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High-Resolution Identification of Chromosomal Abnormalities Using Oligonucleotide Arrays Containing 116,204 SNPs  Howard R. Slater, Dione K. Bailey, Hua.

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Presentation on theme: "High-Resolution Identification of Chromosomal Abnormalities Using Oligonucleotide Arrays Containing 116,204 SNPs  Howard R. Slater, Dione K. Bailey, Hua."— Presentation transcript:

1 High-Resolution Identification of Chromosomal Abnormalities Using Oligonucleotide Arrays Containing 116,204 SNPs  Howard R. Slater, Dione K. Bailey, Hua Ren, Manqiu Cao, Katrina Bell, Steven Nasioulas, Robert Henke, K.H. Andy Choo, Giulia C. Kennedy  The American Journal of Human Genetics  Volume 77, Issue 5, Pages (November 2005) DOI: /497343 Copyright © 2005 The American Society of Human Genetics Terms and Conditions

2 Figure 1 Analysis of Mapping 100K data with use of CNAT. Patient C1 is shown, with the 1.5-Mb deleted region on chromosome 7p indicated by vertical lines. Chromosomal position (in Mb) is indicated on the X-axis for all three panels. Estimated copy-number changes are shown in the upper panel, P values are shown in the middle panel, and the LOH score is shown on the bottom panel. The default window size of 0.5 Mb was used. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

3 Figure 2 A, Duplication (1.4 Mb) at chromosome band 17p11.2 in patient B1: GeneChip Mapping 100K array profiles of copy-number duplication (GSA_CN) and positive P value (GSA_pVal) on chromosome 17 (boxed section), with use of a 1.0-Mb window. X-axis indicates chromosomal position (in Mb); Y-axes indicate estimated copy-number changes (upper panel), P values (middle panel), and LOH score (bottom panel). B, FISH with use of BAC probe RP11-791M8, which contains the PMP22 gene, showing the duplication as an extra signal in interphase nuclei. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

4 Figure 3 Analysis with use of Integrated Genome Browser (Affymetrix). A, GeneChip 100K array LOH profiles of chromosome 5, demonstrating the subtle differences in size and location. Physical position is shown on the X-axis. The Y-axis shows LOH values from CNAT for three different patient samples, with comparison of three deletions in chromosome 5 at band q14.2-q15 in patients A5, A6, and A7. B, Enlargement of deleted regions, showing corresponding genome information. The gene MASS1 (circled) is located in the common region of overlap (boxed section). The default window size of 0.5 Mb was used. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

5 Figure 4 A, Deleted region (4.6 Mb) at chromosome band 17p12-p13.1 in patient A8: GeneChip Mapping 100K array profiles of copy-number deletion (GSA_CN), negative P value (GSA_pVal), and LOH block on chromosome 17 (boxed section). The default window size of 0.5 Mb was used. X-axis indicates chromosomal position (in Mb); Y-axes indicate estimated copy-number changes (upper panel), P values (middle panel), and LOH score (bottom panel). B, Metaphase FISH with use of BAC RP11-601N13, showing the deleted chromosome 17 (white arrow) and the normal chromosome 17 (black arrow) with fluorescence signals. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

6 Figure 5 A, Duplication (7.7 Mb) at chromosome band 6p25 in patient B4: GeneChip Mapping 100K array profiles of copy-number duplication (GSA_CN) and positive P value (GSA_pVal) on chromosome 6 (boxed section). The default window size of 0.5 Mb was used. X-axis indicates chromosomal position (in Mb); Y-axes indicate estimated copy-number changes (upper panel), P values (middle panel), and LOH score (bottom panel). B, Original karyotype showing larger chromosome 6, which was verified by metaphase FISH with use of whole chromosome 6 paint, consistent with the p-arm duplication (white arrow) and normal chromosome 6 (black arrow). The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

7 Figure 6 A, Trisomy 8: GeneChip Mapping 100K array profiles of copy-number duplication (GSA_CN) and positive P value (GSA_pVal) on chromosome 8, with use of a 10-Mb window. B, Partial G-banded karyotype, showing three chromosome 8 homologues in patient C4. X-axis indicates chromosomal position (in Mb); Y-axes indicate estimated copy-number changes (upper panel), P values (middle panel), and LOH score (bottom panel). The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

8 Figure 7 A, Maternal UPD of chromosome 15 of family F1: GeneChip 100K array LOH profiles of chromosome 15 in the child, mother, and father. Note that the child's and mother's profiles are identical except at the arrowed proximal homozygous region (cen-15p12). The default window size of 0.5 Mb was used. B, Diagram illustrating the origin of the isodisomic and heterodisomic regions in the child's chromosome 15 homologues, from a single crossover in the mother's meiosis I (MI), followed by a meiosis II nondisjunction and postfertilization trisomy rescue through loss of the paternal homologue. Physical position is shown on the X-axis. The Y-axis shows LOH values from CNAT for three different patient samples, with comparison of three deletions in chromosome 5 at band q14.2-q15 in patients A5, A6, and A7. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

9 Figure 8 Box plots of GSA_CN and GSA_pVal for all patients. In panels A, B, and C, the GSA_CN box plots are shown for patients A1–A8, B1–B4, and C1–C5, respectively (see table 1). The Y-axis is the GSA_CN as determined by CNAT. In panels D, E, and F, the GSA_pVal box plots are shown for patients A1–A8, B1–B4, and C1–C5, respectively. The Y-axis is the GSA_pVal as determined by CNAT. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

10 Figure 9 Box plots of GSA_CN and GSA_pVal for 42 white reference individuals. In panels A, B, C, and D, the GSA_CN box plots are shown for NA17201-NA17213, NA17214-NA17252, NA17253-NA17278, and NA17172-NA17285, respectively (see tables 4 and 5). The 42 white reference individuals are named as in the catalogue ID from the Coriell Institute. The Y-axis is the GSA_CN as determined by CNAT. In panels E, F, G, and H, the GSA_pVal box plots are shown for NA17201-NA17213, NA17214-NA17252, NA17253-NA17278, and NA17172-NA17285, respectively. The Y-axis is the GSA_pVal as determined by CNAT. The American Journal of Human Genetics  , DOI: ( /497343) Copyright © 2005 The American Society of Human Genetics Terms and Conditions

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