Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

Yap, Chloe X.; Alvares, Gail A.; Henders, Anjali K.; Lin, Tian; Wallace, Leanne; Farrelly, Alaina; McLaren, Tiana; Berry, Jolene; Vinkhuyzen, Anna A. E.; Trzaskowski, Maciej; Zeng, Jian; Yang, Yuanhao; Cleary, Dominique; Grove, Rachel; Hafekost, Claire; Harun, Alexis; Holdsworth, Helen; Jellett, Rachel; Khan, Feroza; Lawson, Lauren; Leslie, Jodie; Levis Frenk, Mira; Masi, Anne; Mathew, Nisha E.; Muniandy, Melanie; Nothard, Michaela; Visscher, Peter M.; Dawson, Paul A.; Dissanayake, Cheryl; Eapen, Valsamma; Heussler, Helen S.; Whitehouse, Andrew J. O.; Wray, Naomi R.; Gratten, Jacob

doi:10.1186/s13229-020-00407-5

Molecular Autism

Table 2 ASD/ID-associated CNVs detected in the AAB dataset

From: Analysis of common genetic variation and rare CNVs in the Australian Autism Biobank

Diagnosed children
Sample ID	Group	Sex	Type	CNV coordinates	ASD/ID-associated CNV	Reference coordinates	Other information
CNVs with a critical gene
1101366	ASD	M	Dup	chr17:1,196,088–1,326,656	17p13.3 (Miller-Dieker syndrome) region (includes YWHAE and PAFAH1B1)^	chr17:1,247,833–2,588,909	Critical gene coordinates: YWHAE: chr17:1,247,569–1,268,350; PAFAH1B1: chr17:2,541,583–2,585,096
1101637	ASD	M	Dup	chr17:29,111,368–30,343,735	17q11.2 recurrent region (includes NF1)	chr17:29,097,069–30,264,027	Critical gene coordinates: chr17:29,422,328–29,701,173
CNVs without a critical gene
4406214	ASD	F	Dup	chr15:22,321,690–32,515,100	15q11q13 recurrent (PWS/AS) region (BP1-BP3, Class 1)	chr15:22,832,519–28,379,874	100.00% overlap
3305166	ASD	M	Del	chr15:29,079,105–32,515,100	15q13.3 recurrent region (D-CHRNA7 to BP5) (includes CHRNA7 and OTUD7A)	chr15:32,019,621–32,445,405	100.00% overlap
1101486	ASD	M	Del	chr15:31,007,901–32,515,100	15q13.3 recurrent region (D-CHRNA7 to BP5) (includes CHRNA7 and OTUD7A)	chr15:32,019,621–32,445,405	100.00% overlap
1101365	ASD	M	Del	chr15:31,115,226–32,515,100	15q13.3 recurrent region (D-CHRNA7 to BP5) (includes CHRNA7 and OTUD7A)	chr15:32,019,621–32,445,405	100.00% overlap
4406241*	ASD	M	Del	chr16:21,973,913–22,414,463	Recurrent 16p12.1 microdeletion (neurodevelopmental susceptibility locus)	chr16:21,946,524–22,467,284	84.60% overlap
3305177	ASD	M	Del	chr16:28,832,565–29,044,745	16p11.2 recurrent region (distal, BP2-BP3) (includes SH2B1)	chr16:28,822,635–29,046,499	94.78% overlap
1101491	ASD	F	Del	chr22:18,877,787–21,461,607	22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1)	chr22:15,912,231–21,465,672	99.84% overlap
4406202	ASD	F	Del	chrX:6,488,784–8,135,053	Xp22.31 recurrent region (includes STS)	chrX:6,455,812–8,133,195	98.02% overlap
Parents
4411283*	MTR	M	Del	chr16:21,956,457–22,414,463	Recurrent 16p12.1 microdeletion (neurodevelopmental susceptibility locus)	chr16:21,946,524–22,467,284	87.95
2215012	MTR	F	Del	chr22:19,036,154–20,244,259	22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1)	chr22:18,912,231–20,287,208	87.86
1116571	MTR	F	Del	chrX:6,456,940–8,135,053	Xp22.31 recurrent region (includes STS)	chrX:6,455,812–8,133,195	99.93

ASD/ID-associated CNVs were taken from ClinGen [47] and DECIPHER [48] datasets, filtering for ASD/ID-associated loci. For reference CNVs with a critical gene, AAB CNVs were annotated where there was any overlap with the critical gene, with the critical gene coordinates provided in the "Other information" column. For reference CNVs without a critical gene, the AAB CNV was called as overlapping with an ASD/ID-associated CNV based on ≥ 80% overlap with the reference coordinates, with percentage overlap provided in the "Other information" column. Genome coordinates are hg19. Biobank Sample IDs have been anonymized
*Refers to parent–child pairs between which ASD/ID-associated CNVs appeared to be inherited in this dataset
^Note that the CNV for ID 1101366 only overlaps the YWHAE critical gene

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ISSN: 2040-2392

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