Precise breakpoint detection in a patient with 9p– syndrome

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 singlebase-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 provided important insight into our patient with 9psyndrome. Altogether, these results indicate that newer technologies can identify precise genomic variants associated with unique patient phenotypes that permit discovery of novel genotype-phenotype correlations and therapeutic strategies.

From karyotypes to precision genomics in 9p deletion and duplication syndromes

“… 26 The absence of high-resolution alignments and precise breakpoint analysis is one factor that has contributed to the difficulty in establishing genotype-phenotype correlations with 9p CNVs. 9 , 64 The advancements of modern sequencing technologies provide an opportunity to precisely resolve breakpoints to the exact base, 33 thus allowing for a better characterization of 9p CNVs both in terms of genomic variation and phenotypes. The power of long-read sequencing technologies (e.g., Oxford Nanopore Technologies and PacBio) is enabling complete genomic variant resolution within individuals, 65 , 66 as shown in the present study.…”

“…Genomic data were collected from the literature where approximate breakpoints are known for 53 individuals with 9p deletion and duplication syndromes. 12 , 14 , 15 , 16 , 17 , 19 , 27 , 29 , 30 , 33 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 …”

“…Bionano optical mapping was carried out as described previously. 33 PacBio HiFi long-read sequencing was performed to a coverage depth of 46.12 for individual 9p.100.p1. The CCS fastq files were aligned to build 38 of the human genome (GRCh38_full_analysis_set_plus_decoy_hla.fa) using pbmm2 ( https://github.com/PacificBiosciences/pbmm2 ) v.1.3.0 align.…”

“… 12 were reported to display ASD or other behavioral issues, and many additional 9p case reports and cohorts include individuals with ASD. 8 , 26 , 31 , 32 , 33 Comparison of 9p CNV individuals with and without ASD and the locations of their CNVs has led to the hypothesis that there is an ASD candidate gene on 9p24. 26 , 31 , 32 …”

Optical Genome Mapping in Routine Human Genetic Diagnostics—Its Advantages and Limitations

“…Recently, the system has been used to successfully detect the breakpoints of chromosomal translocations, for the diagnosis of facioscapulohumeral muscular dystrophy (FSHD) and has been suggested for use as a cytogenomic tool for prenatal diagnostics [ 12 , 13 , 14 , 15 , 16 ]. One study compared OGM using the Saphyr system to conventional point-of-care methods for the detection of 100 different chromosomal aberrations [ 17 ].…”