An International System for Human Cytogenetic Nomenclature (2013)

Transcription

1 ISCN 2013 An International System for Human Cytogenetic Nomenclature (2013) Editors Lisa G. Shaffer Jean McGowan-Jordan Michael Schmid Recommendations of the International Standing Committee on Human Cytogenetic Nomenclature This report should be cited in text as ISCN (2013). The complete citation for reference lists is: ISCN (2013): An International System for Human Cytogenetic Nomenclature, L.G. Shaffer, J. McGowan-Jordan, M. Schmid (eds); S. Karger, Basel 2013 Published in collaboration with

2 Published in collaboration with Cytogenetic and Genome Research under the title ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013) VI p. plus fold-out, 11 fig., 4 tab., 2013 Although produced by the editors and publishers of Cytogenetic and Genome Research, this publication is independent of the subscription. Copies of ISCN 2013 can be ordered from the publishers: S. Karger AG S. Karger Publishers, Inc. Allschwilerstrasse West Avon Road P.O. Box P.O. Box 529 CH 4009 Basel Unionville, CT Switzerland Tel. (860) Tel Fax (860) Fax Toll free: karger@karger.ch Library of Congress Cataloging-in-Publication Data International Standing Committee on Human Cytogenetic Nomenclature. ISCN 2013 : an international system for human cytogenetic nomenclature (2013) / editors, Lisa G. Shaffer, Jean McGowan-Jordan, Michael Schmid. p. ; cm. International system for human cytogenetic nomenclature (2013) Recommendations of the International Standing Committee on Human Cytogenetic Nomenclature. Published in collaboration with Cytogenetic and Genome Research. Includes bibliographical references and index. ISBN (soft cover : alk. paper) I. Shaffer, Lisa G. II. McGowan-Jordan, Jean. III. Schmid, M. (Michael) IV. Cytogenetic and genome research. V. Title. VI. Title: International system for human cytogenetic nomenclature (2013). [DNLM: 1. Cytogenetics--Terminology--English. QU 15] dc Disclaimer. The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publisher and the editor(s). The appearance of advertisements in the book is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements. S. Karger Medical and Scientific Publishers Basel Freiburg Paris London New York Bangalore Bangkok Shanghai Singapore Tokyo Sydney All rights reserved. No part of this publication may be translated into other languages, reproduced, or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher. Copyright 2013 by S. Karger AG, P.O. Box, CH 4009 Basel (Switzerland) Printed in Switzerland by Reinhardt Druck, Basel ISBN

3 Table of Contents 1 Historical Introduction Normal Chromosomes Introduction Chromosome Number and Morphology Non-Banding Techniques Banding Techniques X- and Y-Chromatin Chromosome Band Nomenclature Identification and Definition of Chromosome Landmarks, Regions, and Bands Designation of Regions, Bands, and Sub-Bands High-Resolution Banding Molecular Basis of Banding Symbols and Abbreviated Terms Karyotype Designation General Principles Specification of Breakpoints Designating Structural Chromosome Aberrations by Breakpoints and Band Composition Short System for Designating Structural Chromosome Aberrations Two-Break Rearrangements Three-Break Rearrangements Four-Break and More Complex Rearrangements Detailed System for Designating Structural Chromosome Aberrations Additional Symbols Designating the Band Composition of a Chromosome Derivative Chromosomes Recombinant Chromosomes... 46

4 5 Uncertainty in Chromosome or Band Designation Questionable Identification Uncertain Breakpoint Localization or Chromosome Number Alternative Interpretation Incomplete Karyotype Order of Chromosome Abnormalities in the Karyotype Normal Variable Chromosome Features Variation in Heterochromatic Segments, Satellite Stalks, and Satellites Variation in Length Variation in Number and Position Fragile Sites Numerical Chromosome Abnormalities General Principles Sex Chromosome Abnormalities Autosomal Abnormalities Uniparental Disomy Structural Chromosome Rearrangements General Principles Specification of Structural Rearrangements Additional Material of Unknown Origin Deletions Derivative Chromosomes Dicentric Chromosomes Duplications Fission Fragile Sites Homogeneously Staining Regions Insertions Inversions Isochromosomes Marker Chromosomes Neocentromeres Quadruplications Ring Chromosomes Telomeric Associations Translocations Reciprocal Translocations Whole-Arm Translocations Robertsonian Translocations Jumping Translocations Tricentric Chromosomes Triplications Multiple Copies of Rearranged Chromosomes IV ISCN 2013

5 10 Chromosome Breakage Chromatid Aberrations Non-Banded Preparations Banded Preparations Chromosome Aberrations Non-Banded Preparations Banded Preparations Scoring of Aberrations Neoplasia Clones and Clonal Evolution Definition of a Clone Clone Size Mainline Stemline, Sideline and Clonal Evolution Composite Karyotype Unrelated Clones Modal Number Constitutional Karyotype Meiotic Chromosomes Terminology Examples of Meiotic Nomenclature Correlation between Meiotic Chromosomes and Mitotic Banding Patterns In situ Hybridization Introduction Prophase/Metaphase in situ Hybridization (ish) Use of dim and enh Subtelomeric Metaphase in situ Hybridization Interphase/Nuclear in situ Hybridization (nuc ish) Number of Signals Relative Position of Signals Single Fusion Probes Single Fusion with Extra Signal Probes Dual Fusion Probes Break-Apart Probes In situ Hybridization on Extended Chromatin/DNA Fibers (fib ish) Reverse in situ Hybridization (rev ish) Chromosome Analyses Using Probes Derived from Sorted or Microdissected Chromosomes Chromosome Comparative Genomic Hybridization (cgh) Multi-Color Chromosome Painting Partial Chromosome Paints Table of Contents V

6 14 Microarrays Introduction Examples of Microarray Nomenclature Nomenclature Specific to SNP Arrays Complex Array Results Region-Specific Assays Introduction Examples of RSA Nomenclature for Copy Number Detection Examples of RSA Nomenclature for Balanced Translocations or Fusion Genes References Members of the ISCN Standing Committee and Consultants Appendix Index VI ISCN 2013