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Table 2 Summary of X chromosome 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 CNV Type Start* Size* Platforms Identified CNV Genes Involved Validation Comment on Gene Function
6428 DEL 148 264 112 156 992 Affy IDS NT Expression pattern not consistent with causing MR
2894 DEL 101 266 713 250 045 NimbleGen 5 RefSeq genes NT Expression pattern not consistent with causing MR[45]
3519 DEL 9 454 329 197 920 Affy TBL1X NT Expression pattern not consistent with causing MR[46]
8960 DUP 67 416 262 7 057 217 All 3 platforms 57 RefSeq genes FISH Pos FISH Pos
9313 DEL 9 484 049 165 559 Affy TBL1X NT Expression pattern not consistent with causing MR
3921 DUP 74 811 330 208 698 NimbleGen TTC3L NT Expression pattern not consistent with causing MR[47]
1511 DEL 6 856 649 201 556 Affy HDHD1A NT Expression pattern not consistent with causing MR[48]
2714 DEL 76 534 899 67 182 NimbleGen FGF16 NT Expression pattern not consistent with causing MR[49]
5993 DEL 6 932 549 130 699 NimbleGen HDHD1A NT Expression pattern not consistent with causing MR[48]
4821 DEL 6 625 133 419 230 NimbleGen HDHD1A NT Expression pattern not consistent with causing MR[48]
3921 DUP 74 811330 208 698 NimbleGen MAGEE2 NT Expression pattern not consistent with causing MR[47]
8960 DEL 29 967 317 203 809 Affy MEGB2E NT Expression pattern not consistent with causing MR[50]
1815 DUP 67 767 923 2 019 581 NimbleGen 15 RefSeq genes including DLG3 NT Amplification not reported to cause MR[31]
7093 DUP 73 429 587 263 642 NimbleGen 3 RefSeq genes including SLC16A2 NT Females not affected[28]
3094 DEL 99 293 227 205 443 Affy PCDH19 NT Males not affected[30]
7093 DEL 6 687 308 906 505 Agilent & NimbleGen STS NT Females not affected[29]
  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).
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BMC Medical Genomics

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