array-cgh experiments  (Agilent technologies)

Journal: Nature genetics

Article Title: Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

doi: 10.1038/ng.3120

Figure Lengend Snippet: (a) Different structural rearrangements at the 15q13.3 region include a 2 Mbp microdeletion between BP4 and BP5 , a 430 kbp microdeletion involving the CHRNA7 gene , a 1.8 Mbp polymorphic inversion of the same region (γ inversion) , , , two CNP SDs (CNPα and CNPβ) mapping at BP4 and BP5 of the 15q13.3 microdeletion, and a small inversion (β inversion) overlapping CNPβ at BP4. (b) Read-depth-based copy number estimates of CNPα and CNPβ in 2225 HapMap individuals from the 1000 Genome Project and 86 nonhuman ape, Neanderthal and Denisova genomes (circled in red). The number of individuals from each population is indicated in parentheses. A strong correlation (r=0.82, Pearson correlation which is significant using an F test) in copy number is observed between CNPα and CNPβ in humans but not apes. (c) FISH analysis using a probe mapping at CNPα (WIBR2-1388I24, green) and two probes mapping in the unique sequence (WIBR2-1462O20, red; WIBR2-3158E16, blue) shows a variable copy number between 0 and 1 at BP4 and between 0 and 2 at BP5.

Article Snippet: M.Y.D. performed MIPs experiments, Illumina sequencing libraries construction, array CGH experiments and sequence analysis.

Techniques: Sequencing

Journal: Nature genetics

Article Title: Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

doi: 10.1038/ng.3120

Figure Lengend Snippet: (a) A 210 kbp β inversion was identified, validated, and sequenced using the VMRC54 BAC library (NA12891 individual). Illumina-generated sequences of clones spanning the BP4 CNPβ were mapped to human reference GRCh37. Clones sequenced using PacBio are indicated with asterisks. The copy number (CN) heat map shows the total diploid CN of a region in the CH17 hydatidiform mole cell line. The locations of the β inversion haplotype-tagging variants are pictured as dots. The blue arrows represent the BP4 CNPβ (dark blue) with the flanking 58 kbp inverted SDs (light blue). (b) Homologous sequences of clones, generated using PacBio and assembled into sequence contigs, are connected with colored lines between the direct (Hα 2 ) and inverted (Hα 2 β inv ) haplotypes from NA12891 using Miropeats . Vertical arrows indicate the minimal inversion breakpoints. (c) Homologous sequences (58 kbp) from the BP4 CNPβ flanking inverted SDs were aligned from multiple individuals (NA12891 and CH17) and haplotypes (β direct: SDs 1 and 3, and β inverse: SDs 2 and 4; see for a more detailed alignment) and variant sites compared. Variant positions showing signatures of being within or outside of the β inversion breakpoints are indicated as colored lines under the picture of the distal β inverse SD including: within the inversion (orange; consensus of SDs 1 & 4 and SDs 2 & 3), outside the inversion (yellow; consensus of SDs 1 & 2 and SDs 3 & 4), and gene conversion (gray; consensus of SDs 1 & 3 and SDs 2& 4). The inversion breakpoint, refined to a region in which we observe a transition from orange to yellow lines, is highlighted with a dash-outlined red box.

Article Snippet: M.Y.D. performed MIPs experiments, Illumina sequencing libraries construction, array CGH experiments and sequence analysis.

Techniques: Generated, Clone Assay, Sequencing, Variant Assay

Journal: Nature genetics

Article Title: Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

doi: 10.1038/ng.3120

Figure Lengend Snippet: The genomic structure is schematized within the context of a generally accepted phylogeny of orangutan, gorilla, chimpanzee and human. A tiling path of BAC clones was sequenced for each haplotype (dashed lines Illumina/solid lines PacBio or capillary finished sequence). A total of 66 BACs were completely sequenced and used to determine the SD organization (colored boxes). Colored boxes with lighter shades indicate segments that are single copy but duplicated in other species. Nonhuman primates lack most of the larger duplications (including CNPα and CNPβ) observed in humans but do carry ancestral GOLGA8 repeats. The region has expanded from 1.8–1.9 Mbp in nonhuman apes to 2–3 Mbp in humans as a result of SD accumulation (colored rectangles). The size of each haplotype is indicated on the right, with the size of the duplicated bases in parentheses. The addition of a polymorphic 500 kbp at BP4 occurred specifically in the human lineage, associated with an expansion of the GOLGA8 repeats at BP4 (CN=6 compared to CN=2 in human simpler haplotypes and nonhuman primates). Sequence and FISH data indicate that chimpanzee and orangutan were found to be in direct orientation while gorilla was found to be in inverse orientation for the γ inversion suggesting separate inversion events occurred at this locus across primate species.

Article Snippet: M.Y.D. performed MIPs experiments, Illumina sequencing libraries construction, array CGH experiments and sequence analysis.

Techniques: Clone Assay, Sequencing

Journal: Nature genetics

Article Title: Palindromic GOLGA8 core duplicons promote chromosome 15q13.3 microdeletion and evolutionary instability

doi: 10.1038/ng.3120

Figure Lengend Snippet: Array CGH data for two 15q13.3 microdeletion patient samples are mapped against the GRCh37 human reference. The microdeletion breakpoints map within a 500 kbp region (yellow boxes) where both α and β SDs are mapping. Digital comparative genomic hybridization (dCGH) was used to detect regions of gain or loss in probands (p1) compared to their parents (mo, mother; fa, father). The method measures differences in Illumina sequence read-depth compared to a reference genome to define sites of copy number variation. Paralog-specific read-depth analysis in each proband and their parents was performed at all sites where both parents had the expected copy number of 2. This allowed us to refine proband 13647.p1 breakpoints to a 13 kbp segment and proband 13301.p1 breakpoints to a 30 kbp between BP4 and BP5 (red boxes). The two probands have different breakpoints but in both cases the breakpoints map at or adjacent to the GOLGA8 repeats.

Article Snippet: M.Y.D. performed MIPs experiments, Illumina sequencing libraries construction, array CGH experiments and sequence analysis.

Techniques: Hybridization, Sequencing

Journal: Genome Research

Article Title: Analysis of copy number variations among diverse cattle breeds

doi: 10.1101/gr.105403.110

Figure Lengend Snippet: Cattle copy number variation and segmental duplication regions display a local tandem distribution pattern. CNV regions (177 events, 28 Mb, ∼1% of the bovine genome) reported by 90 array CGH experiments are shown above the chromosomes in green (gain), red (loss), and dark blue (both). The bar height represents their frequencies: short (appeared in 1 sample), median (≥2 samples), and tall (≥5 samples). Segmental duplications (94.4 Mb, 3.1% of the bovine genome) predicted by two independent computational approaches are illustrated on the chromosomes in red (WSSD), blue (WGAC), or purple (both). The patterns are depicted for all duplications for ≥5 kb in length and ≥90% sequence identity. The gaps in the assembly are represented on the chromosomes as white ticks. For clarity, distribution patterns with the unassigned sequence contigs (chrUnAll) are shown separately in Supplemental Figure S1.

Article Snippet: Array CGH experiments were performed as previously described ( Selzer et al. 2005 ).

Techniques: Sequencing