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Table 1 Summary of autosomal de novo CNVs identified on the three main AGH platforms selected for genotype-phenotype analysis.

From: Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation

Trio ID Chr CNV Type Start* Size* Platforms Identified CNV # of RefSeq Genes Validation Comment on Gene Function
1815 3 DEL 196 904 149 54 518 Agilent 1 NT Mucin 20 - Expression pattern not consistent with causing MR[40]
4821 5 DEL 68 950 015 1 329 642 NimbleGen 7 NT Mutations in SMN1 associated with spinal muscle atrophy[41]
8960 5 DUP 180 309 941 55 922 NimbleGen 2 MLPA Pos Expression pattern not consistent with causing MR[42]
1815 6 DEL 111 807 663 9 889 630 All 3 platforms 57 FISH Pos Likely pathogenic based on size
7531 9 DEL 139 496 489 333 935 All 3 platforms 7 FISH Pos CNVs in region previously reported as pathogenic[32]
1815 12 DEL 11 371 263 83 667 NimbleGen 1 MLPA Pos Expression pattern not consistent with causing MR[43]
1056 13 DEL 107 190 506 2 206 948 All 3 platforms 5 FISH Pos Encompassed within de novo CNV in DECIPHER patient with MR
4821 16 DEL 3 862 993 78 891 All 3 platforms 1 MLPA Pos CNVs in region previously reported as pathogenic[35]
3921 17 DEL 41 062 469 657 364 All 3 platforms 8 FISH Pos CNVs in region previously reported as pathogenic[33]
9609 21 DEL 33 902 218 152 885 All 3 platforms 2 MLPA Pos Important in spinal development[37]
9609 22 DEL 19 062 809 728 798 All 3 platforms 19 FISH Pos CNVs in region previously reported as pathogenic[34, 44]
8327 22 DUP 19 412 033 378 797 All 3 platforms 13 MLPA Pos Mutation has been reported in family with normal phenotype[25]
  1. DEL = Deletion; DUP = Amplification, NT - Not tested; Pos = Positive; Neg = Negative; N/T = Not tested
  2. *Start/end coordinates determined from largest region of overlap between any two platforms; size is the difference between these two coordinates (Build 36).