[HTML][HTML] Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for …

MM Li, M Datto, EJ Duncavage, S Kulkarni… - The Journal of molecular …, 2017‏ - Elsevier
Widespread clinical laboratory implementation of next-generation sequencing–based
cancer testing has highlighted the importance and potential benefits of standardizing the …

The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

DR Caswell, P Gui, MK Mayekar, EK Law, O Pich… - Nature Genetics, 2024‏ - nature.com
In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like
(APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven …

Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma

L Au, E Hatipoglu, MR de Massy, K Litchfield, G Beattie… - Cancer cell, 2021‏ - cell.com
ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive
patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma …

Cytosine base editor generates substantial off-target single-nucleotide variants in mouse embryos

E Zuo, Y Sun, W Wei, T Yuan, W Ying, H Sun, L Yuan… - Science, 2019‏ - science.org
Genome editing holds promise for correcting pathogenic mutations. However, it is difficult to
determine off-target effects of editing due to single-nucleotide polymorphism in individuals …

Deterministic evolutionary trajectories influence primary tumor growth: TRACERx renal

S Turajlic, H Xu, K Litchfield, A Rowan, S Horswell… - Cell, 2018‏ - cell.com
The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been
systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients …

Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling

S Hobor, M Al Bakir, CT Hiley, M Skrzypski… - Nature …, 2024‏ - nature.com
The phenomenon of mixed/heterogenous treatment responses to cancer therapies within an
individual patient presents a challenging clinical scenario. Furthermore, the molecular basis …

[HTML][HTML] Tracking cancer evolution reveals constrained routes to metastases: TRACERx renal

S Turajlic, H Xu, K Litchfield, A Rowan, T Chambers… - Cell, 2018‏ - cell.com
Clear-cell renal cell carcinoma (ccRCC) exhibits a broad range of metastatic phenotypes
that have not been systematically studied to date. Here, we analyzed 575 primary and 335 …

Bifrost: highly parallel construction and indexing of colored and compacted de Bruijn graphs

G Holley, P Melsted - Genome biology, 2020‏ - Springer
Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based
assemblers reduce the complexity by compacting paths into single vertices, but this is …

Dissecting the causal mechanism of X-linked dystonia-parkinsonism by integrating genome and transcriptome assembly

T Aneichyk, WT Hendriks, R Yadav, D Shin, D Gao… - Cell, 2018‏ - cell.com
Summary X-linked Dystonia-Parkinsonism (XDP) is a Mendelian neurodegenerative
disease that is endemic to the Philippines and is associated with a founder haplotype. We …

A rationally engineered cytosine base editor retains high on-target activity while reducing both DNA and RNA off-target effects

E Zuo, Y Sun, T Yuan, B He, C Zhou, W Ying, J Liu… - Nature …, 2020‏ - nature.com
Cytosine base editors (CBEs) offer a powerful tool for correcting point mutations, yet their
DNA and RNA off-target activities have caused concerns in biomedical applications. We …