Table 2.
CNA and cnLOH events identified by using three different approaches.
| CNAs and cnLOH events | Conventional Cytogenetics | SNP-Arrays | DECoN | Ginkgo | NGS-Combined | Uniquely by SNP Arrays | Uniquely by NGS |
|---|---|---|---|---|---|---|---|
| Normal karyotype | 37 | 28 | 30 | 31 | 29 | ||
| Clinically relevant CNAs | |||||||
| -Y | 1 | 1 | 1 | 1 | 1 | ||
| del(5q) | 8 | 11 | 11 | 9 | 11 | #151908, 63.8 Mb (only by DECoN); #144969, 5.6 Mb (only by DECoN) | |
| del(12p) | 1 | 5 | 3 | 3 | 3 | #163259, 8 Mb; #162250, 7.9 Mb * | |
| del(20q) | 1 | 3 | 1 | 1 | 1 | #140104, 16.7 Mb; #171224, 27.4 Mb | |
| monosomy 7 | 8 | 4 | 4 | 4 | 4 | ||
| del(7q) | 0 | 5 | 5 | 4 | 5 | #144206, 9.9 Mb(only by DECoN) | |
| trisomy 8 | 2 | 1 | 1 | 1 | 1 | ||
| trisomy 21 | 2 | 1 | 1 | 2 | 2 | #173419, 32.8 Mb (only by Ginkgo) | #144969, trisomy 21 |
| del(17p), i(17)(q10) | 3 | 4 | 3 | 2 | 3 | #144969, 21 Mb; #144304, 4.9 Mb (only by DECoN) | |
| 26 | 35 | 30 | 27 | 31 | |||
| Recurrent CNAs with unknown significance | |||||||
| del(1p) | 1 | 0 | 0 | 0 | 0 | ||
| dup(1p) | 0 | 1 | 1 | 0 | 1 | ||
| dup(2p) | 1 | 1 | 1 | 0 | 1 | ||
| monosomy 3 | 1 | 0 | 0 | 0 | 0 | ||
| del(3p) | 0 | 1 | 1 | 1 | 1 | ||
| del(5p) | 0 | 1 | 0 | 0 | 0 | #144304, 3.3 Mb | |
| dup(5p) | 0 | 1 | 0 | 0 | 0 | #160705, 5.6 Mb | |
| dup(5q) | 1 | 0 | 0 | 0 | 0 | ||
| del(6p) | 0 | 1 $ | 1 $ | 1 $ | 1 $ | ||
| dup(6p) | 0 | 1 $ | 1 $ | 1 $ | 1 $ | ||
| del(7p) | 0 | 2 | 1 | 1 | 1 | #160990, 7.8 Mb (mosaic loss) | |
| dup(7q) | 1 | 1 | 0 | 0 | 0 | #154667, 9.4 Mb | |
| dup(9p) | 0 | 0 | 0 | 1 | 1 | #161780, 5.4 Mb | |
| monosomy 10 | 1 | 0 | 0 | 0 | 0 | ||
| dup(10p) | 0 | 1 | 0 | 1 | 1 | #144969, 36.2 Mb (only by Ginkgo) | |
| del(10q) | 0 | 1 | 0 | 1 | 1 | #144969, 46 Mb (only by Ginkgo) | |
| dup(11q) | 0 | 1 | 1 | 1 | 1 | ||
| dup(12p) | 1 | 0 | 1 | 1 | 1 | #162250, 12.9 Mb * | |
| del(12q) | 0 | 2 $ | 1 $ | 1 $ | 1 $ | #151908, 9.8 Mb | |
| dup(13q) | 2 | 0 | 0 | 0 | 0 | ||
| dup(15p) | 1 | 1 | 0 | 0 | 0 | #151908, 7.6 Mb | |
| del(16p) | 2 | 3 | 3 | 3 | 3 | ||
| dup(16p) | 0 | 1 $ | 1 $ | 1 $ | 1 $ | ||
| dup(16q) | 1 | 0 | 0 | 0 | 0 | ||
| del(17q) | 1 | 1 | 0 | 0 | 0 | #160990, 0.6 Mb | |
| monosomy 18 | 2 | 0 | 0 | 0 | 0 | ||
| del(18q) | 0 | 2 $ | 1 $ | 2 $ | 2 $ | #144969, 10.3 Mb (only by Ginkgo) | |
| monosomy 19 | 1 | 0 | 0 | 0 | 0 | ||
| del(19p) | 0 | 2 | 0 | 0 | 0 | #144206, 6.5 Mb; #144969, 7.5 Mb | |
| dup(19p) | 0 | 2 | 1 | 0 | 1 | #151908, 10 Mb; #144969, 6 Mb (only by DECoN) | |
| dup(19q) | 0 | 1 $ | 1 $ | 0 | 1 $ | #151908, 26.7 Mb (only by DECoN) | |
| monosomy 20 | 1 | 0 | 0 | 0 | 0 | ||
| dup(20p) | 0 | 1 | 0 | 0 | 0 | #151908, 21.8 Mb | |
| del(21q) | 0 | 1 | 1 | 0 | 1 | #162103, 3.2 Mb (only by DECoN) | |
| dup(21q) | 0 | 2 $ | 0 | 0 | 0 | #151908, 8.5 Mb | #144969, trisomy 21 |
| +Y | 0 | 1 | 1 | 1 | 1 | ||
| 17 | 23 | 12 | 11 | 15 | |||
| Copy-neutral LOH | |||||||
| 1p cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 1q cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 2p cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 3q cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 4q cnLOH | NA | 2 | 2 | 2 | 2 | ||
| 7q cnLOH | NA | 4 | 4 | 4 | 4 | ||
| 13q cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 17p cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 20p cnLOH | NA | 1 | 1 | 1 | 1 | ||
| 20q cnLOH | NA | 1 | 1 | 1 | 1 | ||
| NA | 14 | 14 | 14 | 14 | |||
| TOTAL REPORTED LESIONS | 43 | 72 | 56 | 52 | 60 |
$ chromotripsis; * CNAs were differently interpreted. Abbreviations: CNAs, copy number alterations; SNP, single-nucleotide polymorphism; NGS, next-generation sequencing; cnLOH, copy-neutral loss of heterozygosity; Del, deletion; Dup, duplication.