Precise breakpoint detection in a patient with 9p- syndrome.

Cold Spring Harbor Molecular Case Studies
Jeffrey NgTychele N Turner

Abstract

We present a case of 9p- syndrome with a complex chromosomal event originally characterized by the classical karyotype approach as 46,XX,der(9)t(9;13)(p23;q13). We used advanced technologies (Bionano Genomics genome imaging and 10× Genomics sequencing) to characterize the location of the translocation and accompanying deletion on Chromosome 9 and duplication on Chromosome 13 with single-nucleotide breakpoint resolution. The translocation breakpoint was at Chr 9:190938 and Chr 13:50850492, the deletion at Chr 9:1-190938, and the duplication at Chr 13:50850492-114364328. We identified genes in the deletion and duplication regions that are known to be associated with this patient's phenotype (e.g., ZIC2 in dysmorphic facial features, FOXD4 in developmental delay, RNASEH2B in developmental delay, and PCDH9 in autism). Our results indicate that clinical genomic assessment of individuals with complex karyotypes can be refined to a single-base-pair resolution when utilizing Bionano and 10× Genomics sequencing. With the 10× Genomics data, we were also able to characterize other variation (e.g., loss of function) throughout the remainder of the patient's genome. Overall, the Bionano and 10× technologies complemented each other and provi...Continue Reading

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Methods Mentioned

BETA
chip

Software Mentioned

Loupe browser
Loupe genome browser
IGV
Integrated Genomics Viewer ( IGV )
Mosdepth
gnomAD
Long Ranger
Bionano Access
FreeBayes
GATK

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