ArticleScientific reports2019
Deep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Article
- ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.Nature methods · 2026Article
- Lancet2: Improved and accelerated somatic variant calling with joint multi-sample local assembly graphs.NAR genomics and bioinformatics · 2026Article
- Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally Diverse Cohort.bioRxiv : the preprint server for biology · 2026Article
- Proteomic signatures of adipocyte recruitment in breast cancer.Endocrine-related cancer · 2026Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.Genome biology · 2026Article
- Whole-genome sequencing of cell-free DNA for assessment of minimal residual disease in high-risk smoldering multiple myeloma.HemaSphere · 2026Article
- Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.Cell reports · 2025Article
- ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.Nature communications · 2025Article
- A recurrent sequencing artifact on Illumina sequencers with two-color fluorescent dye chemistry and its impact on somatic variant detection.bioRxiv : the preprint server for biology · 2025Article
- Multiplexed, universal probe-based rare variant detection with USE-PCR.Scientific reports · 2025Article
- Evidence for a transgenerational mutational signature from ionizing radiation exposure in humans.Scientific reports · 2025Article
- A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer.NPJ precision oncology · 2025Article
- Article
- Article
- Missense and loss-of-function variants at GWAS loci in familial Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2024Article
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment.Nature medicine · 2024Article
- Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer's disease.Acta neuropathologica · 2024Article
- Childhood cancer mutagenesis caused by transposase-derived PGBD5.Science advances · 2024Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we performed whole-genome sequencing of 3 common cancer cell lines (COLO-829, HCC-1143 and HCC-1187) along with their matched normal cell lines to great sequencing depths (up to 278x coverage) on both Illumina HiSeqX and NovaSeq sequencing instruments. Somatic calling was generally consistent between the two platforms despite minor differences at the read level. We designed and implemented a novel pipeline for the analysis of tumor-normal samples, using multiple variant callers. We show that coupled with a high-confidence filtering strategy, the use of combination of tools improves the accuracy of somatic variant calling. We also demonstrate the utility of the dataset by creating an artificial purity ladder to evaluate the somatic pipeline and benchmark methods for estimating purity and ploidy from tumor-normal pairs. The data and results of the pipeline are made accessible to the cancer genomics community.
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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.