## Description

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:

- Agi: Agilent CGH
- FISH: Inversion FISH assay
- MCD: Clone fingerprint
- NIL: Overlap with "novel" insertion locus
- Nim: NimbleGen CGH
- Seq: Clone sequencing

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

## Methods

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.

## References

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.