Table 1.
Characteristics of the identified copy number alterations
| Patient number | Syndrome | Gene/genomic region (inheritance pattern) | HumanGenome19 coordinates or cytogenetic location | Approximate size of the CNV | Detection method |
|---|---|---|---|---|---|
| 1# | Diamond–Blackfan anemia | RPL35a (AD) | del(chr3:186,550,246–197,837,050)x1 | 11.3 Mb | Array 1 and FISH |
| 2# | Diamond–Blackfan anemia | RPS17 (AD) | del(chr15:83,196,738–84,812,671)x1 | 1.6 Mb | Array 2 |
| 3# | Diamond–Blackfan anemia | RPL5 (AD) | del(chr1:92,932,837–94,018,138)x1 | 1.1 Mb | Array 3 |
| 4# | Diamond–Blackfan anemia | RPL11 (AD) | del(chr1:23,449,116–24,147,166)x1 | 698 kb | Array 4 |
| 5 | TAR syndrome | Chr1q21.1 | del(chr1:145,390,101–145,792,052)x1 | 402 kb | Array 5 |
| RBM8A (AR) | c.−21G>A (chr1:145,507,646G>A) | SNV | |||
| 6 | TAR syndrome | Chr1q21.1 | del(chr1:145,372,550–145,792,064)x1 | 420 kb | Array 5 |
| RBM8A (AR) | c.−21G>A (chr1:145,507,646G>A) | SNV | |||
| 7 | TAR syndrome | Chr1q21.1 | del(chr1:144,100,000–144,290,000)x1* | 190 kb | Quantitative PCR |
| RBM8A (AR) | NA | SNV | |||
| 8 | Trisomy 8 syndrome | Chr8 (aneuploidy) | dup(chr8) | 145.1 Mb | Cytogenetics and FISH |
| 9 | Trisomy 8 syndrome | Chr8 (aneuploidy) | dup(chr8) | 145.1 Mb | Cytogenetics and FISH |
| 10 | Trisomy 8 syndrome | Chr8 (aneuploidy) | dup(chr8) | 145.1 Mb | Cytogenetics and FISH |
| 11# | Fanconi anemia | FANCA (AR) | FANCA deletion exon 31* | 5 kb | MLPA |
| FANCA deletion exons 4–29* | 49 kb | MLPA | |||
| 12# | Fanconi anemia | FANCA (AR) | del(chr16:89,799,574–89,847,471)x1 | 47.9 kb | Array 2 |
| del(chr16:89,824,684–89,869,755)x1 | 45 kb | Array 2 | |||
| 13# | Dyskeratosis congenita | PARN (AR) | del(chr16:14,658,272–14,679,880)x1 | 21.6 kb | Array 5 |
| c.1045C>T (chr16:14,676,047G>A) | SNV | ||||
| 14# | Familial Thrombocytopenia/AML | RUNX1 (AD) | del(chr21:34,965,815–36,781,907)x1 | 1.8 Mb‡ | Array 6 and FISH |
| 15 | Pearson syndrome | mitDNA (mitochondrial) | del(mitDNA)* | 6 kb | Southern blot |
| 16 | SRC1 syndrome | Chr1p13.1 | +r(chr1:116,673,235–152,748,194) | 36.1 Mb | Array 7 and cytogenetics |
| 17 | Wolf–Hirschhorn syndrome | Chr4p | der(4)t(4;8)(p16.3;p23.1)* | 2.5 Mb(del), 9 Mb(dup) | Cytogenetics and FISH |
| 18 | Jacobson syndrome | 11q23 | del(11)(q23.3)x1* | 17 Mb | Cytogenetics |
| 19 | Potocki–Lupski syndrome | 17p11.2 | dup(chr17:16,778,108–18,252,450)x1 | 1.5 Mb | Array 8 and FISH |
#, patients included in the subset analysis; *, for methods without identification of the exact breakpoint, the genomic locations were estimated as well as the total size of the respective CNV; ‡, complex intrachromosomal rearrangement of chromosome 21 including a deletion involving the RUNX1 gene
AD autosomal dominant, AML acute myeloid leukemia, AR autosomal recessive, Array 1 Agilent 105 K Human Genome Oligonucleotide array, Array 2 Agilent 180 K Human Genome Oligonucleotide array, Array 3 GeneDx 180 K microarray v4, Array 4 Agilent Oligo Array – EmArray cyto 6000 custom design, Array 5 Affymetrix SNP Array 6.0, Array 6 CytoSure Syndrome Plus V2, Array 7 Roche NimbleGen 135 K oligonucleotide array, Array 8 Signature Genomic SignatureChipWG Whole genome BAC array, FISH fluorescence in-situ hybridization, MLPA Multiplex Ligation-dependent Probe Amplification, NA not available, SNV single nucleotide variant, SRC1 supernumerary ring chromosome 1, TAR thrombocytopenia absent radius