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

Journal: PLoS Genetics

Article Title: Mechanisms for Complex Chromosomal Insertions

doi: 10.1371/journal.pgen.1006446

Figure Lengend Snippet: (A) Upper panel: CMA and high-density aCGH results of Cplex4. Lower panel: breakpoint junction sequences in Cplex4. Microhomology between distal and proximal sequences are highlighted in red. HD array, high-density aCGH; (+), sequences in the positive strand in the hg19 reference genome. (B) Chromosome idiograms of individual Cplex4 demonstrating the duplicated fragment (segment highlighted in red) on chr14 was inserted and translocated to chr13 with where the deletion of chr13 (segment highlighted in green) occurred. (C) Chromosome idiograms of individual Cplex9 demonstrating the duplicated fragment (right facing arrow) on chr9 was inserted and translocated to chr13 with where the deletion of chr13 (segment highlighted in green) occurred. (D) Chromosome idiograms of individual Cplex12 demonstrating the duplicated fragment (right facing arrow) on chr6 was inserted and translocated to chr5 with where the deletion of chr5 (segment highlighted in green) occurred. Note that in Cplex9 and Cplex12, the inserted fragments were both inverted after the insertion in comparison to the reference genome (left facing arrows). Jct1, Junction 1; Jct2, Junction 2. Polymorphism is defined as the observation that similar CNVs have been documented in multiple healthy, clinically unaffected individuals according to the Database of Genomic Variants (DGV).

Article Snippet: We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH).

Techniques: Comparison

Journal: PLoS Genetics

Article Title: Mechanisms for Complex Chromosomal Insertions

doi: 10.1371/journal.pgen.1006446

Figure Lengend Snippet: (A) CMA and high-density aCGH results of Cplex5. (B) Chromosome idiograms of individual Cplex5 demonstrating a duplication (segment highlighted in magenta) and two deletions (segments highlighted in green and blue, respectively) on chr6, plus a duplication (segment “b” highlighted in red) on chrX. Breakpoint junction mapping indicated that the duplicated fragment of Xq28 (red segment “b”) was inserted to 6q24.2, replacing the deleted region of 6p24.2 (green segment) through Junction 1 and 2, while the duplicated fragment of 6p21 (magenta segment “a”) was inserted to 6q25.1, again replacing the other deleted region of 6q25.1q25.3 (blue segment) through Junction 3 and 4. The overall result in Cplex5 was a rearranged chr6 with inserted fragment from chrX. (C) Chromosome idiograms of individual Cplex6 demonstrating a duplication (segment “a” highlighted in red) at 5pter and a triplication (segment “c” highlighted in blue) embedded in a duplication (segment “b+c+d” highlighted in orange) at Xqter. Junction 1 and 2 led to the insertion and joining of the duplicated region on chr5 (red segment “a”) to the triplication (blue segment “c”) on chrX, both in an inverted orientation in comparison to the reference genome. Note that Junction 3 was a hypothetical breakpoint junction to most parsimoniously explain the putative mechanism for this rearrangement. The overall result in individual Cplex6 was a rearranged chrX with inserted fragment from chr5. Jct1, Junction1; Jct2, Junction 2; Jct3, Junction 3. Dashed purple lines represent potential template switching paths during the generation of the CGRs. ‘??’ indicates hypothetical junction.

Article Snippet: We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH).

Techniques: Comparison

Journal: PLoS Genetics

Article Title: Mechanisms for Complex Chromosomal Insertions

doi: 10.1371/journal.pgen.1006446

Figure Lengend Snippet: (A) CMA and high-density aCGH results of Cplex11. (B) Chromosome idiograms of individual Cplex11 demonstrating two duplications (segments “a” and “b” highlighted in red and cyan) and a deletion (segment highlighted in green) on chr13, plus a duplication (segment “c” highlighted in magenta) and a triplication embedded in the other duplication (segment “e” highlighted in blue embedded in segment “d+e+f” in orange) on chrX. Junction 1 joined the distal side of the chr13 deletion (green) to the proximal side of the first duplication on chr13 (red “a”). Junction 2 joined the distal side of the first duplication on chr13 (red “a”) to the proximal side of the first duplication on chrX (magenta “c”). Junction 3 joined the distal side of the first duplication on chrX (magenta “c”) to the proximal side of the triplication on chrX (blue “e”). Junction 4 joined the distal side of the triplication on chrX (blue “e”) to the distal side of the second duplication on chr13 (cyan “d”). Junction 5 (note this junction is hypothetical) joined the proximal side of the second duplication on chr13 (cyan “d”) to the proximal side of the second duplication on chrX (orange “d+e+f”). Lastly, Junction 6 joined the distal side of the second duplication on chrX (orange “d+e+f”) to the proximal side of the deletion on chr13 (green). The overall result in individual Cplex11 was a rearranged chr13 with multiple inserted fragments from chrX. Jct1 to Jct6, Junction 1 to Junction 6. Dashed purple lines represent potential template switching paths during the generation of the CGRs. ‘??’ indicates hypothetical junction.

Article Snippet: We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH).

Techniques:

Journal: PLoS Genetics

Article Title: Mechanisms for Complex Chromosomal Insertions

doi: 10.1371/journal.pgen.1006446

Figure Lengend Snippet: (A) Pedigree of the family. (B) High-density aCGH results of BAB1379 and BAB1381. (C) Chromosome idiograms of the mother (BAB1381) demonstrating a duplication (segment “a” highlighted in red) on chr19 and a small deletion (segments highlighted in green) plus a small duplication (segment “b” highlighted in magenta) on chrX. The insertion event from chrX to chr19 were generated through Junction 1 and 2: Junction 1 joined the distal side of the duplication on chr19 (red “a”) to the distal side of the small deletion on chrX (green), while Junction 2 joined the distal side of the small duplication on chrX (magenta “b”) to the proximal side of the duplication on chr19 (red “a”). The deletion event on chrX was generated through Junction 3 joining the proximal side of the small deletion on chrX (green) to the proximal side of the small duplication on chrX (magenta “b”). Her affected son (BAB1379) inherited the chrX with the deletion and an intact chr19, while her unaffected son (BAB1380) inherited an intact chrX and a chr19 with the insertion. Note that colored fragments are not in proportion to the actual CNVs’ sizes; i.e. not to scale. Jct1, Junction1; Jct2, Junction 2; Jct3, Junction 3. Dashed purple lines represent potential template switching paths during the generation of the CGRs. Polymorphism is defined as the observation that similar CNVs have been documented in multiple healthy, clinically unaffected individuals according DGV.

Article Snippet: We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH).

Techniques: Generated

Journal: PLoS Genetics

Article Title: Mechanisms for Complex Chromosomal Insertions

doi: 10.1371/journal.pgen.1006446

Figure Lengend Snippet: Upper panel: High-density aCGH showed the deletion at 7p15.2p14.3 in P3, and a small deletion in Mat3 at the distal boundary of the large deletion in her child P3. Lower panel: deletion breakpoint junction sequences shared in P3 and Mat3. An 815 bp insertion from chr9:5874574–5875388 was observed at this junction. (+), sequences in the positive strand in the hg19 reference genome. Jct1, Junction1.

Article Snippet: We identified 16 individuals with complex insertions among 56,000 individuals tested at Baylor Genetics using clinical array comparative genomic hybridization (aCGH) and fluorescence in situ hybridization (FISH).

Techniques:

Journal:

Article Title: High-Resolution Molecular Characterization of 15q11-q13 Rearrangements by Array Comparative Genomic Hybridization (Array CGH) with Detection of Gene Dosage

doi:

Figure Lengend Snippet: Mapping of BP5 by metaphase FISH of patient 03-28. Chromosome 15 homologs are marked by an arrowhead, and the SMC(15) is marked by an arrow. Enlargements of the images are inset, with the top row showing dual color hybridization and the bottom-row red signal arising from the BAC clone. A, Red signals represent clone AC124094 (spot 73), and green signals represent pcm15 (chromosome 15 centromere). Hybridization of AC124094 is seen on the normal homologs and on the SMC(15), with a weaker signal on the SMC(15). B, Red signals represent AC074201 (spot 74), and the green signals represent pcm15. Clone AC074201 hybridizes to the normal chromosome 15 homologs but not to the SMC(15). These data place the breakpoint within clone AC124094, which is consistent with its intermediate fluorescence signal on the array.

Article Snippet: J Med Genet 38:26–3410.1136/jmg.38.1.26 [ PMC free article ] [ PubMed ] [ CrossRef ] Veltman JA, Schoenmakers EF, Eussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG (2002) High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization.

Techniques: Hybridization, Fluorescence

Journal:

Article Title: High-Resolution Molecular Characterization of 15q11-q13 Rearrangements by Array Comparative Genomic Hybridization (Array CGH) with Detection of Gene Dosage

doi:

Figure Lengend Snippet: Characterization of deletions in patients 00-3 and 99-36 by FISH. Array data charts for 00-3 (A) and 99-36 (B) show a relative decrease in signal intensity for clones in the interval between BP1 and BP2. C, FISH analysis of the BP1–BP2 interval, with clone AC011767 (spot 5, red) and with pcm15 (green). The absence of hybridization of clone AC011767 to one chromosome 15 homolog in metaphase spreads from patient 00-3 was consistently detected, although two paired signals were present on the SMC(15). D, FISH with clone AC138649 (spot 6, red) and with pcm15 (green) on metaphase chromosomes from patient 00-3. Signals for the more telomeric clone, AC138649, were present on both chromosome 15 homologs. E, FISH with clone AC138649 (spot 6, red) and with pcm15 (green) on metaphase chromosomes from patient 99-36. The presence of a single paired signal on the SMC(15) for clone AC138649 indicates that there is only one copy of the region. F, FISH with a more distal clone, AC138687 (spot 8, red), and with pcm15 (green) generating a double signal from clone AC138687, consistent with two copies on the idic(15). C–F, Arrowheads indicate chromosome 15 homologs; arrows indicate the SMC(15). Enlargements of the images are inset, with the top row showing dual color hybridization and the bottom-row red signal arising from the BAC clone.

Article Snippet: J Med Genet 38:26–3410.1136/jmg.38.1.26 [ PMC free article ] [ PubMed ] [ CrossRef ] Veltman JA, Schoenmakers EF, Eussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG (2002) High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization.

Techniques: Clone Assay, Hybridization