V. Bafna

Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers

This paper identifies transcription-replication conflict as a vulnerability in ecDNA-containing cancers and demonstrates that CHK1 inhibition selectively kills these tumors.

CoRAL accurately resolves extrachromosomal DNA genomestructures with long-read sequencing

CoRAL improves ecDNA structure reconstruction using long-read sequencing, outperforming short-read methods in simulations and cell-line datasets.

Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change

The paper introduces OM2BFB, an algorithm detecting BFB amplifications using OGMs, showing high precision and recall, and finds BFB events are common in certain cancers but not linked to intratumoral heterogeneity or rapid genome change.

Coordinated inheritance of extrachromosomal DNA species in human cancer cells

This study shows that multiple extrachromosomal DNA species are coordinately inherited in cancer cells through mitotic co-segregation, enabling oncogene cooperation and guiding therapeutic strategies.

Immortalization and transformation of primary cells mediated by engineered ecDNAs

This paper describes a method to engineer large focal amplifications in primary cells using ecDNAs, showing they promote proliferation and transformation.

Transcriptional immune suppression and upregulation of double stranded DNA damage and repair repertoires in ecDNA-containing tumors

The paper identifies transcriptional correlates of ecDNA in tumors, showing upregulation of DNA repair and downregulation of immune pathways.

Variable Number Tandem Repeats (VNTRs) as modifiers of breast cancer risk in carriers of BRCA1 185delAG

This study identifies VNTRs as modifiers of breast cancer risk in BRCA1 185delAG carriers, finding several VNTRs significantly associated with earlier age of onset compared to SNPs.

Epigenetic dysregulation from chromosomal transit in micronuclei

This study shows that chromosomal transit through micronuclei causes epigenetic dysregulation in cancer cells, leading to long-term chromatin accessibility abnormalities.

Targeted profiling of human extrachromosomal DNA by CRISPR-CATCH

This study introduces CRISPR-CATCH, a method to purify and analyze extrachromosomal DNA, revealing hypomethylation and structural details of ecDNA in cancer cells.

The landscape of extrachromosomal circular DNA in medulloblastoma

This study identifies ecDNA in 18% of medulloblastoma patients, linking it to higher relapse and mortality rates and suggesting enhancer rewiring as an oncogenic mechanism.

Principles of ecDNA random inheritance drive rapid genome change and therapy resistance in human cancers

Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA

The paper analyzes clustered mutations in 2,583 cancer genomes, identifying APOBEC3-driven mutagenesis on ecDNA as a significant contributor to cancer evolution.

EcDNA hubs drive cooperative intermolecular oncogene expression

The paper identifies ecDNA hubs as nuclear structures that drive cooperative oncogene expression through intermolecular enhancer-promoter interactions and shows BET inhibitors can disrupt these hubs and kill cancer cells.

Frequent extrachromosomal oncogene amplification drives aggressive tumors

This study shows that extrachromosomal DNA amplification of oncogenes is common in human cancers and is associated with worse patient outcomes.

Cancer avatars derived from genetically engineered pluripotent stem cells allow for longitudinal assessment of tumor development

This paper introduces cancer avatar models using genetically engineered hiPSCs to study tumor development and heterogeneity in glioblastoma.

Assembly-free and alignment-free sample identification using genome skims

The paper introduces Skmer, an alignment-free tool that uses k-mer decomposition to estimate genomic distances from genome skims, achieving high accuracy in identifying closest matches and inferring phylogeny.

Fine-mapping the Favored Mutation in a Positive Selective Sweep

This paper introduces iSAFE, a method to identify the favored mutation in selective sweeps, and demonstrates its effectiveness on simulated and human genomic data.

CLEAR: Composition of Likelihoods for Evolve And Resequence Experiments

The paper introduces CO_SCPLOWLEARC_SCPLOW, a method for detecting selection in evolve-and-resequence experiments, showing improved power and robustness to coverage variation.