1. Diagnostic Genome Profiling in Mental Retardation
Bert B.A. de Vries, Rolph Pfundt, Martijn Leisink, David A. Koolen, Lisenka E.L.M. Vissers, Irene M. Janssen, Simon van Reijmersdal, Willy M. Nillesen, Erik H.L.P.G. Huys, Nicole de Leeuw, Dominique Smeets, Erik A. Sistermans, Ton Feuth, Conny M.A. van Ravenswaaij-Arts, Ad Geurts van Kessel, Eric F.P.M. Schoenmakers, Han G. Brunner, Joris A. Veltman 
The American Journal of Human Genetics 
Volume 77, Issue 4, Pages (October 2005)
DOI: /491719
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

2. Figure 1
Genomic profiles obtained by tiling-resolution array CGH for patients with MR. The arrays contained 32,447 human BAC clones (indicated by small circles representing the log2-transformed and normalized test:reference intensity ratios [“2Log(T/R)”]), ordered from 1pter to Yqter in the two genome profiles and from pter to qter for individual chromosomes, on the basis of physical-mapping positions obtained from the UCSC Genome Browser (May 2004 freeze). A, Examples of de novo alterations, including deletions and duplications, in patients 1, 4, 5, 6, 8, and 9. B, Inherited copy-number variations in patients 117 and 498, including the matching chromosome profiles of one of their parents. The individual chromosome plots show small horizontal lines to indicate the presence of a copy-number alteration (gain shown in green; loss shown in red) detected by HMM analysis. Single-clone changes were ignored.
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

3. Figure 2 Frequency distribution of aneuploid segments per patient
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

4. Figure 3
Size distribution of chromosomal aberrations, divided into de novo alterations (n=10) and polymorphic variants (n=258). Black horizontal bars indicate median size (de novo alteration median 2.76 Mb; genomic variant median 0.43 Mb).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

5. Figure A1
Details on patient 1, showing the genomewide array CGH profile, with the 3.93-Mb deletion on 1p34 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 1 (deletion indicated [red arrow in panel II]), confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III), and confirmation by FISH (panel IV) using clone RP11-708H15 (green) and a centromere probe as the control (red).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

6. Figure A2
Details on patient 2, showing the genomewide array CGH profile, with the 0.92-Mb deletion on 2q23 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 2 (deletion indicated [red arrow in panel II]), confirmation of the de novo deletion by MLPA of patient DNA (panel III), and confirmation by FISH (panel IV) using clone RP11-469G04 (green).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

7. Figure A3
Details on patient 3, showing the genomewide array CGH profile, with the Mb deletion on 3q27-3q29 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 3 (deletion indicated [red arrow in panel II]), confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III), and confirmation by FISH (panel IV) using clone RP11-469G04 (red).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

8. Figure A4
Details on patient 4, showing the genomewide array CGH profile, with the 1.24-Mb duplication on 5q35 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 5 (duplication indicated [red arrow in panel II]), and confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

9. Figure A5
Details on patient 5, showing the genomewide array CGH profile, with the 2.85-Mb deletion on 9q31 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 9 (deletion indicated [red arrow in panel II]), confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III), and confirmation by FISH (panel IV) using clone RP11-177I08 (green) and a centromere probe as the control (red).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

10. Figure A6
Details on patient 6, showing the genomewide array CGH profile, with the 0.54-Mb deletion on 9q33 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 9 (deletion indicated [red arrow in panel II]), confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III), and confirmation by FISH (panel IV) using clone RP11-668H03 (red).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

11. Figure A7
Details on patient 7, showing the genomewide array CGH profile, with the 7.49-Mb deletion on 11q14 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 11 (deletion indicated [red arrow in panel II]), confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III), and confirmation by FISH (panel IV) using clone RP11-118L16 (green) and a centromere probe as the control (red).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

12. Figure A8
Details on patient 8, showing the genomewide array CGH profile, with the 2.3-Mb duplication on 12q24 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 12 (duplication indicated [red arrow in panel II]), and confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

13. Figure A9
Details on patient 9, showing the genomewide array CGH profile, with the interspersed 8.68-Mb duplication on 17p11-17p13 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 17 (duplication indicated [red arrow in panel II]), and confirmation of the de novo deletion by MLPA of both patient and parental DNA (panel III).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions

14. Figure A10
Details on patient 10, showing the genomewide array CGH profile, with the 2.66-Mb deletion on 22q11 (red arrow in panel I), the detailed array CGH profile of the affected chromosome 22 (deletion indicated [red arrow in panel II]), and confirmation of the de novo deletion by FISH (panel IV) using the LSI Tuple (Vysis) probe (red) and a centromere probe as the control (green).
The American Journal of Human Genetics  , DOI: ( /491719)
Copyright © 2005 The American Society of Human Genetics Terms and Conditions