ArticleNucleic acids research2017
NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 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
92 citing papers in PubMed.
- Evolution of AR and Non-AR Alterations in ctDNA of Patients with Metastatic Prostate Cancer Treated in the Phase III Alliance A031201 Trial.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Trial
- Neoadjuvant ipilimumab and nivolumab in resectable cutaneous squamous cell carcinoma: a randomized phase 2 trial.Nature medicine · 2025Trial
- Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity.Nature communications · 2021Trial
- An enhanced genetic model of relapsed IGH-translocated multiple myeloma evolutionary dynamics.Blood cancer journal · 2020Trial
- Putative glioblastoma origin-like cells in the subventricular zone: isolation and characterization.Experimental & molecular medicine · 2026Article
- The PLK4 inhibitor RP-1664 demonstrates potent efficacy in neuroblastoma preclinical models through a dual mechanism of sensitivity.Nature communications · 2026Article
- CREsted: modeling genomic and synthetic cell-type-specific enhancers across tissues and species.Nature methods · 2026Article
- Cell-free DNA methylome and fragmentome analysis for relapse monitoring of Ewing sarcoma.EMBO molecular medicine · 2026Article
- Integrative Multi-omics Analysis of the Human Skeletal Muscle Response to Endurance or Resistance Exercise: Findings from the Molecular Transducers of Physical Activity Consortium (MoTrPAC).bioRxiv : the preprint server for biology · 2026Article
- Multi-Omic, Multi-Tissue Responses to Acute Exercise in Sedentary Adults: Findings from the Molecular Transducers of Physical Activity Consortium.bioRxiv : the preprint server for biology · 2026Article
- Article
- NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.NAR genomics and bioinformatics · 2026Article
- Tailorable porous collagen hydrogels as a physiologically relevant platform for extrachromosomal DNA-associated colorectal cancer research.Theranostics · 2026Article
- Genomic and transcriptomic dynamics in the stepwise progression of lung adenocarcinoma.Cell research · 2025Article
- Clinical, pathological and molecular characteristics of patients with disease recurrence despite pathologic response to neoadjuvant ipilimumab plus nivolumab in stage III melanoma.Communications medicine · 2025Article
- Identification of Sample Processing Errors in Microbiome Studies Using Host Genetic Profiles.bioRxiv : the preprint server for biology · 2025Article
- Multiomic integration reveals subtype-specific predictors of neoadjuvant treatment response in breast cancer.Science advances · 2025Article
- Genotyping from targeted NGS data based on a small set of SNPs correctly matches patient samples.BMC research notes · 2025Article
- SAVANA: reliable analysis of somatic structural variants and copy number aberrations using long-read sequencing.Nature methods · 2025Article
- The Open Pediatric Cancer Project.bioRxiv : the preprint server for biology · 2025Article
32 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies. AVAILABILITY: https://github.com/parklab/NGSCheckMate.
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.