Genomic Characterization of 9p Deletion and Duplication Syndromes

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Presenter(s)

Eleanor Sams

Abstract or Description

Copy number variants (CNVs) involving the p arm of chromosome 9 are rare and progress is needed to establish relationships between the genomic and clinical characteristics of 9p CNVs. To bridge this gap in understanding, we analyzed long and/or short read sequencing data for 19 individuals with 9p CNVs. We determined the precise nucleotide coordinate(s) of the CNV breakpoint(s) for 10 individuals and established breakpoint windows approximately 1,000 base pairs wide for the 9 remaining individuals. We selected three strategies to confirm these 9 low-confidence breakpoints. The first strategy involves performing polymerase chain reactions (PCR) followed by Sanger sequencing and alignment of the sequenced regions. This method effectively confirms the precise breakpoint for interstitial structural variants. The second method, quantitative PCR (qPCR), measures fluorescence as regions surrounding the breakpoint are amplified and detects differences in fluorescence intensity. qPCR confirms the breakpoint window for interstitial and terminal CNVs. The third method involves targeted deep sequencing of fragments from the breakpoint region excised using the CRISPR/Cas9 system. The precise breakpoint of interstitial and terminal CNVs can be determined through read depth analysis. An additional source of 9p CNV data is the Chromosome 9p Minus Network cohort. Cytogenetic data for 719 individuals in this dataset revealed that the chromosome band 9p24 contains the most CNV breakpoints, followed by 9p22. Aggregated data from the Network cohort and the literature revealed that 9q is the most commonly affected chromosome arm in secondary structural variants, due in part to ring chromosome 9. Further analysis of the dataset suggested that the XY sex reversal phenotype commonly observed in individuals with 9p deletions may account for a female gender bias in 9p cohorts. We are hopeful that the methods described in this work will be utilized to further establish genotype-phenotype correlations in 9p deletion and duplication syndromes.