Methods for mapping 3D chromosome architecture

R Kempfer, A Pombo - Nature Reviews Genetics, 2020 - nature.com
Determining how chromosomes are positioned and folded within the nucleus is critical to
understanding the role of chromatin topology in gene regulation. Several methods are …

The emerging clinical relevance of genomics in cancer medicine

MF Berger, ER Mardis - Nature reviews Clinical oncology, 2018 - nature.com
The combination of next-generation sequencing and advanced computational data analysis
approaches has revolutionized our understanding of the genomic underpinnings of cancer …

GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data

M Babadi, JM Fu, SK Lee, AN Smirnov, LD Gauthier… - Nature …, 2023 - nature.com
Copy number variants (CNVs) are major contributors to genetic diversity and disease. While
standardized methods, such as the genome analysis toolkit (GATK), exist for detecting short …

Readfish enables targeted nanopore sequencing of gigabase-sized genomes

A Payne, N Holmes, T Clarke, R Munro… - Nature …, 2021 - nature.com
Nanopore sequencers can be used to selectively sequence certain DNA molecules in a pool
by reversing the voltage across individual nanopores to reject specific sequences, enabling …

Neoantigen vaccine generates intratumoral T cell responses in phase Ib glioblastoma trial

DB Keskin, AJ Anandappa, J Sun, I Tirosh… - Nature, 2019 - nature.com
Neoantigens, which are derived from tumour-specific protein-coding mutations, are exempt
from central tolerance, can generate robust immune responses, and can function as bona …

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

D Liu, B Schilling, D Liu, A Sucker, E Livingstone… - Nature medicine, 2019 - nature.com
Immune-checkpoint blockade (ICB) has demonstrated efficacy in many tumor types, but
predictors of responsiveness to anti-PD1 ICB are incompletely characterized. In this study …

Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes

B Chapuy, C Stewart, AJ Dunford, J Kim, A Kamburov… - Nature medicine, 2018 - nature.com
Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is
a clinically and genetically heterogeneous disease that is further classified into …

Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma

D Miao, CA Margolis, W Gao, MH Voss, W Li… - Science, 2018 - science.org
Immune checkpoint inhibitors targeting the programmed cell death 1 receptor (PD-1)
improve survival in a subset of patients with clear cell renal cell carcinoma (ccRCC). To …

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

MG Filbin, I Tirosh, V Hovestadt, MKL Shaw… - Science, 2018 - science.org
Gliomas with histone H3 lysine27-to-methionine mutations (H3K27M-glioma) arise primarily
in the midline of the central nervous system of young children, suggesting a cooperation …

An immunogenic personal neoantigen vaccine for patients with melanoma

PA Ott, Z Hu, DB Keskin, SA Shukla, J Sun, DJ Bozym… - Nature, 2017 - nature.com
Effective anti-tumour immunity in humans has been associated with the presence of T cells
directed at cancer neoantigens, a class of HLA-bound peptides that arise from tumour …