Table 1. .

CNV Detection with CNAG in Trios^[Note]

Line	Child vs. Father	Child vs. Mother	Father vs. Mother	CNV in Child	Type	Comment(s)
1	Loss	Loss	Loss	Deletion	De novo	The mother may have a duplication that was not inherited by the child.
2	Loss	Loss	No change	Deletion	De novo	Alternatively, both parents might have a duplication that was not inherited by the child.
3	Loss	Loss	Gain	Deletion	De novo	The father may have a duplication that was not inherited by the child.
4	Loss	No change	Gain	Deletion	Inherited from mother	Alternatively, the father may have a duplication that was not inherited by the child.
5	Loss	Gain	Gain	None	…	The father may have a duplication and the mother may have a deletion, but the child has a normal disomic copy number. Both of the child’s copies may be on one chromosome.
6	No change	Loss	Loss	Deletion	Inherited from father	Alternatively, the mother may have a duplication that was not inherited by the child.
7	No change	No change	No change	None	…	Alternatively, the child and both parents may all have the same deletion or duplication.
8	No change	Gain	Gain	Duplication	Inherited from father	Alternatively, the mother may have a deletion that was not inherited by the child.
9	Gain	Loss	Loss	None	…	The father may have a deletion and the mother may have a duplication, but the child has a normal disomic copy number. Both of the child’s copies may be on one chromosome.
10	Gain	No change	Loss	Duplication	Inherited from mother	Alternatively, the father may have a deletion that was not inherited by child.
11	Gain	Gain	Loss	Duplication	De novo	The father may have a deletion that was not inherited by the child.
12	Gain	Gain	No change	Duplication	De novo	Alternatively, both parents may have a deletion that was not inherited by the child.
13	Gain	Gain	Gain	Duplication	De novo	The mother may have a deletion that was not inherited by the child.

Note.— “Loss,” “gain,” or “no change” of copy number refers to the first individual listed in comparison with the second individual listed. Our goal in this trio analysis was to identify de novo CNVs in the affected child. If the child showed the same copy-number change (gain or loss) in comparison with both parents, the child’s CNV was considered to have arisen de novo, regardless of whether the copy number in both parents was the same.