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Source Author Title Publ. Year Bib. FN
Eka/Edelmann Hirschhorn 2009 Lisa Edelmann / Kurt Hirschhorn Clinical Utility of Array CGH for the Detection of Chromosomal Imbalances Associated with Mental Retardation and Multiple Congenital Anomalies 2009 yes yes


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1. INTRODUCTION

1.1 Historical overview

For the past 50 years, since Tjio and Levan first reported that humans have 46 chromosomes (Fig. 1), tremendous effort has been put forth to define the genomic imbalances associated with genetic disease.1 The initial discoveries of whole chromosome trisomies with very specific phenotypes, such as trisomy 21 in Down syndrome and trisomy 13 and 18 in Patau and Edwards syndromes, launched the field of clinical cytogenetics.2,3


1 Tjio J, Levan A: The chromosome number in man. Hereditas 1956; 42: 1-6.

2 Lejeune J, Gautier M, Turpin R: Etude des chromosomes somatiques de neuf enfants mongoliens. Comptes Rendus 1959; 248: 1721-1722.

3 Edelmann L, Hirschhorn K: Clinical utility of array CGH for the detection of chromosomal imbalances associated with mental retardation and multiple congenital anomalies. Ann N Y Acad Sci 2009; 1151: 157-166.

Introduction

Historical Perspective

For the past 50 years, since Tjio and Levan1 first reported that humans have 46 chromosomes, tremendous effort has been put forth to define the genomic imbalances associated with genetic disease. The initial discoveries of whole chromosome trisomies with very specific phenotypes, such as trisomy 21 in Down syndrome and trisomy 13 and 18 in Patau and Edwards syndromes, launched the field of clinical cytogenetics.2–4


1. Tjio, H.J. & A. Levan 1956. The chromosome numbers of man. Hereditas 42: 1–6.

2. Lejeune, J., R. Turpin & M. Gautier. 1959. Mongolism; a chromosomal disease (trisomy). Bull. Acad. Natl. Med. 143: 256–265.

3. Edwards, J.H. et al. 1960. A new trisomic syndrome. Lancet 1: 787–790.

4. Patau, K. et al. 1961. Trisomy for chromosome No. 18 in man. Chromosoma 12: 280–285.

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Source is given in Fn. 3.

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As specialized banding and high resolution techniques became available, including the commonly used giemsa staining following trypsin digestion or G-banding, the ability of the standard karyotype to display more subtle chromosomal aberrations increased significantly. However, even high resolution karyotypes4 are unreliable for detecting many known microdeletion syndromes, which range from 3–5 Mb in size, and cannot detect smaller aberrations.

4 Yunis J: High resolution of human chromosomes. Science 1976; 191: 1268-1270.

As specialized banding and high resolution techniques became available, including the commonly used giemsa staining following trypsin digestion or G-banding, the ability of the standard karyotype to display more subtle chromosomal aberrations increased significantly. However, even high resolution karyotypes5 are unreliable for detecting many known microdeletion syndromes, which range from 3–5 Mb in size, and cannot detect smaller aberrations.

5. Yunis, J.J. 1976. High resolution of human chromosomes. Science 191: 1268–1270.

Anmerkungen
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In the 1990s the introduction of molecular cytogenetic techniques into the clinical laboratory setting represented a major advance in the ability to detect known syndromes and identify chromosomal rearrangements of unknown origin. Fluorescence in situ hybridization (FISH), which is the annealing of fluorescently labelled locus-specific probes to their complimentary sequences in the genome, allowed the detection of specific microdeletion syndromes (Fig. 2).5 There are currently a number of commercially available FISH probes for the most common disorders, and this method is still predominantly used when the clinical phenotype is suggestive of a particular disorder. Several other FISH-based methods, including spectral karyotyping (SKY), multicolour FISH (m-FISH),5 and comparative genomic hybridization (CGH) have proven extremely useful in the identification of unknown chromosomal material. SKY and m-FISH rely mainly on the principal of differentially labelling each chromosome using a unique combination of fluorochromes and are especially beneficial for identifying the origin and content of supernumerary marker chromosomes (SMCs) and complex chromosome rearrangements (CCRs) that involve more than two chromosomes. CGH was originally introduced for the cytogenetic analysis of solid tumors, which can be difficult to culture, and involves the differential labeling of DNA from a test sample and a reference sample (Fig. 3).5 The fluorescently labelled reactions are combined and hybridized to metaphase spreads from chromosomally normal individuals. Gains and losses of the genome in the test sample relative to the control sample are represented as ratios that are quantified from digital image analysis. This method allows the investigation of the whole genome and is very useful for determining the origin of unknown genetic material, such as SMCs and other unbalanced rearrangements.5 However, CGH does not detect balanced rearrangements, and the resolution is on the order of 5–10Mb, and consequently many genomic disorders cannot be detected.3

3 Edelmann L, Hirschhorn K: Clinical utility of array CGH for the detection of chromosomal imbalances associated with mental retardation and multiple congenital anomalies. Ann N Y Acad Sci 2009; 1151: 157-166.

5 Trask BJ: Fluorescence in situ hybridization: applications in cytogenetics and gene mapping. Trends Genet 1991; 7: 149-154.

In the 1990s the introduction of molecular cytogenetic techniques into the clinical laboratory setting represented a major advance in the ability to detect known syndromes and identify chromosomal rearrangements of unknown origin. Fluorescence in situ hybridization (FISH), which is the annealing of fluorescently labeled locus-specific probes to their complimentary sequences in the genome, allowed for the detection of specific microdeletion syndromes.6 There are currently a number of commercially available FISH probes for the most common disorders, and this method is still predominantly used when the clinical phenotype is suggestive of a particular disorder. Several other FISH-based methods, including spectral karyotyping (SKY), multicolor FISH (m-FISH),7,8 and comparative genomic hybridization (CGH), have proven extremely useful in the identification of unknown chromosomal material. SKY and m-FISH rely mainly on the principal of differentially labeling each chromosome using a unique combination of fluorochromes and are especially beneficial for identifying the origin and content of supernumerary marker chromosomes (SMCs) and complex chromosome rearrangements (CCRs) that involve more than two chromosomes. CGH was originally introduced for the cytogenetic analysis of solid tumors, which can be difficult to culture, and involves the differential labeling of DNA from a test sample and a reference sample.9 The fluorescently labeled reactions are combined and hybridized to metaphase spreads from chromosomally normal individuals. Gains and losses of the genome in the test sample relative to the control sample are represented as ratios that are quantified from digital image analysis. This method allows for investigation of the whole genome and is very useful for determining the origin of unknown genetic material, such as SMCs and other unbalanced rearrangements.10 However, CGH does not detect balanced rearrangements, and the resolution is on the order of 5–10Mb, and consequently many genomic disorders cannot be detected.

6. Trask, B.J. 1991. Fluorescence in situ hybridization: Applications in cytogenetics and gene mapping. Trends Genet. 7: 149–154.

7. Speicher,M.R., S. Gwyn Ballard&D.C.Ward. 1996. Karyotyping human chromosomes by combinatorial multi-fluor FISH. Nat. Genet. 12: 368–375.

8. Speicher, M.R. & N.P. Carter. 2005. The new cytogenetics: Blurring the boundaries with molecular biology. Nat. Rev. Genet. 6: 782–792.

9. Kallioniemi, O.P. et al. 1993. Comparative genomic hybridization: A rapid new method for detecting and mapping DNA amplification in tumors. Semin. Cancer Biol. 4: 41–46

Anmerkungen

Source is given in Fn. 3.

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The need to screen the whole genome at a resolution that surpassed the existing technologies led to the implementation of microarray based CGH. The principle is very similar to that employed for traditional CGH, where two differentially labeled specimens are cohybridized in the presence of Cot1 DNA; however, instead of metaphase spreads, the hybridization targets are DNA substrates immobilized on a glass slide.5-7 Subsequently, the arrays are scanned and the resultant data are analyzed by software that computes the log 2 ratios for a variety of copy number differences between a patient and reference sample (Fig. 4) Consequently, array-CGH is an entirely molecular technique with a cytogenetic application and represents a hybrid method that requires the expertise of both specialties. The current limitations of the technology include the inability to detect [balanced chromosome rearrangements and the equivocal nature of copy number alterations of unknown significance that may be identified.]

5 Trask BJ: Fluorescence in situ hybridization: applications in cytogenetics and gene mapping. Trends Genet 1991; 7: 149-154.

6 Pinkel D, Segraves R, Sudar D et al: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998; 20: 207-211.

7 Cai WW, Mao JH, Chow CW, Damani S, Balmain A, Bradley A: Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat Biotechnol 2002; 20: 393-396.

The need to screen the whole genome at a resolution that surpassed the existing technologies led to the implementation of microarray-based CGH. The principle is very similar to that employed for traditional CGH, where two differentially labeled specimens are cohybridized in the presence of Cot1 DNA; however, instead of metaphase spreads, the hybridization targets are DNA substrates are immobilized on a glass slide.11–13 Subsequently, the arrays are scanned and the resultant data are analyzed by software that computes the log 2 ratios for a variety of copy number differences between a patient and reference sample. Consequently, array CGH (aCGH) is an entirely molecular technique with a cytogenetic application and represents a hybrid method that requires the expertise of both specialties. The current limitations of the technology include the inability to detect balanced chromosome rearrangements and the equivocal nature of copy number alterations of unknown significance that may be identified.

11. Solinas-Toldo, S. et al. 1997. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer 20: 399–407.

12. Pinkel,D. et al. 1998. High resolution analysis ofDNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20: 207–211.

13. Cai, W.W. et al. 2002. Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat. Biotechnol. 20: 393–396.

Anmerkungen
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[The current limitations of the technology include the inability to detect] balanced chromosome rearrangements and the equivocal nature of copy number alterations of unknown significance that may be identified. Nevertheless, it is being used routinely in the clinical setting with a normal chromosome result in cases of mental retardation and/or multiple congenital anomalies (MR/MCA); as a result the diagnostic yield in this patient group has increased considerably.

3 1.2 Array – CGH Methodologies

Two major types of array targets are currently being utilized. Initially, bacterial artificial chromosomes (BACs) were the array target of choice.6 However, more recently, oligonucleotide arrays have been adopted due to the increased genome coverage they afford. The design of both array types was made possible by the availability of the complete map and sequence of the human genome. The BAC arrays may contain DNA isolated from large insert clones that range in size from 150–200 kb, spotted directly onto the array or may employ the spotting of PCR products amplified from the BAC clones.8 These arrays are generally very sensitive and results can be directly validated with FISH using the BAC DNA as a probe. However, production of BAC DNA is labor-intensive, and the resolution is limited to 50–100 kb, even on a whole genome tiling path array.9 Oligonucleotide arrays offer a flexible format with the potential for very high resolution and customization. Several different platforms are available for oligonucleotide arrays, some of which were adapted from genomewide SNP-based oligonucleotide markers and others that were created from a library of virtual probes that span the genome, and consequently can be constructed to have extremely high resolution.10 Both BAC and oligonucleotide arrays have been used successfully to detect copy number changes in patients with MR/MCA and autism. A number of different array design approaches have been taken for diagnostic purposes. A targeted array is one that contains specific regions of the genome, such as the subtelomeres and those responsible for known microdeletion/microduplication syndromes, but does not have probes that span the whole genome.11-13 This type of [array was initially used for clinical applications in postnatal specimens but has also been implemented for prenatal specimens with an abnormal ultrasound finding or for general screening purposes.14-16]


6 Pinkel D, Segraves R, Sudar D et al: High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998; 20: 207-211.

7 Cai WW, Mao JH, Chow CW, Damani S, Balmain A, Bradley A: Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat Biotechnol 2002; 20: 393-396.

8 Ylstra B, van den Ijssel P, Carvalho B, Brakenhoff RH, Meijer GA: BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res 2006; 34: 445-450.

9 Ishkanian AS, Malloff CA, Watson SK et al: A tiling resolution DNA microarray with complete coverage of the human genome. Nat Genet 2004; 36: 299-303.

10 Shaikh TH: Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet Med 2007; 9: 617-625.

11 Bejjani BA, Saleki R, Ballif BC et al: Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: is less more? Am J Med Genet A 2005; 134: 259-267.

12 Bejjani BA, Shaffer LG: Application of array-based comparative genomic hybridization to clinical diagnostics. J Mol Diagn 2006; 8: 528-533.

13 Shaffer LG, Kashork CD, Saleki R et al: Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J Pediatr 2006; 149: 98-102.

14 Le Caignec C, Boceno M, Saugier-Veber P et al: Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J Med Genet 2005; 42: 121-128.

15 Sahoo T, Cheung SW, Ward P et al: Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet Med 2006; 8: 719-727.

16 Kitsiou-Tzeli S, Sismani C, Karkaletsi M et al: Prenatal diagnosis of a de novo partial trisomy 10p12.1-12.2 pter originating from an unbalanced translocation onto 15qter and confirmed with array CGH. Prenat Diagn 2008; 28: 770-772.

The current limitations of the technology include the inability to detect balanced chromosome rearrangements and the equivocal nature of copy number alterations of unknown significance that may be identified. Nevertheless, it is being used routinely in the clinical setting with a normal chromosome result in cases of mental retardation and/or multiple congenital anomalies (MR/MCA); as a result the diagnostic yield in this patient group has increased considerably.

Array CGH Methodologies

Two major types of array targets are currently being utilized. Initially, bacterial artificial chromosomes (BACs) were the array target of choice.12 However, more recently, oligonucleotide arrays have been adopted due to the increased genome coverage they afford. The design of both array types was made possible by the availability of the complete map and sequence of the human genome. The BAC arrays may contain DNA isolated from large insert clones that range in size from 150–200 kb, spotted directly onto the array or may employ the spotting of PCR products amplified from the BAC clones.14 These arrays are generally very sensitive and results can be directly validated with FISH using the BAC DNA as a probe. However, production of BAC DNA is labor-intensive, and the resolution is limited to 50–100 kb, even on a whole genome tiling path

[page 159:]

array.15 Oligonucleotide arrays offer a flexible format with the potential for very high resolution and customization. Several different platforms are available for oligonucleotide arrays that range from 25- to 85mers in length, some of which were adapted from genomewide SNP-based oligonucleotide markers and others that were created from a library of virtual probes that span the genome, and consequently can be constructed to have extremely high resolution. 16 Both BAC and oligonucleotide arrays have been used successfully to detect copy number changes in patients with MR/MCA and autism. A number of different array design approaches have been taken for diagnostic purposes. A targeted array is one that contains specific regions of the genome, such as the subtelomeres and those responsible for known microdeletion/ microduplication syndromes, but does not have probes that span the whole genome.17–19 This type of array was initially used for clinical applications in postnatal specimens but has also been implemented for prenatal specimens with an abnormal ultrasound finding or for general screening purposes.20,21


12. Pinkel,D. et al. 1998. High resolution analysis ofDNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 20: 207–211.

13. Cai, W.W. et al. 2002. Genome-wide detection of chromosomal imbalances in tumors using BAC microarrays. Nat. Biotechnol. 20: 393–396.

14. Ylstra, B. et al. 2006. BAC to the future! Or oligonucleotides: A perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 34: 445–450.

15. Ishkanian, A.S. et al. 2004. A tiling resolution DNA microarray with complete coverage of the human genome. Nat. Genet. 36: 299–303.

16. Shaikh, T.H. 2007. Oligonucleotide arrays for highresolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet. Med. 9: 617–625.

17. Bejjani, B.A. et al. 2005. Use of targeted array-based CGH for the clinical diagnosis of chromosomal imbalance: Is less more? Am. J. Med. Genet. A 134: 259– 267.

18. Bejjani, B.A. & L.G. Shaffer. 2006. Application of array-based comparative genomic hybridization to clinical diagnostics. J. Mol. Diagn. 8: 528–533.

19. Shaffer, L.G. et al. 2006. Targeted genomic microarray analysis for identification of chromosome abnormalities in 1500 consecutive clinical cases. J. Pediatr. 149: 98–102.

20. Le Caignec, C. et al. (2005. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J. Med. Genet. 42: 121–128.

21. Sahoo, T. et al. 2006. Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet. Med. 8: 719–727.

Anmerkungen
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[This type of] array was initially used for clinical applications in postnatal specimens but has also been implemented for prenatal specimens with an abnormal ultrasound finding or for general screening purposes.14-16 A whole genome or tiling path array offers full genome coverage with a resolution that is dependent on the spacing of the probes. For clinical testing the resolution generally involves a spacing of 50 kb to 1 Mb between adjacent probes on the array often with additional coverage at the subtelomeric regions.17-19 The enhanced coverage of whole genome arrays identifies an additional 5% of abnormalities when compared to a targeted array.19,20 For research purposes, very high density oligonucleotide whole genome arrays and region specific custom arrays have been instrumental in defining new syndromes, detecting target gene deletions and characterizing breakpoint regions.3,21-24

14 Le Caignec C, Boceno M, Saugier-Veber P et al: Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J Med Genet 2005; 42: 121-128.

15 Sahoo T, Cheung SW, Ward P et al: Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet Med 2006; 8: 719-727.

16 Kitsiou-Tzeli S, Sismani C, Karkaletsi M et al: Prenatal diagnosis of a de novo partial trisomy 10p12.1-12.2 pter originating from an unbalanced translocation onto 15qter and confirmed with array CGH. Prenat Diagn 2008; 28: 770-772.

17 Veltman JA, de Vries BB: Diagnostic genome profiling: unbiased whole genome or targeted analysis? J Mol Diagn 2006; 8: 534-537; discussion 537-539.

18 Toruner GA, Streck DL, Schwalb MN, Dermody JJ: An oligonucleotide based array-CGH system for detection of genome wide copy number changes including subtelomeric regions for genetic evaluation of mental retardation. Am J Med Genet A 2007; 143A: 824-829.

19 Baldwin EL, Lee JY, Blake DM et al: Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet Med 2008; 10: 415-429.

20 Veltman JA, de Vries BB: Whole-genome array comparative genome hybridization: the preferred diagnostic choice in postnatal clinical cytogenetics. J Mol Diagn 2007; 9: 277.

21 Selzer RR, Richmond TA, Pofahl NJ et al: Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 2005; 44: 305-319.

22 Urban AE, Korbel JO, Selzer R et al: High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc Natl Acad Sci U S A 2006; 103: 4534-4539.

23 Wong LJ, Dimmock D, Geraghty MT et al: Utility of oligonucleotide arraybased comparative genomic hybridization for detection of target gene deletions. Clin Chem 2008; 54: 1141-1148.

24 Balikova I, Lehesjoki AE, de Ravel TJ et al: Deletions

This type of array was initially used for clinical applications in postnatal specimens but has also been implemented for prenatal specimens with an abnormal ultrasound finding or for general screening purposes.20,21 A whole genome or tiling path array offers full genome coverage with a resolution that is dependent on the spacing of the probes. For clinical testing the resolution generally involves a spacing of 50 kb to 1 Mb between adjacent probes on the array often with additional coverage at the subtelomeric regions.22–24 The enhanced coverage of whole genome arrays identifies an additional 5% of abnormalities when compared to a targeted array.24–25 For research purposes, very high density oligonucleotide whole genome arrays and region-specific custom arrays have been instrumental in defining new syndromes and characterizing breakpoint regions.26,27

20. Le Caignec, C. et al. (2005. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J. Med. Genet. 42: 121–128.

21. Sahoo, T. et al. 2006. Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet. Med. 8: 719–727.

20. Le Caignec, C. et al. (2005. Detection of genomic imbalances by array based comparative genomic hybridisation in fetuses with multiple malformations. J. Med. Genet. 42: 121–128.

21. Sahoo, T. et al. 2006. Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization. Genet. Med. 8: 719–727.

22. Veltman, J.A. & B.B. de Vries. 2006. Diagnostic genome profiling: Unbiased whole genome or targeted analysis? J. Mol. Diagn. 8: 534–537; discussion 537–539.

23. Toruner, G.A. et al. 2007. An oligonucleotide based array-CGH system for detection of genome wide copy number changes including subtelomeric regions for genetic evaluation of mental retardation. Am. J. Med. Genet. A 143A: 824–829.

24. Baldwin, E.L. et al. 2008. Enhanced detection of clinically relevant genomic imbalances using a targeted plus whole genome oligonucleotide microarray. Genet. Med. 10: 415–429.

25. Veltman, J.A. & B.B. de Vries. 2007. Whole-genome array comparative genome hybridization: The preferred diagnostic choice in postnatal clinical cytogenetics. J. Mol. Diagn. 9: 277.

26. Selzer, R.R. et al. 2005. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305–319.

27. Urban, A.E. et al. 2006. High-resolution mapping of DNA copy alterations in human chromosome 22 using high-density tiling oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 103: 4534–4539.

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