Fine-scale mapping of human genome structural variation
Fine-scale mapping of human genome structural variation
A review of Mapping and sequencing of structural variation from eight human genomes
Note: This is a review of the published article listed below. All information, quotes, figures, methods, and findings mentioned in this review are from that article, and are the property of its authors and/or the publication in which the article originally appeared.
Adapted by permission from Macmillan Publishers Ltd: Nature 453(7191):56-64, 2008.
Intermediate scale human genetic structural variations (insertions, duplications, deletions, and inversions of DNA comprising a few thousand to a few million base pairs) are quite common and represent more nucleotides than single nucleotide polymorphisms. It is increasingly evident that these structural variations are important to human diversity as well as disease susceptibility. Dr. Evan Eichler and researchers from multiple institutions present the first high-resolution sequence map of human structural variation for genomes of eight individuals of Asian, European, and African ancestry from the HapMap Project. Using a clone-based approach, they localized 1,695 sites of structural variation (Figure 1). They also identified 525 regions of novel euchromatic sequence in the examined genomes that are not included in the human reference genome (Figure 2), compelling evidence that the human genome sequence is incomplete. The researchers used custom Agilent microarrays to assess the copy number status of the unannotated sequences by array comparative genomic hybridization (array CGH). More than 40% of the novel sequences showed copy number variation. Their map of human structural variation is highly consistent with previous high-resolution CNV studies that found a considerably smaller size distribution for CNV regions compared to studies that employed bacterial artificial chromosome (BAC)-based array CGH, and predicts that the current database of copy number variation is overstated. The study’s clone-based method enabled mapping and complete sequencing of many CNV regions, enabling valuable insights into the mechanisms that mediate human structural variation.
Figure 1. Map of structural variation in the human genome.
The location of 724 insertions (blue), 747 deletions (red) and 224 inversions (green) that have been experimentally validated are mapped onto the human genome (build35). Sites are arranged according to individuals in rows above each chromosome, in order of the nine individual genomic libraries (G248 (first row), then ABC7–ABC14); the Coriell IDs are listed in Table 1. All sites have been validated by array CGH, MCD analysis, or sequencing in at least one reference individual. The location of 525 novel sequence loci are depicted as arrows below each chromosome. Those mapping to gaps (black) are distinguished from those mapping to regions not associated with gaps (orange). The Y chromosome is not shown because samples were primarily from females.
Figure 2. Discovery of novel human sequences that are CNV.
a, Clusters of clones where one end is mapped to the genome (build35) but the other does not map are shown schematically on the basis of their orientation (blue and yellow lines). Three categories are distinguished: clones mapping around a site already spanned by a discordant fosmid ESP (spanned), regions where no discordant clones are identified (unspanned), and clones mapping adjacent to sequence gaps (gap). b, Array CGH experiment based on an oligonucleotide microarray designed to a sequence assembly of these novel sequences (525 distinct loci). Of the spanned and unspanned loci, 45% show copy-number variation (gains, orange; losses, blue) in comparison with a reference sample (NA15510). Each data point represents the average log2 intensity values for all of the probes from a single contig. Within each of the three categories, contigs are ordered on the basis of their chromosomal anchored positions. The bottom row represents the results of one of three self-versus-self hybridizations with sample NA15510. c, A novel insertion of 130 kbp on chromosome 6 identified by OEA fosmid clones (blue and gold arrows) and confirmed by optical mapping of DNA from the GM15510 cell line. Optical images of SwaI-restricted DNA are aligned to the reference (build35) genome. This large insertion maps intergenically to a region rich in conserved sequence elements and is confirmed in all eight libraries. This region does not correspond to a known gap in the human genome and does not appear CNV in our eight samples. d, Validation of a CNV region by fluorescence in situ hybridization. Hemizygous signals are detected by fluorescence in situ hybridization on metaphase chromosomes (with OEA clone ABC7_42397600_G7 as probe), corresponding to samples where no signal intensity difference was observed with respect to the reference by array CGH.
Title: Mapping and sequencing of structural variation from eight human genomes
Authors: Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, Haugen E, Zerr T, Yamada NA, Tsang P, Newman TL, Tüzün E, Cheng Z, Ebling HM, Tusneem N, David R, Gillett W, Phelps KA, Weaver M, Saranga D, Brand A, Tao W, Gustafson E, McKernan K, Chen L, Malig M, Smith JD, Korn JM, McCarroll SA, Altshuler DA, Peiffer DA, Dorschner M, Stamatoyannopoulos J, Schwartz D, Nickerson DA, Mullikin JC, Wilson RK, Bruhn L, Olson MV, Kaul R, Smith DR, Eichler EE.
Journal: Nature. 2008 May 1;453(7191):56-64.
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