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Cited by 64Genomic variations and chromosomal abnormalitiesGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

Analysis of chromosomal aberrations and recombination by allelic bias in RNA-Seq

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Weissbein, Uri, Schachter, Maya, Egli, Dieter, Benvenisty, Nissim·2016·Nature Communications
DOI 10.1038/ncomms12144PMC PMC4941052
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Abstract

Genomic instability has profound effects on cellular phenotypes. Studies have shown that pluripotent cells with abnormal karyotypes may grow faster, differentiate less and become more resistance to apoptosis. Previously, we showed that microarray gene expression profiles can be utilized for the analysis of chromosomal aberrations by comparing gene expression levels between normal and aneuploid samples. Here we adopted this method for RNA-Seq data and present eSNP-Karyotyping for the detection of chromosomal aberrations, based on measuring the ratio of expression between the two alleles. We demonstrate its ability to detect chromosomal gains and losses in pluripotent cells and their derivatives, as well as meiotic recombination patterns. This method is advantageous since it does not require matched diploid samples for comparison, is less sensitive to global expression changes caused by the aberration and utilizes already available gene expression profiles to determine chromosomal aberrations.

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  • eSNP-Karyotyping is based on measuring the ratio of expressed heterozygous to homozygous SNPs.

    “eSNP-Karyotyping is based on measuring the ratio of expressed heterozygous to homozygous SNPs.”

    From Frequent loss of heterozygosity in CRISPR-Cas9–edited early human embryos (2021) · cites this paper as [26]

    The Results and Methods sections on loss of heterozygosity say eSNP-Karyotyping compares counts of homozygous and heterozygous expressed SNPs, using a homozygous-to-heterozygous ratio. But the Methods section on chromosomal duplications uses the major-to-minor allele read ratio for each SNP. The claimed ratio describes one application, not the method as a whole. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • eSNP-Karyotyping relies on SNP calls from gene expression data and is very sensitive to depth and breadth of sequencing.

    “Since eSNP-Karyotyping relies on SNP calls from gene expression data, it is very sensitive to depth and breadth of sequencing (26).”

    From Frequent loss of heterozygosity in CRISPR-Cas9–edited early human embryos (2021) · cites this paper as [26]

    The Results section (page unavailable) says the method calls SNPs from RNA-Seq data and that detection power depends on read depth; it reports good detection with 15–20 million mapped reads. The paper does not separately establish sensitivity to the breadth of sequencing, so that part of the claim is not supported by our copy. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • Weissbein et al. developed eSNP-Karyotyping for the detection of LOH in chromosome arms.

    “In addition, Weissbein et al. developed a pipeline, called eSNP-Karyotyping, for the detection of LOH in chromosome arms (26).”

    From Frequent loss of heterozygosity in CRISPR-Cas9–edited early human embryos (2021) · cites this paper as [26]

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References 41 · Cited by 64

Research works printed but not linked: 37

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Authors
Weissbein, U., Schachter, M., Egli, D., & Benvenisty, N.
Affiliations
  • Hebrew University of Jerusalem (IL)
  • New York Stem Cell Foundation (US)
Corresponding author
Benvenisty, Nissim
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2016-07-07
Volume
7
Issue
1
Pages
12144-12144
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/ncomms12144
PMC
PMC4941052
OpenAlex
W2469297379
Cited by
64
References
41
Citations by year
2026: 6 · 2025: 8 · 2024: 5 · 2023: 6 · 2022: 12 · 2021: 5 · 2020: 7 · 2019: 10 · 2018: 3 · 2017: 2
FWCI
4.04
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • New York Stem Cell Foundation
  • Rosetrees Trust (M108-F1)
  • Israel Science Foundation (269/12)
  • Azrieli Foundation
  • National Institute of Diabetes and Digestive and Kidney Diseases (P30DK026687)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
chromosomal abnormalities, allelic bias, RNA-seq, aneuploidy, genomic instability, pluripotent cells, meiotic recombination, gene expression profiling, karyology, chromosomal gains and losses
MeSH terms
Alleles, Cell Line, Chromosome Aberrations, Feasibility Studies, Humans, Karyotyping, Recombination, Genetic, RNA, Sensitivity and Specificity, Sequence Analysis, RNA, Gene Expression Profiling, Pluripotent Stem Cells, Genomic Instability

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