ArticleNucleic acids research2019
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed.
- Hepatitis B virus protein X promotes survival and loss of hepatocyte identity in a differentiated human liver organoid system.Cell death and differentiation · 2026Article
- The HepG2 Cell Line as a Model for Studying Metabolic Dysfunction-Associated Steatotic Liver Disease.International journal of molecular sciences · 2026Review
- Accurate prediction of cohesin and RNA Polymerase II-associated chromatin interactions using convolutional neural networks.Nucleic acids research · 2026Article
- Evaluation of the Immortalized Primary Human Hepatocyte Cell Line Fa2N-4 as a Model for Metabolic Dysfunction-Associated Steatotic Liver Disease.Gastro hep advances · 2026Article
- Review
- Effects of the Polar Fraction ofInternational journal of molecular sciences · 2025Article
- Haplotype-resolved assemblies of the MHC region in five widely used tumor cell lines.Genes & diseases · 2025Article
- Optimizing Cell Density and Unveiling Cytotoxic Profiles of DMSO and Ethanol in Six Cancer Cell Lines: Experimental and In Silico Insights.Methods and protocols · 2025Article
- Review
- Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits.Genome research · 2025Article
- Current Understanding of Pathogenic Mechanisms and Disease Models of Citrin Deficiency.Journal of inherited metabolic disease · 2025Review
- Distinct roles of Constitutive Photomorphogenesis Protein 1 homolog (COP1) in human hepatocyte models.Frontiers in molecular biosciences · 2025Article
- Article
- Characterizing the allele-specific gene expression landscape in high hyperdiploid acute lymphoblastic leukemia with BASE.Scientific reports · 2024Article
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- CRISPR in Nucleic Acids Research: the sequel.Nucleic acids research · 2024Article
- hcHCR: High-Throughput Single-Cell Imaging of RNA in Human Primary Immune Cells.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Systematic elucidation of genetic mechanisms underlying cholesterol uptake.Cell genomics · 2023Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
Abstract
HepG2 is one of the most widely used human cancer cell lines in biomedical research and one of the main cell lines of ENCODE. Although the functional genomic and epigenomic characteristics of HepG2 are extensively studied, its genome sequence has never been comprehensively analyzed and higher order genomic structural features are largely unknown. The high degree of aneuploidy in HepG2 renders traditional genome variant analysis methods challenging and partially ineffective. Correct and complete interpretation of the extensive functional genomics data from HepG2 requires an understanding of the cell line's genome sequence and genome structure. Using a variety of sequencing and analysis methods, we identified a wide spectrum of genome characteristics in HepG2: copy numbers of chromosomal segments at high resolution, SNVs and Indels (corrected for aneuploidy), regions with loss of heterozygosity, phased haplotypes extending to entire chromosome arms, retrotransposon insertions and structural variants (SVs) including complex and somatic genomic rearrangements. A large number of SVs were phased, sequence assembled and experimentally validated. We re-analyzed published HepG2 datasets for allele-specific expression and DNA methylation and assembled an allele-specific CRISPR/Cas9 targeting map. We demonstrate how deeper insights into genomic regulatory complexity are gained by adopting a genome-integrated framework.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.