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["A) CNV detection within trios using a reference set of 2"]
[]
["Child vs. Father","Child vs. Mother","Father vs. Mother","CNV in child","CNV in father","CNV in mother"]
["loss","loss","loss","deletion","none","duplication"]
["loss","loss","no change","deletion*","duplication*","duplication*"]
["loss","loss","gain","deletion","duplication","none"]
["loss","no change","gain","deletion*","duplication*","deletion*"]
["loss","gain","gain","none","duplication","deletion"]
["no change","loss","loss","deletion*","deletion*","duplication*"]
["no change","no change","no change","none","none","none"]
["no change","gain","gain","duplication*","duplication*","deletion*"]
["gain","loss","loss","none","deletion","duplication"]
["gain","no change","loss","duplication*","deletion*","duplication*"]
["gain","gain","loss","duplication","deletion","none"]
["gain","gain","no change","duplication*","deletion*","deletion*"]
["gain","gain","gain","duplication","none","deletion"]
[]
["*It is possible that only one or two of the CNVs called in the trio are real. To detect as many CNVs as possible, we accepted all three potential candidate CNVs in these cases."]
[]
[]
[]
["B) CNV detection using a reference set 50, 106 or 214"]
[]
["Child vs. reference set","Father vs. reference set","Mother vs. reference set","CNV in child","CNV in father","CNV in mother"]
["loss","loss","loss","deletion","deletion","deletion"]
["loss","loss","no change","deletion","deletion","none"]
["loss","loss","gain","deletion","deletion","duplication"]
["loss","no change","loss","deletion","none","deletion"]
["loss","no change","no change","deletion","none","none"]
["loss","no change","gain","deletion","none","duplication"]
["loss","gain","loss","deletion","duplication","deletion"]
["loss","gain","no change","deletion","duplication","none"]
["loss","gain","gain","deletion","duplication","duplication"]
["no change","loss","loss","none","deletion","deletion"]
["no change","loss","no change","none","deletion","none"]
["no change","loss","gain","none","deletion","duplication"]
["no change","no change","loss","none","none","deletion"]
["no change","no change","no change","none","none","none"]
["no change","no change","gain","none","none","duplication"]
["no change","gain","loss","none","duplication","deletion"]
["no change","gain","no change","none","duplication","none"]
["no change","gain","gain","none","duplication","duplication"]
["gain","loss","loss","duplication","deletion","deletion"]
["gain","loss","no change","duplication","deletion","none"]
["gain","loss","gain","duplication","deletion","duplication"]
["gain","no change","loss","duplication","none","deletion"]
["gain","no change","no change","duplication","none","none"]
["gain","no change","gain","duplication","none","duplication"]
["gain","gain","loss","duplication","duplication","deletion"]
["gain","gain","no change","duplication","duplication","none"]
["gain","gain","gain","duplication","duplication","duplication"]

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