array comparative genomic hybridization (acgh) analysis  (Agilent technologies)

Journal: European Journal of Human Genetics

Article Title: CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a three-generation pedigree

doi: 10.1038/ejhg.2013.302

Figure Lengend Snippet: aCGH and FISH analyses. (a) Upper panel: clinical CMA V.8.1 OLIGO (individual III-2), lower panel: NimbleGen 4.2 M array, both showing copy number gain in 15q13.3, encompassing the CHRNA7 gene. Log ratios of 0.7–1.0 suggest triplication of the respective area. (b) FISH analysis, using test probe G248P89177H7 within the first 4 exons of the CHRNA7 gene (red) and control probe G248P85751G8 outside the CHRNA7 gene on 15q13.3 (green). Triplication of 15q13.3 in one copy of chromosome 15, as indicated by yellow arrows, is seen in the proband (III-2, upper panels) and his twin brother (III-3, middle panels), but not in a control individual (lower panels). Left panels: interphase cells, showing three red signals cluster with one green signal, whereas one separate red signal is next to another green signal. Right panels: metaphase cells, showing red signals that are stronger and bigger on one copy of chromosome 15, whereas green signals have comparable size and intensity on both copies of chromosome 15.

Article Snippet: The index case was referred to the Medical Genetics Laboratories at Baylor College of Medicine (BCM), Houston, TX, USA, for clinical array comparative genomic hybridization (aCGH) analysis.

Techniques: Control

Journal: European Journal of Human Genetics

Article Title: CHRNA7 triplication associated with cognitive impairment and neuropsychiatric phenotypes in a three-generation pedigree

doi: 10.1038/ejhg.2013.302

Figure Lengend Snippet: Agilent high-resolution tiling-path aCGH. (a) CNV results for individual III-2, shown in the context of the genomic human reference (hg19). LCRs present within the region color coded according to nucleotide similarity as presented in UCSC genome browser (orange >99%, light to dark grey 90–98% similarity). The triplicated segment is represented by a blue rectangle; duplicated segment is represented by red rectangles. Note that BP4 seems duplicated likely due to the high similarity between probes that span BP4 and BP5 (purple rectangle). (b) Close view of aCGH proximal DUP-TRP breakpoint showing location of primers used to amplify and sequence the junction (sequence is shown on the aCGH view to the right). Of note, primers R2.1 and R1.1 have the same orientation in the reference genome but produce a patient-specific PCR product that reveals that the triplication is inverted in orientation regarding the small duplication. Sequencing data is color-coded to show transition from the duplicated to the triplicated segment.

Article Snippet: The index case was referred to the Medical Genetics Laboratories at Baylor College of Medicine (BCM), Houston, TX, USA, for clinical array comparative genomic hybridization (aCGH) analysis.

Techniques: Sequencing