Cytopia – the future of cytogenetics. Before we jump into how Bionano Optical Genome Mapping with Saphyr is going to revolutionize cytogenetics, first you need to know how we got here.


What is cytogenetics?

Cytogenetics is the study of chromosomes through a microscope.1 It uses techniques that visualize the individual chromosomes for analysis. By examining chromosomes in detail, cytogeneticists can identify broken, missing, or extra chromosomes.


Specific genetic diseases and cancers can have changes in individual chromosomes that can be identified. If damaged, missing, rearranged, or extra chromosomes are established, it can help diagnose disease and potentially define treatment options for that disease.


What is cytogenomics?

Advances in the field have allowed for the incorporation of molecular techniques to analyze chromosomes. This is cytogenomics. Cytogenomics focuses on the genomic variations and architecture at microscopic, submicroscopic, and molecular resolutions. It can shed light on genome behavior that causes cancer or genetic disorders.


Cytogenomic technology can detect absent chromosome imbalances much smaller than what can be seen with traditional cytogenetic microscope technology. These tiny imbalances are called microdeletions or microinsertions.


Evolution from Cytogenetics to Cytogenomics

Due to innovations in molecular biology and instrumentation technology, cytogenetics has evolved considerably over the last few decades resulting in cytogenomics.3 Some of the key developments are noted in the timeline below:


  • The 1960s-1970s The revolution of conventional cytogenetics (karyotyping). Scientists developed chromosomal banding methods to identify individual chromosomes as unique entities based on their specific banding patterns4.
  • 1968 Chromosome banding techniques 3
  • 1969 Molecular hybridization of radioactive DNA to the DNA 3
  • 1973 Philadelphia chromosome is the result of t(9;22) 3
  • 1976 High Resolution Banding 3
  • 1979 Flow Cytogenetics (flow chromosome sorting) 3
  • The 1980s- The introduction of molecular cytogenetics. By observing particular DNA sequences in the chromosomes and nuclei of cancer cells, it led to the precise identification of clinically relevant genetic abnormalities. FISH was the primary technique introduced for molecular cytogenetic characterization4.
  • 1981 In situ hybridization, biotin labeled (non-radioactive) 3
  • 1982 Indirect FISH 3
  • 1984 Direct FISH 3
  • 1986 Interphase FISH 3
  • 1988 In situ hybridization, digoxigenin labeled 3
  • 1988 Use of cot 1 DNA to reduce background signals 3
  • 1989 Combinatorial Labeling 3
  • 1989 Primed In situ Labeling (PRINS) 3
  • The 1990’s- Scientists used FISH technology to develop a genome-wide screening analysis known as the CGH technique4.
  • 1990 Identification of translocation in interphase cell by FISH 3
  • 1992 DOP PCR labeling of probe 3
  • 1992 Comparative Genomic Hybridization (CGH) 3
  • 1992 Quantitative Fluorescent PCR 3
  • 1993 Fiber FISH
  • 1996 Multiplex FISH (M FISH) 3
  • 1996 Spectral Karyotyping (SKY FISH) 3
  • 1997 DNA array (matrix) CGH 3
  • 1998 Array CGH using BAC clones 3
  • 1999 Array CGH using oligonucleotides probes 3
  • 1999 Array CGH using SNP oligonucleotides probes 3
  • The 2000’s- A significant step forward in cytogenomic technology and the cancer field, and consequently in personalized cancer genomics, with the development of NGS. 4.
    • 2008 Next Generation Sequencing 3


Revolutionizing Cytogenomics

Cytogenomic technology has evolved. Traditional cytogenetic methods have limited resolution and speed. The Saphyr system from Bionano Genomics can detect all structural variant types at high sensitivities. Even those present at low allele fractions in heterogeneous cancer samples, in an unbiased genome-wide manner.


The Saphyr system has revolutionized cytogenomics by showing a 100% concordance to traditional cytogenetic methods – array CGH, karyotyping, and FISH. It allows for a better resolution and a more complete picture of complex aberrations. Stay tuned for more on Cytopia, but in the meantime, visit our videos page and watch recordings from our recent Next-Generation Cytogenomics Symposium to learn more about how Saphyr outperforms the gold standard.







  1. NCI Dictionary of Cancer Terms. National Cancer Institute. Published 2021. Accessed January 5, 2021.
  2. Papadakis M, McPhee S, Bernstein J. Quick Medical Diagnosis & Treatment 2020. McGraw Hill; 2020:40-09.
  3. Halder A, Jain M. Cytogenetics to Cytogenomics: Transition from Chromosome to DNA Sequence. Global Journal of Human Genetics & Gene Therapy. 2014:53-67. doi:10.14205/2311-0309.2014.02.01.5
  4. Ribeiro I, Melo J, Carreira I. Cytogenetics and Cytogenomics Evaluation in Cancer. Int J Mol Sci. 2019;20(19):4711. doi:10.3390/ijms20194711
  5. Genetics vs. Genomics Fact Sheet. Published 2021. Accessed January 6, 2021.



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