Cited by 129Genomics and Chromatin DynamicsGenetic Associations and EpidemiologyEpigenetics and DNA Methylation

Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants

Open access
Zhang, Siwei, Zhang, Hanwen, Zhou, Yifan, Qiao, Min, Zhao, Siming, Kozlova, Alena, Shi, Jianxin, Sanders, Alan R. +13 more·2020·Science

Abstract

Effects of allele-specific open chromatin: Genetic variants in noncoding regions of the genome may underlie the development of disease. However, we are just beginning to tease apart the function of such variants associated with neuropsychiatric disease. Using five types of neural progenitor cells derived from 20 human induced pluripotent stem cell lines, Zhang et al. looked at allele-specific open chromatin (ASoC) variants. Many ASoC variants overlapped with genomic elements, such as transcription factor binding sites, and loci identified in genome-wide association studies for neurological traits. From the experimental and computational analyses, they identified single-nucleotide polymorphisms and illuminate how one schizophrenia-associated variant affects neurodevelopment. Science , this issue p. 561

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  • eSNP-karyotyping was performed for all cell lines used to eliminate potential chromosomal abnormalities.

    “eSNP-karyotyping was performed for all cell lines used to eliminate potential chromosomal abnormalities, as previously described20,21.”

    From PICALM Alzheimer’s risk allele causes aberrant lipid droplets in microglia (2025) · cites this paper as [20]

    The paper’s passage describing the 20 iPSC lines and their assays (section labeled Abstract, page unavailable) does not say they underwent eSNP-karyotyping. Searches for eSNP-karyotyping and chromosomal-abnormality screening found only a reference to a separate chromosomal-aberration assay, not a statement that this procedure was performed on all cell lines. (LLM, conf=0.72)

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Research works printed but not linked: 1

  1. [70]Willer CJ, Discovery and refinement of loci associated with lipid levels. Nat Genet 45, 1274– 1283 (2013). 24097068 PMC3838666

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Authors
Zhang, S., Zhang, H., Zhou, Y., Qiao, M., Zhao, S., Kozlova, A., Shi, J., Sanders, A. R., Wang, G., Luo, K., Sengupta, S., West, S., Qian, S., Streit, M., Avramopoulos, D., Cowan, C. A., Chen, M., Pang, Z. P., Gejman, P. V., He, X., & Duan, J.
Affiliations
  • Endeavor Health (US)
  • University of Chicago (US)
  • National Cancer Institute (US)
  • Johns Hopkins University (US)
  • Harvard University (US)
  • Rutgers, The State University of New Jersey (US)
Corresponding author
  • Zhang, Siwei
  • Zhang, Hanwen
  • Zhou, Yifan
  • Qiao, Min
  • Zhao, Siming
  • He, Xin
  • Duan, Jubao
Venue
Science
Published
2020-07-31
Volume
369
Issue
6503
Pages
561-565
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
OpenAlex
W3046891017
Cited by
127
References
88
Citations by year
2026: 13 · 2025: 14 · 2024: 17 · 2023: 25 · 2022: 30 · 2021: 20 · 2020: 8
FWCI
6.81
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
NIH Office of the Director (R01MH106575, R01MH116281, R01AG063175, R01MH110531, R01AA023797, R01MH113215)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
non-coding variants, chromatin accessibility, iPSC-derived neurons, brain development, transcription factor binding, enhancers, expression quantitative trait loci, chromatin interactions
MeSH terms
Alleles, Brain, Chromatin, Enhancer Elements, Genetic, Humans, Risk, Schizophrenia, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Induced Pluripotent Stem Cells

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