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      American College of Medical Genetics guideline on the cytogenetic evaluation of the individual with developmental delay or mental retardation

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          Abstract

          The following are the recommendations of the American College of Medical Genetics (ACMG) Professional Practice and Guidelines Committee, which was convened to assist health care professionals in making decisions regarding cytogenetic diagnostic testing and counseling for mental retardation (MR) and developmental delay (DD). This document reviews available evidence concerning the value of conventional and molecular cytogenetic testing for the identification of chromosomal anomalies that play a role in the etiology of MR/DD, and, based on this evidence, specific recommendations for each method of testing are provided.

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          High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays.

          D. Pinkel, R. Segraves, D. Sudar … (1998)
          Gene dosage variations occur in many diseases. In cancer, deletions and copy number increases contribute to alterations in the expression of tumour-suppressor genes and oncogenes, respectively. Developmental abnormalities, such as Down, Prader Willi, Angelman and Cri du Chat syndromes, result from gain or loss of one copy of a chromosome or chromosomal region. Thus, detection and mapping of copy number abnormalities provide an approach for associating aberrations with disease phenotype and for localizing critical genes. Comparative genomic hybridization (CGH) was developed for genome-wide analysis of DNA sequence copy number in a single experiment. In CGH, differentially labelled total genomic DNA from a 'test' and a 'reference' cell population are cohybridized to normal metaphase chromosomes, using blocking DNA to suppress signals from repetitive sequences. The resulting ratio of the fluorescence intensities at a location on the 'cytogenetic map', provided by the chromosomes, is approximately proportional to the ratio of the copy numbers of the corresponding DNA sequences in the test and reference genomes. CGH has been broadly applied to human and mouse malignancies. The use of metaphase chromosomes, however, limits detection of events involving small regions (of less than 20 Mb) of the genome, resolution of closely spaced aberrations and linking ratio changes to genomic/genetic markers. Therefore, more laborious locus-by-locus techniques have been required for higher resolution studies. Hybridization to an array of mapped sequences instead of metaphase chromosomes could overcome the limitations of conventional CGH (ref. 6) if adequate performance could be achieved. Copy number would be related to the test/reference fluorescence ratio on the array targets, and genomic resolution could be determined by the map distance between the targets, or by the length of the cloned DNA segments. We describe here our implementation of array CGH. We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer.
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            Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors.

            A Kallioniemi, D. Pinkel, D. Sudar … (1992)
            Comparative genomic hybridization produces a map of DNA sequence copy number as a function of chromosomal location throughout the entire genome. Differentially labeled test DNA and normal reference DNA are hybridized simultaneously to normal chromosome spreads. The hybridization is detected with two different fluorochromes. Regions of gain or loss of DNA sequences, such as deletions, duplications, or amplifications, are seen as changes in the ratio of the intensities of the two fluorochromes along the target chromosomes. Analysis of tumor cell lines and primary bladder tumors identified 16 different regions of amplification, many in loci not previously known to be amplified.
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              Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances.

              Ronald A. Benner, S Stilgenbauer, S S Toldo … (1997)
              Comparative genomic hybridization (CGH) to metaphase chromosomes has been widely used for the genome-wide screening of genomic imbalances in tumor cells. Substitution of the chromosome targets by a matrix consisting of an ordered set of defined nucleic acid target sequences would greatly enhance the resolution and simplify the analysis procedure, both of which are prerequisites for a broad application of CGH as a diagnostic tool. However, hybridization of whole genomic human DNA to immobilized single-copy DNA fragments with complexities below the megabase pair level has been hampered by the low probability of specific binding because of the high probe complexity. We developed a protocol that allows CGH to chips consisting of glass slides with immobilized target DNAs arrayed in small spots. High-copy-number amplifications contained in tumor cells were rapidly scored by use of target DNAs as small as a cosmid. Low-copy-number gains and losses were identified reliably by their ratios by use of chromosome-specific DNA libraries or genomic fragments as small as 75 kb cloned in PI or PAC vectors as targets, thus greatly improving the resolution achievable by chromosomal CGH. The ratios obtained for the same chromosomal imbalance by matrix CGH and by chromosomal CGH corresponded very well. The new matrix CGH protocol provides a basis for the development of automated diagnostic procedures with biochips designed to meet clinical needs.
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                Author and article information

                Contributors
                : On behalf of : on behalf of the American College of Medical Genetics (ACMG) Professional Practice and Guidelines Committee
                Journal
                Journal ID (nlm-ta): Genet Med
                Title: Genetics in Medicine
                Publisher: Lippincott, Williams & Wilkins
                ISSN (Print): 1098-3600
                ISSN (Electronic): 1530-0366
                Publication date (Print): Nov-Dec 2005
                Volume: 7
                Issue: 9
                Pages: 650-654
                Affiliations
                From the Health Research and Education Center, Washington State University Spokane, WA.
                Article
                Publisher ID: 16301868
                DOI: 10.1097/01.gim.0000186545.83160.1e
                PMC ID: 3110947
                PubMed ID: 16301868
                SO-VID: f9d68ace-3187-491e-abe9-51fd773b3d1d
                Copyright © Copyright © American College of Medical Genetics. Unauthorized reproduction of this article is prohibited.
                History
                Categories
                Subject: ACMG Practice Guideline

                ScienceOpen disciplines: Genetics
                Keywords: karyotype,developmental delay,mental retardation,cytogenetic analysis,chromosomes
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: karyotype, developmental delay, mental retardation, cytogenetic analysis, chromosomes

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