Karyogram viewer online: ISCN karyotype and pedigree integration

Short version. A karyogram is the visual representation of a person's chromosomes arranged in standard order, used in clinical cytogenetics to show numerical and structural abnormalities. ISCN — the International System for Human Cytogenomic Nomenclature — provides the notation for describing karyotypes and structural variants, as in 46,XX,t(9;22)(q34;q11.2). In many clinical contexts the pedigree and the karyogram need to be read together, particularly when a balanced translocation in one generation produces unbalanced offspring in the next. Evagene's built-in karyogram viewer brings both into the same workspace.

What a karyogram shows

A karyogram is a systematically arranged display of chromosomes, typically from a metaphase spread in which chromosomes are condensed and individually distinguishable. The classical human karyogram shows 22 autosome pairs plus the sex chromosomes, labelled in order of size and identified by their banding pattern after Giemsa staining (G-banding) or other techniques.

Clinical karyograms are used to detect two broad classes of abnormality.

Numerical abnormalities. The wrong number of chromosomes. Trisomies — an extra copy of a chromosome, as in trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), trisomy 13 (Patau syndrome). Monosomies — a missing copy, as in monosomy X (Turner syndrome). Polyploidies — a full extra set, as in triploidy. Sex chromosome variations including Klinefelter syndrome (47,XXY), 47,XYY, 47,XXX.

Structural abnormalities. Rearrangements within or between chromosomes. Balanced reciprocal translocations exchange material between two chromosomes without gain or loss; Robertsonian translocations fuse two acrocentric chromosomes at the centromere. Deletions lose a segment of a chromosome; duplications add an extra copy of a segment. Inversions reverse a segment within a chromosome. Rings form when a chromosome's ends join. Isochromosomes have two identical arms.

Modern clinical cytogenetics extends traditional karyotyping with chromosomal microarray, FISH, optical genome mapping, and sequencing-based approaches that detect submicroscopic changes not visible on G-banded metaphases. ISCN accommodates results from these techniques within the same notational framework.

Reading ISCN notation

ISCN notation has a specific grammar that, once learned, is compact and precise. The headline conventions:

• Chromosome number and sex. Start with the total chromosome count, followed by the sex chromosomes. 46,XX for a typical female, 46,XY for a typical male.
• Abnormality shorthand. After the chromosome count and sex, any abnormality is listed with standard abbreviations: + for an extra chromosome (47,XY,+21 for Down syndrome), - for a missing chromosome (45,X for Turner syndrome), del for deletion, dup for duplication, t for translocation, inv for inversion, i for isochromosome.
• Band notation. A band is identified by chromosome, arm (p for short arm, q for long arm), region, and band within region. 9q34 means the band at the 4th band of the 3rd region of the long arm of chromosome 9. Sub-bands are added with a decimal: 11q23.3.
• Breakpoints. Structural changes are annotated with the breakpoints involved. t(9;22)(q34;q11.2) means a reciprocal translocation between chromosome 9 at band q34 and chromosome 22 at band q11.2 — the classical Philadelphia translocation seen in chronic myeloid leukaemia.
• Clone notation. For cancer cytogenetics, multiple clones and their frequencies are annotated in brackets.

A clinical cytogenetic report might read 46,XX,t(11;22)(q23.3;q11.2) for a balanced maternal translocation, alongside an affected child's result of 46,XX,der(22)t(11;22)(q23.3;q11.2)mat for an unbalanced derivative. The mat indicates the derivative chromosome was inherited from the mother.

When the karyotype and pedigree need to be read together

Several clinical scenarios require the karyogram and the pedigree to be considered as a single unit.

Balanced translocations across generations. A balanced reciprocal translocation is usually phenotypically silent in the carrier, because there is no net gain or loss of genetic material. At meiosis, however, the translocation can produce unbalanced gametes, leading to miscarriage, stillbirth, or live-born children with chromosomal imbalance. A pedigree with recurrent miscarriages and an affected child often points to a parental balanced translocation; testing the parents and mapping the result onto the pedigree is the next step.

Robertsonian translocations. Fusion of two acrocentric chromosomes (13, 14, 15, 21, 22) produces a derivative chromosome with 45 chromosomes counted but no loss of genetic material. Robertsonian carriers are at elevated risk of trisomy in their offspring — famously, Robertsonian translocation-associated Down syndrome.

Inversions and their reproductive consequences. Pericentric and paracentric inversions can produce recombinant unbalanced gametes when large enough. A family history of recurrent miscarriage combined with an inversion in a parent is a common reason for pedigree-karyotype combined review.

Ring chromosomes and X-autosome translocations. These have specific segregation patterns and phenotypic consequences that are best understood in the family context.

Cancer cytogenetics in families. Some inherited cancer predispositions have characteristic cytogenetic signatures; pedigree-karyotype combined views support the interpretation.

A short history of cytogenetics in clinical pedigrees

Until the mid-twentieth century, the human chromosome count itself was not reliably known. The development of tissue culture, hypotonic swelling, and metaphase spreading in the 1950s allowed Tjio and Levan to establish the correct human count as 46. The first chromosomal disease — trisomy 21 — was identified shortly after. G-banding, developed in the early 1970s, made individual chromosomes and specific bands reliably identifiable, and the first ISCN was published in 1971. Subsequent editions (1978, 1981, 1985, 1991, 1995, 2005, 2009, 2013, 2016, 2020) have expanded the nomenclature to cover FISH, microarray, optical mapping, and sequencing results.

The integration of karyogram and pedigree into a single clinical record is a relatively recent development. For most of the history of clinical cytogenetics, the pedigree lived in the clinical notes while the karyotype sat in the laboratory report; bringing them onto the same screen is a feature of modern clinical software, not a long-standing convention.

What to look for in a karyogram viewer

A clinical karyogram viewer needs to do more than render an attractive image. Practically useful features include:

• Accurate banding patterns. The viewer should render chromosomes with realistic G-banding that corresponds to published ideograms, not a stylised cartoon.
• Hover and click annotations. Hovering over a band should reveal its identity and approximate coordinates; clicking should pin an information panel for reference while reading another part of the karyogram.
• Structural abnormality rendering. Translocations, deletions, duplications, and inversions should be drawn in a way that makes the abnormality visible rather than hidden in a text label.
• ISCN round-trip. The viewer should accept ISCN as input and emit ISCN as output, so clinical reports can be generated from the diagram and diagrams can be constructed from report strings.
• Embedding. In a clinical pedigree platform, the karyogram should sit inside the pedigree workspace without a context switch — ideally on the same canvas as the pedigree itself.
• Export. PNG and SVG export for clinical reports; SVG is preferable for print-quality reports because it scales without aliasing.

Limitations of karyogram viewers

A karyogram viewer is not a cytogenetic laboratory. It renders data derived from laboratory analysis; it does not generate the data itself. Several limits follow.

A viewer can show what is provided as input, but it cannot infer what is not provided. Submicroscopic changes below the resolution of the underlying technique are not visible. Mosaicism — different cells with different karyotypes — requires specific annotation; a single karyogram does not convey it by default.

Clinical interpretation rests with the cytogenetic laboratory and the clinical geneticist, not with the viewer. A viewer supports communication and reasoning, but diagnostic classification depends on laboratory-grade analysis and clinical judgement.

How Evagene supports karyograms

Evagene includes an interactive karyogram viewer designed to sit within the pedigree workspace rather than as a separate application. Karyotype data can be attached to individuals in the pedigree, so a balanced translocation carrier and their affected offspring can be viewed side-by-side without switching contexts. The viewer renders chromosomes with standard G-banding at conventional resolution, supports hover tooltips for band annotation, and supports click-to-pin information panels for sustained reference.

The karyogram can be embedded on the same canvas as the pedigree, so a clinician can hold the pedigree and the karyotype in one view while drafting a clinical interpretation or a report. PNG and SVG export preserve the karyogram for inclusion in clinical letters and publications. ISCN notation is used throughout the platform for description and for report generation; clinicians can enter an ISCN string and see it rendered, or adjust the rendering and see the ISCN update.

For integration with broader pedigree workflows, karyotype data flows through the same data model as disease annotations and other individual-level information, so REST API, webhooks, MCP server, and embeddable viewer expose karyotype data alongside the rest of the pedigree.

Frequently asked questions

Related reading

• Pedigree drawing software: standard notation
• Clinical genetics pedigree tool
• Rare disease pedigree software
• Mendelian inheritance calculator
• Pedigree OCR: scanning legacy pedigree images
• Evagene platform: API and embeddable viewer