Nir Friedman
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View article: Figure S5 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure S5 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Heterogeneity in patient derived samples, related to Figure 5
View article: Figure S2 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure S2 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Validation of ecDNA in SCLC, related to Figure 2
View article: Table S3 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S3 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Methylation array derived beta values derived from EPIC array used to compare methylation of ecDNA positive and negative regions within several cell lines at the MYC, MYCL and MYCN loci.
View article: Figure 2 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure 2 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Cell line AmpliconArchitect assemblies, related to figure 1 and Figure 2
View article: Figure S1 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure S1 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
ecDNA in SCLC, related to Figure 1
View article: Figure 1 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure 1 extended data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Patient sample AmpliconArchitect assemblies, related to Figure 1
View article: Table S6 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S6 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Enhancer-enhancer interaction results of MYC and MYCL ecDNAs in the DMS-273 cell line.
View article: Table S8 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S8 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Experimental validation of copy-number of the MYC locus in NCI-H889, DMS-114, NCI-H446 and RA022 patient derived cell lines and number of ecDNA and HSR positive cells in the RA022 patient derived cell lines
View article: Table S7 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S7 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Amplified genes identified from cell-free ChIP-seq of patient plasma samples.
View article: Figure S3 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure S3 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Fusion landscape and ecDNA RLF-MYCL fusions, related to Figure 3.
View article: Table S2 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S2 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Enhancer-enhancer interaction analysis derived from H3K27ac HiChIP in the NCI-H889 and NCI-H524 cell lines. Interaction strength of proximal enhancers was calculated from the “.hic” files generated by the JuiceBox suite.
View article: Table S1 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S1 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Expression and copy-number status of recurrently highly amplified genes in patient and cell line samples. The tables summarize copy-number signal and AmpliconArchitect curation, expression of key genes and results of the multivariate analy…
View article: Table S5 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S5 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Amplicon design used for the targeted single-cell copy-number analysis. Normalized depth of MYC and MYCL amplicons in single-cells for the DMS-273 cell line are shown, as well as comparison of MYC amplicon depths in single cells between th…
View article: Figure S4 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure S4 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
ecDNA heterogeneity in SCLC, related to Figure 4
View article: Table S4 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S4 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Fusion analysis results calculated with STARfusion and summary of RLF exon1 and exon2 expression for the CCLE cohort. Table summarizes the RLF-MYCL expression qPCR results.
View article: Diagnosis and Prediction of Precursor States in Multiple Myeloma using Cell-free Chromatin
Diagnosis and Prediction of Precursor States in Multiple Myeloma using Cell-free Chromatin Open
Multiple myeloma (MM) is a hematological malignancy that, in many cases, is preceded by monoclonal gammopathy of undetermined significance (MGUS) and smoldering multiple myeloma (SMM), pre-MM conditions with a lifelong risk of progression …
View article: Epigenetic liquid biopsies reveal endothelial turnover and erythropoiesis in asymptomatic COVID-19
Epigenetic liquid biopsies reveal endothelial turnover and erythropoiesis in asymptomatic COVID-19 Open
Understanding the full spectrum of tissues affected by SARS-CoV-2 is crucial for deciphering the heterogeneous clinical course of COVID-19. We analyzed DNA methylation and histone modifications in circulating chromatin to assess cell type–…
View article: P-272 Ovarian follicular fluid: liquid biopsy insights via cfChIP-seq in IVF and oocyte preservation
P-272 Ovarian follicular fluid: liquid biopsy insights via cfChIP-seq in IVF and oocyte preservation Open
Study question How can cfChIP-seq analysis be used to characterize functional gene expression signatures in follicular fluid and be used to assess ovarian function and oocyte competence? Summary answer CfChIP-seq analysis revealed intact m…
View article: VarNMF: non-negative probabilistic factorization with source variation
VarNMF: non-negative probabilistic factorization with source variation Open
Motivation Non-negative matrix factorization (NMF) is a powerful tool often applied to genomic data to identify non-negative latent components that constitute linearly mixed samples. It is useful when the observed signal combines contribut…
View article: Diagnostic accuracy of point-of-care ultrasound (PoCUS) for the diagnosis of hip effusion in the pediatric emergency department
Diagnostic accuracy of point-of-care ultrasound (PoCUS) for the diagnosis of hip effusion in the pediatric emergency department Open
View article: Urine cf-Nucleosomes: A Non-invasive Window into Human Physiology and Disease
Urine cf-Nucleosomes: A Non-invasive Window into Human Physiology and Disease Open
Urine contains fragments of cell-free DNA, which hold valuable molecular insights into the processes occurring within the urinary system and the whole body. It is unknown whether these fragments are in the form of chromatin, as in the cell…
View article: <scp>SLAM‐Drop</scp> ‐seq reveals <scp>mRNA</scp> kinetic rates throughout the cell cycle
<span>SLAM‐Drop</span> ‐seq reveals <span>mRNA</span> kinetic rates throughout the cell cycle Open
View article: Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma
Polyclonal lymphoid expansion drives paraneoplastic autoimmunity in neuroblastoma Open
View article: Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients
Epigenetic liquid biopsies reveal elevated vascular endothelial cell turnover and erythropoiesis in asymptomatic COVID-19 patients Open
The full spectrum of tissues affected by SARS-CoV-2 infection is crucial for deciphering the heterogenous clinical course of COVID-19. Here, we analyzed DNA methylation and histone modification patterns in circulating chromatin to assess c…
View article: Identification of hepatocyte immune response in Autoimmune Hepatitis from human plasma cfChIP-seq
Identification of hepatocyte immune response in Autoimmune Hepatitis from human plasma cfChIP-seq Open
Autoimmune hepatitis (AIH) is a self-perpetuating inflammatory liver disease with significant morbidity and mortality risks. Patients undergo liver biopsy to confirm diagnosis and affirm subsequent remission. Advances in liquid biopsies sh…
View article: Elevated cfDNA after exercise is derived primarily from mature polymorphonuclear neutrophils, with a minor contribution of cardiomyocytes
Elevated cfDNA after exercise is derived primarily from mature polymorphonuclear neutrophils, with a minor contribution of cardiomyocytes Open
View article: Data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Data from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Small-cell lung cancer (SCLC) is an aggressive neuroendocrine lung cancer. Oncogenic MYC amplifications drive SCLC heterogeneity, but the genetic mechanisms of MYC amplification and phenotypic plasticity, characterized by neu…
View article: Table S7 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S7 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Amplified genes identified from cell-free ChIP-seq of patient plasma samples.
View article: Figure S4 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Figure S4 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
ecDNA heterogeneity in SCLC, related to Figure 4
View article: Table S3 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes
Table S3 from Extrachromosomal DNA Amplification Contributes to Small Cell Lung Cancer Heterogeneity and Is Associated with Worse Outcomes Open
Methylation array derived beta values derived from EPIC array used to compare methylation of ecDNA positive and negative regions within several cell lines at the MYC, MYCL and MYCN loci.