine and immunotherapeutic approaches have become
increasingly popular in oncology. Early clinical trials reported promising results, but …