Relative burden of large CNVs on a range of neurodevelopmental phenotypes

Abstract

While numerous studies have implicated copy number variants (CNVs) in a range of neurological phenotypes, the impact relative to disease severity has been difficult to ascertain due to small sample sizes, lack of phenotypic details, and heterogeneity in platforms used for discovery. Using a customized microarray enriched for genomic hotspots, we assayed for large CNVs among 1,227 individuals with various neurological deficits including dyslexia (376), sporadic autism (350), and intellectual disability (ID) (501), as well as 337 controls. We show that the frequency of large CNVs (>1 Mbp) is significantly greater for ID-associated phenotypes compared to autism (p = 9.58 × 10(-11), odds ratio = 4.59), dyslexia (p = 3.81 × 10(-18), odds ratio = 14.45), or controls (p = 2.75 × 10(-17), odds ratio = 13.71). There is a striking difference in the frequency of rare CNVs (>50 kbp) in autism (10%, p = 2.4 × 10(-6), odds ratio = 6) or ID (16%, p = 3.55 × 10(-12), odds ratio = 10) compared to dyslexia (2%) with essentially no difference in large CNV burden among dyslexia patients compared to controls. Rare CNVs were more likely to arise de novo (64%) in ID when compared to autism (40%) or dyslexia (0%). We observed a significantly increased large CNV burden in individuals with ID and multiple congenital anomalies (MCA) compared to ID alone (p = 0.001, odds ratio = 2.54). Our data suggest that large CNV burden positively correlates with the severity of childhood disability: ID with MCA being most severely affected and dyslexics being indistinguishable from controls. When autism without ID was considered separately, the increase in CNV burden was modest compared to controls (p = 0.07, odds ratio = 2.33).

Figure 1. CNV burden in neurodevelopmental disorders.

(A) The figure shows the population frequency of the largest CNV (as a survivor function) in individuals with ID, autism, dyslexia, and controls. (B) Population frequency of the largest CNV is shown for ID, ID with MCA, autism with ID, autism without ID, dyslexia, and NIMH control individuals. (C) Histograms depicting deletions per individual at each size range are shown. Note that 35 NIMH control samples carried an approximately 560 kbp deletion involving PRAME on distal 22q11.2. (D) Duplications per individual at each size range are shown. The hotspot chip has higher coverage over segmental duplication regions and therefore there is an expected abundance of duplications per individual compared to deletions.

Figure 2. Rare CNVs and de novo rates in neurodevelopmental disorders.

(A) The proportion of rare CNVs as a function of size is shown for NIMH controls and dyslexia, autism, and ID cohorts. To identify rare CNVs, we compared the pattern of CNVs from each of these cohorts to the CNV frequency map from 8,329 controls genotyped on Illumina arrays. (B) The proportion of de novo occurrence of CNVs among the three cohorts is shown for each size range. Note that the CNVs from the dyslexia cohort are all inherited. DNA from parents of NIMH controls was not available and hence not tested for de novo CNV frequency.

Figure 3. Pedigree shows the inheritance of a 669 kbp duplication encompassing AUTS2 and WBSCR17 from a father to the daughter.

(A) The father has features of dyslexia with a verbal IQ (VIQ) of 122, WATT^a 93, WRAT3sp^b 83 and WIATsp^c 94. The daughter's scores are VIQ 122, WID^d 86, WATT 91, WRAT3sp 90, and WIATsp 94. (B) In this pedigree the 84 kbp deletion within AUTS2 is transmitted to the proband (VIQ 122, WATT 97, WRAT3sp 96, WIATsp 94) from the affected paternal grandmother (VIQ 118, WATT 88) through the unaffected father. (C) A deletion within IMMP2L is shown for this family. The deletion is transmitted to the proband (VIQ 111, WID 83, WATT 82, WRAT3sp 85, WIATsp 81) from his affected father (VIQ 84, WRAT3sp 68, WIAT-2sp 66). Interestingly, IMMP2L variants have been associated with Tourette syndrome, ADHD, and autism. (D) A 1.2 Mbp deletion within EYS is shown in several family members of this large pedigree. While the proband (VIQ 107, WID 56, WATT 81, WRAT3sp 87, WIATsp 87) and his affected brother (VIQ 101, WID 66, WATT 82, WRAT3sp 78, WIATsp 85) carried the deletion, so did many other unaffected relatives, including the father. Although no inference can be drawn for its role in dyslexia, as the deletion does not segregate with the phenotype, recessive mutations in EYS have been associated with retinitis pigmentosa. ^aWATT- WRMT-R Woodcock Reading Mastery Test – Revised; Word Attack subtest . A measure of untimed reading of single non-words. ^bWRAT3sp - Wide Range Achievement Tests – Third Addition; Spelling subtest . Spelling of single words from dictation in writing. ^cWIAT(2)sp - Wechsler Individual Achievement Test (2^nd edition); Spelling subtest . Spelling of single words from dictation in writing. ^dWID - WRMT-R Woodcock Reading Mastery Test – Revised; Word Identification subtest . A measure of untimed reading of single words.

Figure 4. FOXP1 deletions in individuals with autism and ID.

Two deletions (5 Mbp and 6.6 Mbp) are shown intersecting at a common region of 1.16 Mbp containing FOXP1. Note that the deletion in the autism individual also covers ROBO2 and CNTN3.

Figure 5. Novel CNVs identified in the ID cohort.

(A) Overlapping deletions on chromosome 9p24 are shown. Deletions of this region containing DMRT1 and DMRT3 have also been associated with urogenital abnormalites and sex reversal. (B) A ∼3 Mbp deletion on 6q16 is shown encompassing SIM1. Larger deletions of this region were previously reported and have been associated with obesity. Orange bars denote deletions and gray regions are non-deleted regions from previous studies . Taken together with other published studies, this deletion narrows down the critical region (dotted box) to about 2.9 Mbp.

Figure 6. Two large CNV hits in a case with ID/MCA.

A 3.3 Mbp deletion containing PITX2 as well as the 3.4 Mbp paternally inherited 16p13.33 duplication is shown for an individual with ID plus MCA. This individual has features of Rieger syndrome including visual defects, mild hypotonia, right congenital glaucoma, left microophalmia, and anterior segment dysgenesis. Other features include cleft uvula, hypodontia and conical teeth, hyperplasia of frenulum of tongue, midface hypoplasia, strabismus, and deafness.