ArticlePloS one2016
A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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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.
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Who cites it
22 citing papers in PubMed.
- Telomere-to-telomere genome assembly of pumpkin (Horticulture research · 2026Article
- The repertoire of short tandem repeats across the tree of life.Genome biology · 2025Article
- BiU-Net: A Biologically Informed U-Net for Genotype Imputation.Research square · 2025Article
- iPSC-modelling reveals genetic associations and morphological alterations of oligodendrocytes in schizophrenia.Translational psychiatry · 2025Article
- In vitro HIV DNA integration in STAT3 drives T cell persistence-A model of HIV-associated T cell lymphoma.PLoS pathogens · 2025Article
- Article
- Polygenic risk for schizophrenia converges on alternative polyadenylation as molecular mechanism underlying synaptic impairment.bioRxiv : the preprint server for biology · 2024Article
- Assessing Genetic Distinctness and Redundancy of Plant Germplasm Conserved Ex Situ Based on Published Genomic SNP Data.Plants (Basel, Switzerland) · 2023Article
- Identification and validation of quantitative trait loci for fertile spikelet number per spike and grain number per fertile spikelet in bread wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Recommendations, guidelines, and best practice for the use of human induced pluripotent stem cells for neuropharmacological studies of neuropsychiatric disorders.Neuroscience applied · 2023Review
- Contribution of schizophrenia polygenic burden to longitudinal phenotypic variance in 22q11.2 deletion syndrome.Molecular psychiatry · 2022Article
- Amplification of human interneuron progenitors promotes brain tumors and neurological defects.Science (New York, N.Y.) · 2022Article
- Article
- Twelve years of SAMtools and BCFtools.GigaScience · 2021Article
- Cystatin B is essential for proliferation and interneuron migration in individuals with EPM1 epilepsy.EMBO molecular medicine · 2020Article
- Characterization of Prevalence and Health Consequences of Uniparental Disomy in Four Million Individuals from the General Population.American journal of human genetics · 2019Article
- Genomic integrity of human induced pluripotent stem cells: Reprogramming, differentiation and applications.World journal of stem cells · 2019Review
- Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT.BMC genomics · 2019Article
- Systems-Wide Approaches in Induced Pluripotent Stem Cell Models.Annual review of pathology · 2019Review
- A homozygous G insertion in MPLKIP leads to TTDN1 with the hypergonadotropic hypogonadism symptom.BMC medical genetics · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Genomic screening for chromosomal abnormalities is an important part of quality control when establishing and maintaining stem cell lines. We present a new method for sensitive detection of copy number alterations, aneuploidy, and contamination in cell lines using genome-wide SNP genotyping data. In contrast to other methods designed for identifying copy number variations in a single sample or in a sample composed of a mixture of normal and tumor cells, this new method is tailored for determining differences between cell lines and the starting material from which they were derived, which allows us to distinguish between normal and novel copy number variation. We implemented the method in the freely available BCFtools package and present results based on induced pluripotent stem cell lines obtained in the HipSci project.
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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.