Pathogenic copy number variants that affect gene expression contribute to genomic burden in cerebral palsy

Abstract

Cerebral palsy (CP) is the most frequent movement disorder of childhood affecting 1 in 500 live births in developed countries. We previously identified likely pathogenic de novo or inherited single nucleotide variants (SNV) in 14% (14/98) of trios by exome sequencing and a further 5% (9/182) from evidence of outlier gene expression using RNA sequencing. Here, we detected copy number variants (CNV) from exomes of 186 unrelated individuals with CP (including our original 98 trios) using the CoNIFER algorithm. CNV were validated with Illumina 850 K SNP arrays and compared with RNA-Seq outlier gene expression analysis from lymphoblastoid cell lines (LCL). Gene expression was highly correlated with gene dosage effect. We resolved an additional 3.7% (7/186) of this cohort with pathogenic or likely pathogenic CNV while a further 7.7% (14/186) had CNV of uncertain significance. We identified recurrent genomic rearrangements previously associated with CP due to 2p25.3 deletion, 22q11.2 deletions and duplications and Xp monosomy. We also discovered a deletion of a single gene, PDCD6IP, and performed additional zebrafish model studies to support its single allele loss in CP aetiology. Combined SNV and CNV analysis revealed pathogenic and likely pathogenic variants in 22.7% of unselected individuals with CP.

PDCD6IP, encoding a regulator of the ESCRT complex, is mutated in microcephaly

“…In this study, we report a Saudi consanguineous family with pri- show complete loss of one allele, yet showed no clinical abnormality, which would be markedly different from the previously reported de novo heterozygous deletion in two males that was associated with cerebral palsy, 15 so further study will be needed to understand the effects of heterozygous loss of PDCD61P.…”

“…14,26 Zebrafish with knock-down of pdcd6ip showed significant effects on movement including hyperactivity and erratic swimming behavior when compared with controls. 15 Other morphological features such as microcephaly, mild, moderate or severe developmental abnormalities, loss of pigment in eye, decreased eye size, gray matter hindbrain, small head, domed cranium, cardiac abnormality, decreased body size and tail curvature or kinking and cardiac oedema were also seen following knock down of the pdcd6ip expression in zebrafish compared to the control, 15 suggesting that Pdcd6ip has effects on many cell types in the body. Importantly, we report that homozygous loss of function has significantly more severe clinical outcome than previously reported case of heterozygous loss through whole gene deletion.…”

“…Whole exome sequencing was used to identify a candidate gene for the disorder supported by common phenotypic features observed in mouse and zebrafish models. 14,15 2 | PATIENT AND METHODS…”

Targeted resequencing identifies genes with recurrent variation in cerebral palsy

“…The gene list used in this study was derived from published known and candidate CP genes from our studies and those of others; 8–11,15,25,34–40 however, this panel has flexibility to be regularly updated with novel published CP genes. Since the design of this gene panel, pathogenic variants in a number of other genes have been identified in individuals with CP and future designs should include these candidates; for example, CTNNB1 , 18,41 PDCD6IP , 42 AMPD2 , 18 ITPR1, KCNC3 and SPTBN2 . 17…”

The Cerebral Palsies—Using a Common Language in Research Allows New Insights

“…Taken together, they accounted for around 30% of CP cases, which is somewhat higher to what is reported in studies on findings of pathogenic and likely pathogenic variants, when it concerns unselected individuals with CP. 8 A third paper addresses the impact of associated impairments in CP and suggests an "impairment index" characterizing severity of impairments and their combinations. 9 An important message is that on a population basis, CP is not always a severe condition: 30% of children with CP can walk unaided and have a normal or near-normal intellect without additional problems (concerning vision, hearing, or epilepsy) which is defined as low impairment index.…”