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| Status |
Public on Dec 18, 2023 |
| Title |
Break-induced replication underlies formation of inverted triplications and generates unexpected diversity in haplotype structures |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by array
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| Summary |
The duplication-triplication/inverted-duplication (DUP-TRP/INV-DUP) structure is a type of complex genomic rearrangement (CGR). Although it has been identified as an important mutation signature of pathogenicity for genomic disorders and cancer genomes, its architecture remains unresolved. Here we studied the genomic architecture of DUP-TRP/INV-DUP by investigating the DNA of 24 patients identified by array comparative genomic hybridization (aCGH) on whom we found evidence for the existence of 4 out of 4 predicted structural variant (SV) haplotypes. Using a combination of short-read genome sequencing (GS), long-read GS, optical genome mapping and StrandSeq the haplotype structure was resolved in 18 samples. The point of template switching in 4 samples was shown to be a segment of ~2.2-5.5 kb of 100% nucleotide similarity. These data provide experimental evidence supporting the hypothesis that inverted LCRs act as a recombinant substrate. This type of CGR can result in multiple conformers which contributes to generate diverse SV haplotypes in susceptible loci.
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| Overall design |
The goal of this experiment was to determine the precise genomic architecture of patients harboring a duplication-triplication/inverted-duplication complex genomic rearrangement.
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| Contributor(s) |
Grochowski CM, Carvalho CM |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 18, 2023 |
| Last update date |
Dec 19, 2023 |
| Contact name |
Christopher Grochowski |
| E-mail(s) |
Christopher.Grochowski@bcm.edu
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| Organization name |
Baylor College of Medicine
|
| Department |
Molecular and Human Genetics
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| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77006 |
| Country |
USA |
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| Platforms (2) |
| GPL34011 |
Agilent-086099 MECP2 ReReDesign G4125A |
| GPL34013 |
Agilent-085948 MECP2_V3 G4125A |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA1054092 |
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