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Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment
In solid tumor oncology, circulating tumor DNA (ctDNA) is poised to transform care through accurate assessment of minimal residual disease (MRD) and therapeutic response monitoring. To overcome the sparsity of...
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Open AccessMost large structural variants in cancer genomes can be detected without long reads
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole geno...
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Open AccessLong-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers
Homologous recombination (HR) deficiency is associated with DNA rearrangements and cytogenetic aberrations1. Paradoxically, the types of DNA rearrangements that are specifically associated with HR-deficient cance...
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Faster detection of somatic structural variants
The algorithmic detection of cancer-associated variants can be accelerated by leveraging machine-learning classifiers to filter out reads matched to pan-genome k-mer sets.
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Open AccessAuthor Correction: The evolutionary history of 2,658 cancers
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Open AccessAuthor Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
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Open AccessAuthor Correction: Patterns of somatic structural variation in human cancer genomes
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Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer
Fanconi anaemia (FA), a model syndrome of genome instability, is caused by a deficiency in DNA interstrand crosslink repair resulting in chromosome breakage1–3. The FA repair pathway protects against endogenous a...
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Article
Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing
High-order three-dimensional (3D) interactions between more than two genomic loci are common in human chromatin, but their role in gene regulation is unclear. Previous high-order 3D chromatin assays either mea...
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Open AccessPublisher Correction: Recurrent somatic mutations as predictors of immunotherapy response
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Open AccessRecurrent somatic mutations as predictors of immunotherapy response
Immune checkpoint blockade (ICB) has transformed the treatment of metastatic cancer but is hindered by variable response rates. A key unmet need is the identification of biomarkers that predict treatment respo...
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Open AccessSomatic whole genome dynamics of precancer in Barrett’s esophagus reveals features associated with disease progression
While the genomes of normal tissues undergo dynamic changes over time, little is understood about the temporal-spatial dynamics of genomes in premalignant tissues that progress to cancer compared to those that...
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Open AccessStructural variant evolution after telomere crisis
Telomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of experimental telomere crisis identified in prev...
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Open AccessShotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV...
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Histone H1 loss drives lymphoma by disrupting 3D chromatin architecture
Linker histone H1 proteins bind to nucleosomes and facilitate chromatin compaction1, although their biological functions are poorly understood. Mutations in the genes that encode H1 isoforms B–E (H1B, H1C, H1D an...
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Open AccessAnalyses of non-coding somatic drivers in 2,658 cancer whole genomes
The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from ...
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Open AccessPatterns of somatic structural variation in human cancer genomes
A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1–7. Here we develop methods t...
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Open AccessThe evolutionary history of 2,658 cancers
Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing inf...
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Next-generation characterization of the Cancer Cell Line Encyclopedia
Large panels of comprehensively characterized human cancer models, including the Cancer Cell Line Encyclopedia (CCLE), have provided a rigorous framework with which to study genetic variants, candidate targets...
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Clinical hallmarks in whole cancer genomes
Fraser and colleagues describe the whole-genome sequencing (WGS) profiles of over 200 localized intermediate-risk prostate cancers. WGS has been widely used in research but not, thus far, in clinical settings....
