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Autor     Marwan Shinawi and Sau Wai Cheung
Titel    The array CGH and its clinical applications
Zeitschrift    Drug Discovery Today
Verlag    Elsevier
Ausgabe    13
Datum    September 2008
Nummer    17/18
Seiten    760–770
Anmerkung    PubMed ID: 18617013
DOI    10.1016/j.drudis.2008.06.007
URL    http://www.sciencedirect.com/science/article/pii/S1359644608002201, http://www.ncbi.nlm.nih.gov/pubmed/18617013, http://www.researchgate.net/publication/5235676_The_array_CGH_and_its_clinical_applications/links/0912f507661710afc6000000

Literaturverz.   

yes
Fußnoten    yes
Fragmente    3


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[1.] Mmu/Fragment 008 01 - Diskussion
Zuletzt bearbeitet: 2014-11-18 19:11:53 Singulus
Fragment, Gesichtet, KomplettPlagiat, Mmu, SMWFragment, Schutzlevel sysop, Shinawi and Cheung 2008

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Seite(n): 761-762, 763, Zeilen: 761:right col. 5-8.11 - 762:left col. 1.4-10; Figure 2: legend 6-7; 763:left col. 6-11, right col. 10-12
The higher resolution and throughput with possibilities for automation, robustness, simplicity, high reproducibility and precise mapping of aberrations are the most significant advantages of aCGH over cytogenetic methods. In addition, there is no need for cell culture, making the turn around time shorter than in cytogenetic methods. As with other clinical diagnostic methods, there are limitations in aCGH technology. aCGH is not able to identify balanced rearrangements such as translocations and inversions and low-level mosaicism for unbalanced numeric or structural rearrangements.

1.2 Array – CGH Methodologies

In aCGH, equal amounts of labelled genomic DNA from a test and a reference sample are co-hybridized to an array containing the DNA targets. Genomic DNA of the patient and control are differentially labelled with Cyanine 3 (Cy3) and Cyanine 5 (Cy5). The slides are scanned into image files using a microarray scanner. The spot intensities are measured and the image files are quantified using feature extraction software, and text file outputs from the quantitative analyses are imported into software programs for copy number analysis (Fig.2) (Cheung 2005, Lu 2007). The resulting ratio of the fluorescence intensities is proportional to the ratio of the copy numbers of DNA sequences in the test and reference genomes.


17. Cheung S.W. et al. (2005) Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet. Med. 7, 422–432

43. Lu, X. et al. (2007) Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS ONE 2, e327

[Page 761]

aCGH methodology

In aCGH, equal amounts of labeled genomic DNA from a test and a reference sample are cohybridized to an array containing the DNA targets. [...] Genomic DNA of the patient and control are differen-

[Page 762]

tially labeled with Cyanine 3 (Cy3) and Cyanine 5 (Cy5) (Fig. 2a). [...] The spot intensities are measured (Fig. 2c) and the image files are quantified using feature extraction software, and text file outputs from the quantitative analyses are imported into software programs for copy number analysis (Fig. 2d) [4,9]. The resulting ratio of the fluorescence intensities is proportional to the ratio of the copy numbers of DNA sequences in the test and reference genomes.


FIGURE 2

[...] (b) The slides are scanned into image files using a specific microarray scanner.

[Page 763]

The advantages and limitations of diagnostic aCGH

The higher resolution and throughput with possibilities for automation, robustness, simplicity, high reproducibility and precise mapping of aberrations are the most significant advantages of aCGH over cytogenetic methods. In addition, there is no need for cell culture, making the turn around time shorter than in cytogenetic methods. [...]

As with other clinical diagnostic methods, there are limitations in aCGH technology. aCGH is not able to identify balanced rearrangements such as translocations and inversions.


4 Cheung, S.W. et al. (2005) Development and validation of a CGH microarray for clinical cytogenetic diagnosis. Genet. Med. 7, 422–432

9 Lu, X. et al. (2007) Clinical implementation of chromosomal microarray analysis: summary of 2513 postnatal cases. PLoS ONE 2, e327

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(Graf Isolan), SleepyHollow02

[2.] Mmu/Fragment 010 01 - Diskussion
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1.3.1 Discovering new syndromes

Deletion and duplication syndromes represent recurrent chromosomal abnormalities that are associated with distinct phenotypes. These microdeletions/microduplications often occur between low copy repeats (LCRs) and are commonly because of non-allelic homologous recombination (NAHR) events (Lupski 1998). The detection of a de novo genomic imbalance in a single patient does not prove pathogenicity. Only the identification of similar genomic imbalances with a recognizable phenotype can help clarify the role of these genomic changes in causing the specific clinical features and will ultimately define a genetic syndrome.


45. Lupski JR. 1998. Genomic disorders: Structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet 14:417.

Identification of new syndromes by aCGH

Deletion and duplication syndromes represent recurrent chromosomal abnormalities that are associated with distinct phenotypes. These microdeletions/microduplications often occur between low copy repeats (LCRs) and are commonly because of nonallelic homologous recombination (NAHR) events [37]. The detection of a de novo genomic imbalance in a single patient does not prove pathogenicity. Only the identification of similar genomic imbalances with a recognizable phenotype can help clarify the role of these genomic changes in causing the specific clinical features and will ultimately define a genetic syndrome.


37 Lupski, J.R. (1998) Genomic disorders: structural features of the genome can lead to DNA rearrangements and human disease traits. Trends Genet. 14, 417–422

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(Graf Isolan), SleepyHollow02

[3.] Mmu/Fragment 012 09 - Diskussion
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Some of these aberrations are apparently benign CNVs and are usually inherited from a parent (Lee 2007). If identical alterations are found either in one of the unaffected parents, or in independent normal controls, they most probably have no direct phenotypic

consequences; however, low penetrance and variable expressivity of the phenotype may complicate the analysis and genetic counseling. Currently, the publicly available CNV databases assist in making decisions about the clinical significance of imbalances detected by microarrays. Examples of such databases are the Database of Genomic Variants (http://projects.tcag.ca/variation). When determined as de novo in origin genomic imbalances are considered more likely pathological (Tyson 2005). This can be further supported if the implicated region contains gene(s) with functions compatible with the abnormal clinical findings or previously described patients with a similar genomic imbalance and a similar phenotype. The de novo occurrence of copy number alteration is, however, not an absolute evidence of its pathogenicity and caution must be exercised for possible non paternity.


40. Lee JA, Carvalho CM, Lupski JR. A DNA replication mechanism for generating nonrecurrent rearrangements associated with genomic disorders. Cell. 2007 Dec 28;131(7):1235-47.

41. Lee, C., Iafrate A.J., and Brothman A.R., Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet, 2007. 39(7 Suppl): p. S48-54.

79. Tyson C, et al. Submicroscopic deletions and duplications in individuals with intellectual disability detected by array-CGH. Am J Med Genet A. 2005 Dec 15;139(3):173-85.

are apparently benign CNVs and are usually inherited from a parent [10]. If identical alterations are found either in one of the unaffected parents, or in independent normal controls, they most probably have no direct phenotypic consequences; however, low penetrance and variable expressivity of the phenotype may complicate the analysis and genetic counseling. Currently, the publicly available CNV databases assist in making decisions about the clinical significance of imbalances detected by microarrays. Examples of such databases are the Database of Genomic Variants (http://www.projects.tcag.ca/variation/, http://www.genome.ucsc.edu/ and http://www.sanger.ac.uk/PostGenomics/decipher/). Investigations of the parents and additional family members may often be necessary to interpret and clarify these results. The elimination of such regions from the new generations of microarray can improve the specificity and subsequently facilitate the genetic counseling.

When determined as de novo in origin genomic imbalances are considered pathogenic. This can be further supported if the implicated region contains gene(s) with functions compatible with the abnormal clinical findings or previously described patients with a similar genomic imbalance and a similar phenotype. The de novo occurrence of copy number alteration is, however, not an absolute evidence of its pathogenicity and caution must be exercised for possible nonpaternity.


10 Lee, C. et al. (2007) Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat. Genet. 39, S48–54

Anmerkungen

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"(Lee 2007)" cannot be uniquely resolved by the references given by Mmu.

Sichter
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