@article {715, title = {Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants.}, journal = {Genome Med}, volume = {11}, year = {2019}, month = {2019 12 09}, pages = {80}, abstract = {

BACKGROUND: We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated.

METHODS: Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis.

RESULTS: High-density customized array showed that the majority of cases (33/50; ~ 66\%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34\%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54\% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32\% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches).

CONCLUSIONS: These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.

}, issn = {1756-994X}, doi = {10.1186/s13073-019-0676-0}, author = {Bahrambeigi, Vahid and Song, Xiaofei and Sperle, Karen and Beck, Christine R and Hijazi, Hadia and Grochowski, Christopher M and Gu, Shen and Seeman, Pavel and Woodward, Karen J and Carvalho, Claudia M B and Hobson, Grace M and Lupski, James R} } @article {346, title = {Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication.}, journal = {PLoS Genet}, volume = {11}, year = {2015}, month = {2015 Mar}, pages = {e1005050}, abstract = {

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM$\#$300260) and Pelizaeus-Merzbacher disease (PMD, MIM$\#$312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

}, keywords = {Chromosome Breakpoints, Chromosome Inversion, Gene Dosage, Gene Duplication, Humans, Myelin Proteolipid Protein, Pelizaeus-Merzbacher Disease}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005050}, author = {Beck, Christine R and Carvalho, Claudia M B and Banser, Linda and Gambin, Tomasz and Stubbolo, Danielle and Yuan, Bo and Sperle, Karen and McCahan, Suzanne M and Henneke, Marco and Seeman, Pavel and Garbern, James Y and Hobson, Grace M and Lupski, James R} }