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: Molecular Vision

Article Title: Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression

doi:

Figure Lengend Snippet: Schematic representation of the PRPF31 region and of the deletions identified. The structure of the PRPF31 (green) and TFPT (red) genes is indicated (introns, lines; noncoding exons, light-blue boxes; coding exons, dark blue boxes). The deletions detected in families MOL0931 and TB228 are indicated by the black lines. Repeated DNA elements are indicated by boxes in color (SINE, short interspersed nuclear elements; LINE, long interspersed nuclear elements; LTR, long-terminal repeats; SAT, microsatellites). Results of real-time PCRs on the genomic DNA from members of the MOL0931 family are shown by the graphs at the bottom, indicating the presence of two DNA copies (+/+) or one DNA copy of the region investigated (+/−). Because of space constraints, only eight primer pairs of the 12 used are depicted in this image. TEL, telomere; CEN, centromere.

Article Snippet: Genomic DNA samples of MOL0931–1 and MOL0931–2 were tested with array-based comparative genomic hybridization (aCGH) targeted for PRPF31 at GeneDx (Gaithersburg, MD).

Techniques:

Journal: Molecular Vision

Article Title: Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression

doi:

Figure Lengend Snippet: Sequences of the breakpoints. Electropherograms of the breakpoints of the two deletions. The red lines indicate the junction between DNA originating from intron 2 of TFPT (on the left) and DNA originating from intron 1 of PRPF31 (right).

Article Snippet: Genomic DNA samples of MOL0931–1 and MOL0931–2 were tested with array-based comparative genomic hybridization (aCGH) targeted for PRPF31 at GeneDx (Gaithersburg, MD).

Techniques:

Journal: Molecular Vision

Article Title: Heterozygous deletions of noncoding parts of the PRPF31 gene cause retinitis pigmentosa via reduced gene expression

doi:

Figure Lengend Snippet: Real-time PCR from lymphoblastoid cell lines from family MOL0931 and from controls. Relative PRPF31 expression in 13 controls, patients from family MOL0931 (931–1, 931–2, and 931–5), and individual 931–3 (unaffected carrier of the mutation) are shown. Error bars indicate standard deviations. The difference in gene expression between controls and patients is statistically significant (p = 1.3 × 10 −4 , by t test).

Article Snippet: Genomic DNA samples of MOL0931–1 and MOL0931–2 were tested with array-based comparative genomic hybridization (aCGH) targeted for PRPF31 at GeneDx (Gaithersburg, MD).

Techniques: Real-time Polymerase Chain Reaction, Expressing, Mutagenesis, Gene Expression

Journal: Genes & Development

Article Title: Delineation of two multi-invasion-induced rearrangement pathways that differently affect genome stability

doi: 10.1101/gad.350618.123

Figure Lengend Snippet: MIR frequently causes additional unselected rearrangements. ( A ) Experimental system in diploid S. cerevisiae . The heterozygous DSB-inducible YS -HOcs construct replaces URA3 on chromosome V. The LY and S2 donors consist in the two halves of the LYS2 gene (2090 and 2089 bp, respectively) at its locus on chromosome II. This DSB donor configuration is referred to as interchromosomal with allelic donors. Translocation of the LY and S2 donors restores a functional LYS2 gene. Approximately 10% of induced Lys + colonies are small on the initial plate and exhibit a higher proportion of additional SVs than bigger colonies. ( B – D ) Twelve small MIR recombinants were analyzed by Southern blot ( B ), PFGE ( C ), and high-throughput shotgun sequencing ( D ). Strains labeled in green were additionally analyzed by aCGH and nanopore long-read sequencing. ( C ) The ladder corresponds to a S. cerevisiae strain from the YPH80 background, marginally different from our W303 parental strain. Ladder size is in kilobases. Chromosome V and chromosome VIII comigrate in the W303 background. (*) Chromosomal abnormality. ( E ) Deduced genome structure of the 12 MIR recombinants. The number of nanopore (NP) reads encompassing the unselected rearrangements is indicated.

Article Snippet: Array comparative genomic hybridization (aCGH) copy number profiling and characterization of rearrangement junctions through Oxford nanopore long-read sequencing were carried out following procedures described previously ( ; ).

Techniques: Construct, Translocation Assay, Functional Assay, Southern Blot, High Throughput Screening Assay, Shotgun Sequencing, Labeling, Sequencing