Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Capability of the oligo array CGH platform to detect and map chromosomal aberrations. Genome-wide profiles are shown that were obtained from hybridization of BT474 DNA ( A ) with human male reference DNA or ( B ) normal male with normal female DNA on a 29 K human oligonucleotide array. Log2ratios were calculated with a weighted moving average as described using a window of 250 kb and are displayed as a function of their position in the genome. Log2ratios of the odd and even chromosomes are shown in aqua blue and black, respectively. Chromosome numbers are indicated. Smoothed values of the log2ratios were calculated using a dedicated smoothing algorithm (red). Note the many breakpoints, gains, losses and amplifications in the BT474 profile and the lack of those in the male–female profile. Detailed profiles of chromosome 17 for the BT474 ( C ) and male–female ( D ) hybridizations. Log2ratios were calculated without moving average and are displayed in black as a function of their position on chromosome 17. Smoothed values of the log2ratios (red). The arrow in C indicates a fifth amplification in the BT474 profile on chromosome 17 that was not observed in a 1 Mb BAC array .

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques: Genome Wide, Hybridization, Amplification

Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Performance of the oligo array CGH platform. ( A ) DNA from the cell line GM01750 was hybridized against normal female reference DNA. Copy number changes were detected using the smoothing algorithm . Blue: median values and SDs (error bars) were calculated for the areas with different copy numbers and are displayed as a function of the theoretical log2ratio. The different areas were the X-chromosome (theoretical ratio = 1/2, log2ratio = −1), chromosomes 1–8, 10–13 and 15–22 (theoretical ratio = 2/2, log2ratio = 0) and the gain in chromosome 9 (theoretical ratio = 3/2, log2ratio = 0.58). The correlation coefficient is 0.98 and the slope is 0.38. Red: same values calculated after applying a moving average of 3 to the data. Note that the red error bars do not overlap. ( B ) Detailed profile of chromosome 9 of the GM01750 hybridization. Log2ratios were calculated without moving average and are displayed in black as a function of their position on chromosome 9. Smoothed values of the log2ratios (red).

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques: Hybridization

Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Reproducibility of the oligo array CGH platform. BT474 DNA was hybridized four times against normal human male reference DNA on four different days and on three different batches of 29 K human oligo arrays. Log2ratios were calculated without moving average and are displayed in different colours as indicated for each experiment as a function of their position on chromosome 2.

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques:

Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Detection of a homozygous deletion by the oligo array CGH platform. DNA from the cell lines MDA-MB-468 ( A ) and SUM159 ( C ) was hybridized with normal male reference DNA on a human oligo array. Log2ratios were calculated without moving average and are displayed in black as a function of their position on chromosome 13. The smoothed values of the log2ratios are displayed in red and the position of the RB1 oligo is indicated by the green circle in A and the arrow in C. Note the lack of the deletion in SUM159. Validation of the HD by FISH analysis in cell lines: MDA-MB-468 ( B ) and SUM159 ( D ). The green signal from the RB1 probe clearly shows the presence of RB1 in SUM159 (D), but is absent from MDA-MB-468 (B). Chromosome 13 paint (red) shows the presence of three normal copies of chromosome 13 and two marker chromosomes with chromosome 13 material.

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques: Marker

Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Detection of a heterozygous deletion by the oligo array CGH platform. ( A ) DNA from the cell line SKBR7 was hybridized with normal male reference DNA on a human oligo array. Log2ratios were calculated without moving average and are displayed in black as a function of their position on chromosome 12. The smoothed values of the log2ratios are displayed in red. ( B ) Validation of the heterozygous deletion on 12q24 by FISH analysis of cell line SKBR7. Chromosome 12 paint (dark blue) shows two copies of seemingly normal chromosome 12. FISH using 3 BACs, RP11-340F14 (red), RP11-44F24 (green) and RP11-7M8 (aqua blue) confirmed the interstitial deletion on one copy of chromosome 12 (arrow). Overlapping FISH signals from different BACs show up in white.

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques:

Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Validation of the oligo array CGH platform with DNA obtained from FFPE tissue. DNA from an FFPE gastric tumour was hybridized with normal human reference DNA on a human oligo array ( A ) and a 1 Mb human BAC array ( B ). Log2ratios were calculated without moving average and are displayed for chromosomes 19–21 as a function of their position on the genome. Log2ratios of the odd and even chromosomes are shown in aqua blue and black, respectively. Chromosome numbers are indicated. Smoothed values of the log2ratios (red).

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques:

Journal: Nucleic Acids Research

Article Title: Human and mouse oligonucleotide-based array CGH

doi: 10.1093/nar/gni191

Figure Lengend Snippet: Validation of the mouse oligo array CGH platform. DNA from a mouse tumour was hybridized with normal mouse reference DNA on a 21 K mouse oligo array ( A ). Log2ratios were calculated with a weighted moving average as described using a window of 250 kb and are displayed as a function of their position in the genome. The same mouse tumour and reference DNA was hybridized in a paired fluor-reversed experiment (dye-swap) to a 1 Mb mouse BAC array ( B ). Log2ratios were calculated as described and displayed as a function of their position in the genome. Log2ratios of the odd and even chromosomes are shown in aqua blue and black, respectively. Smoothed values of the log2ratios (red).

Article Snippet: Although tiling resolution BAC arrays have been developed ( ) and now several commercial oligo array CGH platforms are available (Agilent, Nimblegen), we have shown here that in-house spotting of commercially available oligonucleotide libraries can be a cost-effective way to produce high quality, high resolution results.

Techniques:

Journal: BMC Medical Genomics

Article Title: The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome

doi: 10.1186/1755-8794-4-16

Figure Lengend Snippet: Copy number alterations (CNAs) found in a genome of MCF-7 cells with ultra-dense array CGH platforms . Genomic DNA from MCF-7 cells was hybridized to slides containing either 244 K oligonucleotide probes ( green ) or 1 M oligonucleotide probes ( red ). (A) The whole genome view of overlaid moving averages (2 Mb window) for log 2 ratios of fluorescence between labeled MCF-7 DNA and the differentially labeled normal human reference. (B) Zoom-in on chromosome 3 showing overlaid moving averages and aberrations found with the ADM-2 algorithm. Aberrations smaller than 1 Mb in genomic length are indicated; those found with both 244 K and 1 M platforms (*) and those found with the 1 M platform only (#). (C) Zoom-in on the smallest aberration, 8 Kb amplification, found only with the 1 M platform. Overlaid data points for log 2 ratios obtained with 1 M platform and 244 K platform are shown (green: values below log 2 = -0.5; red: values above log 2 = 0.5; black: values above log 2 = -0.5 and below log 2 = 0.5). Aberrations called by the ADM-2 algorithm are identified by a shaded area, and the presence of CNVs is indicated with red boxes (bottom).

Article Snippet: In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities.

Techniques: Fluorescence, Labeling, Amplification

Journal: BMC Medical Genomics

Article Title: The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome

doi: 10.1186/1755-8794-4-16

Figure Lengend Snippet: Three intra-genic "breaks" detected with ultra-dense array CGH analysis, mapping to known gene fusions in the MCF-7 genome . Each panel shows data points and moving averages for log 2 ratios of fluorescence between labeled MCF-7 DNA and the differentially labeled normal human reference obtained with 1 M platform (top, shown in red) or 244 K platform (middle, shown in green). Aberrations are identified and the presence of common CNVs is indicated with red boxes (bottom). (A) Amplification affecting DEPDC1B and ELOVL7 genes. Note that the amplification starts within the DEPDC1B gene and ends within the ELOVL7 gene, corresponding to an intrachromosomal translocation involving the N-terminus of DEPDC1B gene and the C-terminus of the ELOVL7 gene . (B) A view of large amplified segment centered around a "relative" DNA copy number loss within the BCAS3 (Breast Carcinoma Amplified Sequence 3) gene, corresponding to a gene fusion event involving exons 6-24 or the middle part of the BCAS3 gene . (C) Two genes, PTPRG and ATXN7 (indicated by solid arrows) involved in two different gene fusion events in MCF-7 cells and flanking large amplified segments of chromosome 3 (shaded area) adjacent to the FRA3B fragile site, which contains the FHIT gene (broken arrow).

Article Snippet: In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities.

Techniques: Fluorescence, Labeling, Amplification, Translocation Assay, Sequencing

Journal: BMC Medical Genomics

Article Title: The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome

doi: 10.1186/1755-8794-4-16

Figure Lengend Snippet: Array CGH using 1 M platform and whole genome amplified DNA reveals artifacts due to whole genome amplification . Array CGH of whole-genome amplified DNA from the MCF-7 cell line compared to non-amplified DNA, with magnification of two small segments in chromosomes 1 and 2. (A, B) Data obtained with 1 M platform. In three independent experiments (top 3 sections) DNA was amplified using the Phi29 polymerase kit. The fourth experiment (bottom section) was performed without WGA. Arrows indicate some of the WGA artifacts. (C, D) Array CGH results from the 1 M platform shown as overlaid moving averages obtained in 4 experiments; 3 with WGA-DNA ( blue, green, red ) and 1 without amplification ( purple ). (C) Zoom-out on chromosome 1. (D) Zoom-out on chromosome 2. (E, F) Data obtained with 244 K platform. In three independent experiments (top 3 sections) DNA was amplified using Phi29 polymerase kit. The fourth experiment (bottom section) was performed without WGA. Note the small "wave" effects are seen only in the 1 M arrays when using WGA.

Article Snippet: In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities.

Techniques: Amplification, Whole Genome Amplification

Journal: Molecular Cytogenetics

Article Title: Prenatal diagnosis of Wolf-Hirschhorn syndrome confirmed by comparative genomic hybridization array: report of two cases and review of the literature

doi: 10.1186/1755-8166-5-12

Figure Lengend Snippet: a. a-CGH profile of chromosome 4 showing an terminal deletion . To the left, the whole chromosome 4 view. To the right, the enlarged view of the rearrangement as provided by Agilent Technologies, CGH Analytics 3.5.14. The overall size of the deletion was about 14.7 Mb. b . a-CGH profile of chromosome 4 showing a terminal deletion. To the left, the whole chromosome 4 view. To the right, the enlarged view of the rearrangement as provided by Agilent Technologies, CGH Analytics 3.5.14. The overall size of the deletion was about 19.3 Mb.

Article Snippet: Molecular karyotyping was carried out through oligonucleotide array-CGH platforms (Agilent Technologies, Santa Clara, CA) as described elsewhere [ ].

Techniques: