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The first rearrangement was a 708 kb duplication containing DAX1 in case 13.
This analysis showed that all duplication containing haplotypes are associated with higher anxiety-like behavior, which is consistent with a direct role for the duplication in behavior.
We considered separately the two strains that were members of the duplication containing haplotype blocks but had apparently lost the duplication (BTBR_T+_tf/J and PERA/EiJ; red boxes, Figure 3); their anxiety-like behavior was similar to the average behavior of the non-duplication containing strains (Figure 4E).
However, it has enough of the typical properties of TEs and enough full-length copies to correspond to a true TE, rather than a mere segmental duplication containing TE fragments.
We did, however, detect a smaller ∼430-kbp 15q13.3 duplication containing CHRNA7 in one individual with PD.
This is consistent with duplication in tandem spanning the full length of the HPR gene, corresponding to the annotated segmental duplication containing the HPR gene.
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Because this duplication contains 4 genes it is not immediately clear which gene is responsible for the observed behavioral differences.
As such, we relax the condition requiring that the trapezoids induced by the same tandem duplication contain the breakpoint coordinates of duplication.
The deleted region contains 70 RefSeq genes including HLXB9, SHH and EN2, while the duplication contains 82 genes (Table 1) > -wrap-foot>.
Because the telomeric limit of the duplication contained greater than 95% repetitive sequence, we designed probes to span the centromeric limit.
For example, artifactual events were observed more frequently if the syntenic homolog, i.e. the gene copy that retained the genome neighbourhood after duplication, contained suspicious segments.
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