Definition and research guide
This page combines a MeSH definition, publication statistics and selected research abstracts. It is a starting point for reading the literature, not a medical textbook or a systematic evidence review.
Content available: 4 complete abstracts (620 words), 10 references. Full article text is not stored or reproduced here; follow the PMID, DOI or PMC links to read the original sources and their access terms.
Definition
Examination of chromosomes to diagnose, classify, screen for, or manage genetic diseases and abnormalities. Following preparation of the sample, karyotyping is performed and/or the specific chromosomes are analyzed.
Definition: NLM Medical Subject Headings (MeSH) scope note (Public domain (U.S. National Library of Medicine); attribution requested). View the MeSH record.
Also known as: Analyses, Cytogenetic; Analysis, Cytogenetic; Cytogenetic Analyses; Cytogenetic Technics; Cytogenetic Technic; Technic, Cytogenetic; Technics, Cytogenetic; Cytogenetic Techniques.
Where it fits in the MeSH classification
- Broader topics
- Cytological Techniques; Genetic Techniques
- Narrower topics
- Chromosome Banding; Karyotyping; Mitotic Index; Comparative Genomic Hybridization; In Situ Hybridization, Fluorescence; Sex Determination Analysis
- See also
- Chromosome Aberrations; Chromosome Mapping; Cytogenetics; Genetic Testing; Karyometry; Molecular Diagnostic Techniques
Related concepts
- Chromosomes
- Karyotyping
Research landscape
PubMed indexes 118,796 records tagged with the MeSH heading “Cytogenetic Analysis” (counts retrieved 2026-10-29). 9,588 of them (8.1%) were published from 2020 onward, and the busiest period so far is through 1999 with 49,866 records.
Reviews account for 7,985 records (6.7%) and meta-analyses for 139. Randomized controlled trials number 385 (0.3%) as a share of all records on the topic. Randomized trials make up only a small share of this literature, so much of what is known comes from laboratory, observational or descriptive work.
Show the data
| Period | Records |
|---|---|
| through 1999 | 49,866 |
| 2000-2009 | 31,124 |
| 2010-2019 | 28,218 |
| 2020 onward | 9,588 |
Publication-type chart data
| Type | Records | Share |
|---|---|---|
| Reviews | 7,985 | 6.7% |
| Meta-analyses | 139 | 0.1% |
| Randomized controlled trials | 385 | 0.3% |
Method: PubMed query "Cytogenetic Analysis"[MeSH Terms] with publication-type and date filters, retrieved 2026-10-29.
Reading the evidence in genetics and genomics
Genetic findings vary widely in strength. A variant linked to a condition in one study may not replicate in other ancestries, and most common variants have small effects that are meaningful only in aggregate. Studies of rare, high-impact variants can support strong causal claims about a gene, while association studies describe statistical links that need functional and independent replication. Check the sample size, the ancestry of participants, whether results were replicated, and whether a laboratory or clinical outcome was actually measured.
Evidence from open-access studies
These open-access studies come from PubMed’s best-match results for this heading (papers whose main topic it is), ranked here by citation count, with one recent addition. Each abstract is reproduced in full under its recorded open licence so that you can read the authors’ own words. They illustrate the literature; they are not a systematic summary of it. Citation counts measure attention, not reliability or clinical benefit.
| Study / authors | Year | Source label / design | Europe PMC citations | Licence / source |
|---|---|---|---|---|
| Deep-tissue transcriptomics and subcellular imaging at high spatial resolution | 2025 | Research article Design not recorded in structured metadata | 62 | cc by PMID 39977545 · DOI · PMC12005972 |
| Three-dimensional single-cell transcriptome imaging of thick tissues | 2024 | Research article Design not recorded in structured metadata | 52 | cc by PMID 39727221 · DOI · PMC11677232 |
| Single-molecule live-cell RNA imaging with CRISPR-Csm | 2025 | Research article Design not recorded in structured metadata | 47 | cc by PMID 39966655 · DOI · PMC12700784 |
| Social lives of bacteria as revealed through CLASI-FISH | 2026 | Review article Design not recorded in structured metadata | 1 | cc by PMID 42614111 · DOI · PMC13538133 |
Deep-tissue transcriptomics and subcellular imaging at high spatial resolution [1]
Abstract reading summary — source excerpts
- Opening excerpt
- Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens.
- Closing excerpt
- cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (124 words)
Limited color channels in fluorescence microscopy have long constrained spatial analysis in biological specimens. We introduce cycle hybridization chain reaction (cycleHCR), a method that integrates multicycle DNA barcoding with HCR to overcome this limitation. cycleHCR enables highly multiplexed imaging of RNA and proteins using a unified barcode system. Whole-embryo transcriptomics imaging achieved precise three-dimensional gene expression and cell fate mapping across a specimen depth of ~310 μm. When combined with expansion microscopy, cycleHCR revealed an intricate network of 10 subcellular structures in mouse embryonic fibroblasts. In mouse hippocampal slices, multiplex RNA and protein imaging uncovered complex gene expression gradients and cell-type-specific nuclear structural variations. cycleHCR provides a quantitative framework for elucidating spatial regulation in deep tissue contexts for research and has potential diagnostic applications.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 39977545 · DOI · PMC12005972
Three-dimensional single-cell transcriptome imaging of thick tissues [2]
Abstract reading summary — source excerpts
- Opening excerpt
- Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues.
- Closing excerpt
- We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (110 words)
Multiplexed error-robust fluorescence in situ hybridization (MERFISH) allows genome-scale imaging of RNAs in individual cells in intact tissues. To date, MERFISH has been applied to image thin-tissue samples of ~10 µm thickness. Here, we present a thick-tissue three-dimensional (3D) MERFISH imaging method, which uses confocal microscopy for optical sectioning, deep learning for increasing imaging speed and quality, as well as sample preparation and imaging protocol optimized for thick samples. We demonstrated 3D MERFISH on mouse brain tissue sections of up to 200 µm thickness with high detection efficiency and accuracy. We anticipate that 3D thick-tissue MERFISH imaging will broaden the scope of questions that can be addressed by spatial genomics.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 39727221 · DOI · PMC11677232
Single-molecule live-cell RNA imaging with CRISPR-Csm [3]
Abstract reading summary — source excerpts
- Opening excerpt
- Understanding the diverse dynamic behaviors of individual RNA molecules in single cells requires visualizing them at high resolution in real time.
- Closing excerpt
- This method has the potential to unlock principles governing the spatiotemporal organization of native transcripts in health and disease.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (140 words)
Understanding the diverse dynamic behaviors of individual RNA molecules in single cells requires visualizing them at high resolution in real time. However, single-molecule live-cell imaging of unmodified endogenous RNA has not yet been achieved in a generalizable manner. Here, we present single-molecule live-cell fluorescence in situ hybridization (smLiveFISH), a robust approach that combines the programmable RNA-guided, RNA-targeting CRISPR-Csm complex with multiplexed guide RNAs for direct and efficient visualization of single RNA molecules in a range of cell types, including primary cells. Using smLiveFISH, we track individual native NOTCH2 and MAP1B transcripts in living cells and identify two distinct localization mechanisms including the cotranslational translocation of NOTCH2 mRNA at the endoplasmic reticulum and directional transport of MAP1B mRNA toward the cell periphery. This method has the potential to unlock principles governing the spatiotemporal organization of native transcripts in health and disease.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 39966655 · DOI · PMC12700784
Social lives of bacteria as revealed through CLASI-FISH [4]
Abstract reading summary — source excerpts
- Opening excerpt
- The spatial organization of microbiomes illuminates their structure, function, and relationship to their host.
- Closing excerpt
- Collectively, visualizing the spatial organization of host-associated microbiomes reveals spatial relationships among taxa and between microbes and host and serves to generate predictions about the dynamics of the host-microbiome interaction.
- Interpretation limits
- Verbatim excerpts from the authors’ abstract; the closing excerpt may describe a finding, limitation or recommendation. Design, population, effect size and uncertainty have not been independently extracted or appraised. Read the complete abstract and linked paper before interpreting the findings.
Read complete abstract (246 words)
The spatial organization of microbiomes illuminates their structure, function, and relationship to their host. Using fluorescence spectral imaging to discriminate up to 16 fluorophores and using combinations of probes to generate unique spectral signatures, combinatorial labeling and spectral imaging-fluorescence in situ hybridization (CLASI-FISH) has been deployed to analyze spatial organization in oral, gut, and marine microbiomes. In dental plaque, imaging revealed the structural role of Corynebacterium matruchotii in organizing the plaque biofilm and revealed previously unrecognized complexity in dental plaque corncob structures. Tongue dorsum biofilms showed a patchy organization around a core of host epithelial cells projecting from the tongue surface, with anaerobes located near the core and oxygen-tolerant taxa near the surface. Taxa that are prominent in these tongue dorsum communities can reduce nitrate to nitrite and thus may play an important role in human nitrate metabolism. In contrast with the highly structured organization of oral biofilms, analysis of the gut microbiome by CLASI-FISH showed a mixed community, indicating that the rate of mixing in the gut is high enough to overcome the tendency of bacterial replication to generate single-taxon patches. Application of CLASI-FISH to blades of kelp showed a dense biofilm with clusters of cocci near the kelp surface, bacteria invading the kelp tissue, and rod-shaped and filamentous bacteria extending into the water column. Collectively, visualizing the spatial organization of host-associated microbiomes reveals spatial relationships among taxa and between microbes and host and serves to generate predictions about the dynamics of the host-microbiome interaction.
Abstract reproduced from the open-access article under the recorded cc by licence; © the authors. PMID 42614111 · DOI · PMC13538133
Key reviews and meta-analyses
The most cited review-type papers among PubMed’s best-match results for this heading, listed with bibliographic details only. Follow the links for the full text and access terms.
- Research article Prenatal diagnosis by chromosomal microarray analysis [5]
- Research article The aneuploidy paradox: costs and benefits of an incorrect karyotype [6]
- Research article Comparison of telomere length measurement methods [7]
- Research article Noninvasive fetal sex determination using cell-free fetal DNA: a systematic review and meta-analysis [8]
- Research article Detecting metabolic activities in single cells, with emphasis on nanoSIMS [9]
- Research article Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review [10]
References
- Gandin V, Kim J, Yang LZ, Lian Y, Kawase T, Hu A, et al.. Deep-tissue transcriptomics and subcellular imaging at high spatial resolution. . 2025. PMID 39977545 · DOI · PMC12005972
- Fang R, Halpern A, Rahman MM, Huang Z, Lei Z, Hell SJ, et al.. Three-dimensional single-cell transcriptome imaging of thick tissues. . 2024. PMID 39727221 · DOI · PMC11677232
- Xia C, Colognori D, Jiang XS, Xu K, Doudna JA. Single-molecule live-cell RNA imaging with CRISPR-Csm. . 2025. PMID 39966655 · DOI · PMC12700784
- Mark Welch JL. Social lives of bacteria as revealed through CLASI-FISH. . 2026. PMID 42614111 · DOI · PMC13538133
- Levy B, Wapner R. Prenatal diagnosis by chromosomal microarray analysis. Fertil Steril. 2018. PMID 29447663 · DOI · PMC5856154
- Sheltzer JM, Amon A. The aneuploidy paradox: costs and benefits of an incorrect karyotype. Trends Genet. 2011. PMID 21872963 · DOI · PMC3197822
- Lai TP, Wright WE, Shay JW. Comparison of telomere length measurement methods. Philos Trans R Soc Lond B Biol Sci. 2018. PMID 29335378 · DOI · PMC5784071
- Devaney SA, Palomaki GE, Scott JA, Bianchi DW. Noninvasive fetal sex determination using cell-free fetal DNA: a systematic review and meta-analysis. JAMA. 2011. PMID 21828326 · DOI · PMC4526182
- Musat N, Foster R, Vagner T, Adam B, Kuypers MM. Detecting metabolic activities in single cells, with emphasis on nanoSIMS. FEMS Microbiol Rev. 2012. PMID 22092433 · DOI
- Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, et al.. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol. 2017. PMID 28129707 · DOI
About this article
- Sources
- NLM Medical Subject Headings (definition, synonyms); NCBI PubMed (counts, identifiers); Europe PMC (open-access abstracts and citation counts).
- Verification
- Every reference was resolved against PubMed on 2026-10-31; title, year and DOI matched.
- Review state
- automated source verified; no human expert review has been recorded yet.
- Version
- 1, last updated 2026-10-29.
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Evidence strength
EvidenceHelix's computed view of the study designs behind this topic: how common meta-analyses, randomized trials and reviews are, how recent the literature is, and a plain-language reading. It describes the design mix of the literature. It is not a quality appraisal of any study, and it is not medical advice.