Data from Human Genome Structural Variation Project. This track shows validated regions of structural variation in nine individuals from Kidd, et al.. Deletions, insertions and inversions are included. For inversions, sites corresponding to both breakpoints may be depicted. Clones corresponding to only a single breakpoint were selected to validate the site. Coordinates correspond to the variant region predicted by end-sequence pairs (ESPs), not to sequence-derived breakpoints.
Each site was validated by at least one of these methods:
Each individual's validated sites are in a different subtrack. The nine individuals' labels used in Kidd, et al., populations of origin, and Coriell Cell Repository catalog IDs are shown here:
| Individual | Population | Coriell ID |
| ABC14 | CEPH | NA12156 |
| ABC13 | Yoruba | NA19129 |
| ABC12 | CEPH | NA12878 |
| ABC11 | China | NA18555 |
| ABC10 | Yoruba | NA19240 |
| ABC9 | Japan | NA18956 |
| ABC8 | Yoruba | NA18507 |
| ABC7 | Yoruba | NA18517 |
| G248 | Unknown | NA15510 |
Excerpted from Kidd, et al.:
|
We selected eight individuals as part of the first phase of the Human
Genome Structural Variation Project. This included four individuals of
Yoruba Nigerian ethnicity and four individuals of non-African
ethnicity. For each individual we constructed a whole genomic library
of about 1 million clones by using a fosmid subcloning strategy.
Each library was arrayed and both ends of each clone insert were
sequenced to generate a pair of high-quality end sequences (termed an
end-sequence pair (ESP)).
The overall approach generated a physical clone map for each
individual human genome, flagging regions discrepant by size or
orientation on the basis of the placement of end sequences against the
reference assembly.
Across all eight libraries, we mapped 6.1 million clones to distinct
locations against the reference sequence
(http://hgsv.washington.edu).
Of these, 76,767 were discordant by length and/or orientation,
indicating potential sites of structural variation. About 0.4%
(23,742) of the ESPs mapped with only one end to the reference
assembly despite the presence of high-quality sequence at the other
end (termed one-end anchored (OEA) clones).
Fosmid clones discordant by size (n = 3,371 fosmid clones) were subjected to fingerprint analysis using four multiple complete restriction enzyme digests (MCD analysis) to confirm insert size and eliminate rearranged clones. Two high-density customized oligonucleotide microarrays (Agilent and NimbleGen) were designed to confirm sites of deletion and insertion (GEO accessions GSE10008 and GSE10037). We developed a new, expectation maximization-based clustering approach to genotype deletions with the use of data from the Illumina Human1M BeadChip collected for 125 HapMap DNA samples. We found that more than 98% of the children's genotypes were consistent with mendelian transmission on the basis of an analysis of 28 parent-child trios. |
Kidd JM, Cooper GM, Donahue WF, Hayden HS, Sampas N, Graves T, Hansen N, Teague B, Alkan C, Antonacci F, et al. Mapping and sequencing of structural variation from eight human genomes. Nature. 2008 May 1;453(7191):56-64.