Chromosomes

Interactive software tool to train users to identify chromosomes
Free to use (does not require an account)
A Lesson in Chromosome Matching - provides a helpful tutorial to get started, including the Chromosome Descriptions page (hover over each chromosome to see tips on how to recognize)
Six sets to practice matching chromosomes and 10 practice cases

Tips and tricks of G-banded chromosome recognition

This slide deck includes images of each chromosome at varying levels of resolution with helpful tips for chromosome recognition.

Nomenclature

ISCN 2020: An International System for Human Cytogenomic Nomenclature (2020) | Books Gateway | Karger Publishers

Human cytogenetics nomenclature book which provides guidelines for describing cytogenomic abnormalities including chromosomal analysis, CGH and SNP arrays, and other cytogenomic methods.

ISCN online forum

Requires subscription access (options include purchasing textbook + one year online access, subscription for four years of online access, or lifetime access). A free trial is available on request.
Provides online access to ISCN as well as a discussion forum to post ISCN questions (reviewed by ISCN committee).

ISCN 2024 Update

This Spotlight Symposium talk at the 2023 CGC annual meeting by Dr. Hastings (ISCN Standing Committee Chair) highlights the upcoming changes to the forthcoming 2024 ISCN nomenclature.

Visualization tool for chromosome abnormalities

CyDAS: free online tool for drawing structural chromosome aberrations - Drawing a Karyogram Online

CyDAS was created in the late 1980s with funding from the German Research Foundation as a free software to help resolve ISCN nomenclature errors that occur during cytogenetic data mining and statistical analyses. This resource provides you a visual representation of various chromosomal rearrangements including translocations and derivative chromosomes in a karyotype. Banding resolutions are for the 400, 550, and 850 band levels.
Allows you to enter ISCN nomenclature and generate ideograms showing the abnormality.
This document provides more information on how to use CyDAS.

Technical standards and guidelines

ACMG Technical Standards for Clinical Genetics Laboratories (2021 revision)

Voluntary standards that establish criteria for clinical labs to provide accurate and reliable testing
Seven sections, including personnel and general lab policies
Clinical Cytogenetics (section E) - Includes guidelines for cell culture, prenatal diagnosis, constitutional studies, neoplastic studies, reporting standards
New in 2024 - updates to Section E6
- Cytogenomic studies of acquired chromosomal abnormalities in solid tumors (PMID: 38376505)
- Cytogenomic studies of acquired chromosomal abnormalities in neoplastic blood, bone marrow, and lymph nodes (PMID: 38349293)

Helpful readings and textbooks

The Principles of Clinical Cytogenetics | SpringerLink

A very comprehensive book about cytogenetics, the clinical and laboratory practices of a cytogenetics laboratory, and including various culturing procedures and techniques.

Human Chromosome Variation: Heteromorphism, Polymorphism and Pathogenesis | SpringerLink

Provides a comprehensive list of common polymorphisms by chromosome that has been observed in the general population.

Clinical Cytogenetics: Current Practices and Beyond

This article provides a detailed analysis of the history of the field of cytogenetics, the advantages and limitations of current cytogenomics technologies including conventional G-banding, FISH, chromosomal microarray, optical genome mapping (OGM) and whole genome sequencing (WGS).
Additionally, it details the history of FISH, the three types of array platforms, introduces OGM, the gaps this technology is expected to fill, and discusses the limitation of WGS for replacing all current standard cytogenetics and molecular technologies.

Report Drafting: Cytogenetic Abnormalities | Wiley Online Books by Susan Mahler Zneimer

This book provides sample clinical reports for common cytogenetic abnormalities (including somatic as well as germline changes) and includes chromosome, FISH, and microarray-based clinical reporting.

The AGT Cytogenetics Laboratory Manual

This textbook produced by the Association of Genetic Technologists provides valuable scientific background for cytogenetic laboratory techniques.
Includes laboratory protocols and practical advice
Chapters on germline and somatic alterations as well as lab management and other topics

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Constitutional Cytogenomics

Recommended readings

Gardner and Sutherland’s Chromosome Abnormalities and Genetic Counseling (5th Edition)

This textbook provides helpful background on the mechanisms of germline chromosome abnormalities, description of different abnormalities and the associated syndromes, as well as implications for genetic counseling.

Examples of common constitutional abnormalities with images

Common Constitutional Chromosomal Syndromes

This document describes several common chromosome abnormalities, the associated syndromes and phenotypes, and shows example images of the abnormal chromosomes.

Unique - Rare chromosome and single gene disorders

Unique - Rare Chromosome and Single Gene Disorders

Unique is a UK-based charity organization established in 1984 to support and provide information for families and medical genetics professionals about specific rare chromosomal and single gene disorders. The website also provides resources for families and a genotype database documenting the clinical history of more than 27,000 members of all ages affected by various disorders.
This document provides more information about how to use the site.

Marker Chromosome Website

Liehr T. 2024. Small supernumerary marker chromosomes

This database includes >7000 cases reported in the literature of individuals with sSMCs
Useful for genotype-phenotype correlation in cases where you identify a small supernumerary chromosome
- Search by chromosome.
- Each page includes a summary of whether or not these individuals had clinical findings and what the phenotypes were.
- Click on Cases with clinical findings or Cases without clinical findings to see individual case info, including chromosomal breakpoints, symptoms, and reference.

Estimation of reproductive risk in balanced translocation carriers

This paper describes some of the challenges with estimating reproductive risk in balanced translocation carriers and provides tools to calculate this risk for translocation of interest.

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Acquired Cytogenomics

Recommended readings

Cancer Cytogenetics: Chromosomal and Molecular Genetic Aberrations of Tumor Cells (Editors: Heim and Mitelman)

This book provides a comprehensive description of recurrent cytogenetic abnormalities in cancer and their clinical significance, with chapters organized by disease.

ACMG Technical Laboratory Standards

Section E6.1-6.6 (Heme and Lymph Nodes)
Section E6.7-6.12 (Solid Tumors)

Molecular/Cytogenetic Education for Hematopathology Fellows: A Recommended Curriculum From the Society for Hematopathology and the Association for Molecular Pathology (PMID 32444878)

While this article is meant for hemepath fellows, it provides a helpful introduction for any trainee
Provides an introduction to cytogenetics and molecular assays as well as a summary of important genetic findings in both myeloid and lymphoid neoplasms

The AGT Cytogenetics Laboratory Manual | Wiley Online Books 4th Edition

Figure 11.2 pg. 512-513- lists common hematological rearrangements seen in conventional G-banding analysis.

Coming Soon! Mayo Clinic Hematology Cytogenetics Reference Sheet

Helpful resources for clinical/pathology background and for evaluating significance of chromosome abnormalities

Clinical/pathology background

WHO Blue Books
National Comprehensive Cancer Network (NCCN) Guidelines

Evaluating significance of chromosome abnormalities

For more information about how and when to use these and other resources, check out this page of Cancer Genomics Resources.

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Data and information obtained from the Cancer Genomics Consortium (CGC) and the Geneticist Toolkit are provided as an educational resource only; they should not be used as a stand-alone resource for clinical decision making or reporting, as they may contain errors or omissions. Review of the data by an appropriately trained medical professional is required for clinical reporting. Some of these resource pages may include links to content created by commercial entities and/or which require a fee for service; the inclusion of such material is meant for educational purposes only and does not represent an endorsement of these entities by the CGC.
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