Table 1. Overview of the detected aberrations in 30 patients with ID/MCA.
| Genomic position (GRCh37) | Detected by | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Patients | Aberration | Karyotyping | Array | Mate pair | Inheritance pattern | Array CGH | Clustering | Coverage analysis | LCRs | Trio analysis | Genes in region | Genes in breakpoint region |
| Nonrecurrent aberrations | ||||||||||||
| Patient 1 | del | 46,XY | chr16:21806318–22448172 | chr16:21795323–22563293 | Unknown | + | + | + | 11 genes | LOC653786 | ||
| Patient 2 | Tandem dup | 46,XX | chr15:57656004–57763906 | chr15:57644360–57778338 | Maternal | + | + | + | – | CGNL1 | CGNL1 | |
| Tandem dup | chr18:77326777–77529494 | chr18:77308690–77531555 | Paternal | + | + | + | – | CTDP1 | – | |||
| Patient 3 | Tandem dup | 46,XY | chr12:24771140–25398348 | chr12:24769808–25401031 | Maternal | + | + | + | – | 5 genes | KRAS | |
| Patient 4 | del | 46,XY | chr12:73241458–73357773 | chr12:73227890–73369478 | Unknown | + | + | + | – | - | – | |
| del | chr12:121297228–121618126 | chr12:121289330–121625939 | Maternal | + | + | + | – | 4 genes | SPPL3, P2RX7 | |||
| Patient 5 | dup | 46,XY | chrX:130608951–130950183 | chrX:130580626–130958687 | Maternal | + | + | + | OR13H1 | IGSF1, LOC286467 | ||
| Patient 6 | del | 46,XX | chr7:110520319–110722966 | chr7:110511762–110707768 | Paternal | + | + | + | – | IMMP2L | IMMP2L | |
| Patient 7 | Tandem dup | 46,XX | chr11:107779704–108157951 | chr11:107777875–108164503 | De novo | + | + | + | – | 4 genes | ATM | |
| Patient 8 | del | 46,XX | chr8:141294618–141403896 | chr8:141293153–141399016 | Unknown | + | + | – | TRAPPC9 | TRAPPC9 | ||
| Patient 9 | Interspersed dup | 46,XX | chr4:172013456–172341313 | chr4:172013259–172366770 | De novo | + | + | + | – | – | – | |
| chr4:174790209–175298661 | chr4:174806588–175303104 | – | FBXO8, CEP44 | – | ||||||||
| Patient 10 | Tandem dup | 46,XY | chr9:131395721–132073928 | chr9:131395733–132070993 | De novo | + | + | + | – | + | 20 genes | SPTAN1 |
| Patient 11 | Tandem dup | 46,XY | chr19:54187022–54602946 | chr19:54184569–54603393 | De novo | + | + | + | – | + | C19MC cluster, 9 coding genes | NDUFA3 |
| Patient 12 | del | 46,XY | chr1:92834493–93617701 | chr1:92826568–93627209 | De novo | + | + | + | – | + | 7 genes | RPAP2, TMED5 |
| Tandem dup | chr1:93794057–93857706 | chr1:93789807–93856418 | De novo | + | + | + | – | DR1 | LOC100131564 | |||
| Patient 13 | Tandem dup | 46,XY | chr4:103533732–10400665 | chr4:103522991–104009288 | De novo | + | + | + | – | + | 5 genes | NFKB1, BDH2 |
| Tandem dup | chr8:53505877–55140480 | chr8:53503328–55161235 | De novo | + | + | + | – | 8 genes | – | |||
| Tandem dup | chr8:80536950–81934189 | chr8:80538184–81944843 | De novo | + | + | + | – | 6 genes | STMN2, PAG1 | |||
| dup | chr14:71023626–72238032 | chr14:71027050–72258758 | De novo | + | + | − | 7 genes | – | ||||
| Microdeletion/duplication syndromes | ||||||||||||
| Patient 14 | del | 46,XX | chr7:72685734–74172854 | chr7:72714024–74155970 | De novo | + | + | + | WBS region | |||
| Patient 15 | dup | 47,XY,+del(15)(q13.1) | chr15:20190547–28305525 | chr15:20186026–28290176 | Unknown | + | + | + | PWS/AS region | |||
| Patient 16 | del | 46,XY | chr17:16663504–18853898 | chr17:16695511–19139094 | De novo | + | + | + | SMS region | |||
| Patient 17 | del | 46,XY | chr17:34823124–36248858 | chr17:34723963–36357595 | De novo | + | + | + | region associated with renal cysts and diabetes | |||
| Patient 18 | del | 46,XX | chr17:44683–2444275 | chr17:10802–2473314 | De novo | + | + | – | Miller–Dieker region | |||
| Patient 19 | del | 46,XY | chr22:18894834–21505357 | chr22:18918731–21469569 | Maternal | + | + | + | VCFS region | |||
| Patient 20 | del | 46,XY | chr22:18953012–20311704 | chr22:18891194–23003094 | De novo | + | + | + | VCFS region | |||
| Patient 21 | dup | 46,XY | chr22:18706001–21505358 | chr22:18918992–21448778 | De novo | + | + | + | VCFS region | |||
| Apparently balanced translocations/inversions | ||||||||||||
| Patient 22 | Translocation | 46,X,t(X;1)(q26;q25) | – | chr1:175823563–175825129 | De novo | + | – | – | ||||
| chrX:130560260–130562008 | IGSF1 | |||||||||||
| Patient 23 | Translocation | 46,XX,t(3;5)(p24;q14) | – | chr3:29299498–29300608 | De novo | + | – | – | ||||
| chr5:88597544–88598474 | MEF2C | |||||||||||
| Patient 24 | Translocation | 46,Y,t(X;3)(p11.2;q13.1) | – | chrX: 47104033–47104034 | De novo | + | – | USP11 | ||||
| chr3:107477586–107477586 | BBX | |||||||||||
| Patient 25 | Translocation | 46,X,t(X;7)(q12;q22) | – | - | De novo | – | – | |||||
| Patient 26 | Inversion | 46,XY,inv(4)(q21;q31.3) | – | chr4:82872172–155552374 | De novo | + | – | DQ266889 | ||||
| Patient 27 | Complex translocation | 46,XY,t(2;14)(p22;q24.3) | – | chr2:38344860–38345669 | De novo | + | – | |||||
| chr14:79133247–79136029 | De novo | NRXN3 | ||||||||||
| chr14:71207318–82091783 | De novo | MAP3K9 | ||||||||||
| Complex rearrangements | ||||||||||||
| Patient 28 | dup | 46,XX | chrX:129569453–130234890 | chrX:129553399–130251499 | De novo | + | + | + | – | BC043223, FAM45A, ENOX2, ARHGAP36 | – | |
| dup | chrX:153297312–153676716 | chrX:153298107–153679735 | + | + | – | 13 genes | MECP2, FAM50A | |||||
| dup | chrX:153828822–154351545 | chrX:153875203–154368527 | + | + | – | 10 genes | - | |||||
| Patient 29 | Chromothripsis/complex trisomy 21 | 46,XX,der(21)t(21;21) | See Figure 4 | See Figure 4 + Table 2 | De novo | + | + | + | – | |||
| Patient 30 | Chromothripsis/complex trisomy 18 | 46,XX,der(18) | See Figure 4 | See Figure 4 + Table 2 | De novo | + | + | + | – | |||
For each patient, the inheritance pattern, the karyotyping result and the genomic position obtained with array CGH, cluster analysis and/or coverage analysis of the mate pair data are given. Columns 7–9 display whether an aberration was detected by array CGH, cluster analysis or coverage analysis. When low copy repeats (LCRs) are present at the breakpoint regions, this is shown in column 10. For five patients, trio analysis was performed, which is highlighted in the last column.