Using a new analytic approach for genotyping and phenotyping chromosome 9p deletion syndrome

Abstract

Using a new analytic method ("unique non-overlapping region" (UNOR) analysis), we characterized the genotypes and phenotypes of a large cohort of individuals diagnosed with chromosome 9p deletion syndrome (9PMS) and defined critical genomic regions. We extracted phenotypic information from 48 individuals with 9PMS from medical records and used a guided interview with caregivers to clarify ambiguities. Using high-resolution whole-genome sequencing for breakpoint definition, we aligned deletions and drew virtual breakpoints to obtain UNORs associated with phenotypic characteristics. We next extracted genotype and phenotype data for 57 individuals identified from a systematic review of the 9PMS literature and analyzed these as above. Common phenotypic features included developmental delay/intellectual disability, dysmorphic features, hypotonia, genital defects in XY individuals, psychiatric diagnoses, chronic constipation, atopic disease, vision problems, autism spectrum disorder, gastroesophageal reflux disease, trigonocephaly, congenital heart disease, and neonatal hypoglycemia. Our approach confirmed previous literature reports of an association of FREM1 with trigonocephaly and suggested a possible modifier element for this phenotype. In conclusion, the UNOR approach delineated phenotypic characteristics for 9PMS and confirmed the critical role of FREM1 and a possible long-distance regulatory element in pathogenesis of trigonocephaly that will need to be replicated in future studies.

Fig. 1. Schematic representation of the delimitation of unique non-overlapping regions (UNORs).

Each horizontal line represents a hypothetical patient, except the last one (in gray), which represents a hypothetical, or virtual, chromosome composited from all of the breakpoints in patient’s real chromosomes 9. Red regions represent deleted regions. Blue regions represent non-deleted regions. Dashed vertical lines represent breakpoints.

Fig. 2. Flowchart of systematic review results.

Study selection flowchart.

Fig. 3. Maximal overlapping regions.

Each plot includes only individuals that were positive for a single, given phenotype. Horizontal red lines represent deleted areas of single individuals in subcohort 1. Horizontal blue lines represent deleted areas of single individuals in subcohort 2. The horizontal brown line, when present, represents the maximal overlapping deleted region.

Fig. 4. Unique non-overlapping region (UNOR) analysis per phenotype.

Each Manhattan plot represents the UNOR analysis for a single phenotype. UNORs are arrayed in geographical order, starting at the most telomeric (UNOR 1). Log-transformed p-values are plotted for the association between the deletion of each UNOR and the phenotype for the given plot. Significance is achieved at a log-transformed p-value ≥3.0. Coordinates for UNORs that achieved statistical significant are: UNOR 1: 1–190,938; UNOR 3: 1,374,920–1,657,320; UNOR 4: 1,657,321–1,998,155; UNOR 5: 1,998,156–3,418,240; UNOR 9: 5,341,747–9,247,652; UNOR 10: 9,247,653–9,461,126; UNOR 11: 9,461,127–10,307,066; UNOR 12: 10,306,720–10,327,386; UNOR 15: 11,020,189–11,079,032; UNOR 16: 11,079,033–12,743,642; UNOR 17: 12,732,126–13,041,178; UNOR 18: 13,041,179–13,276,084; UNOR 19: 13,276,085–14,543,329; UNOR 20: 14,543,330–14,550,891; UNOR 21: 14,550,892–14,608,632; UNOR 22: 14,608,633–14,745,360; UNOR 23: 14,745,361–16,301,691; UNOR 24: 16,301,692–16,637,545; UNOR 25: 16,637,546–16,684,627; UNOR 26: 16,684,628–17,102,299.