Table 1.
Tested Samples Ordered by CNV Size, Sequencing Detection, and Fetal-Fraction Estimation
| Sample No. | Outcome | CNV Size (Mb)a | How Outcome Was Determined | Gestation (Weeks + Days) | CNV Position (kb) |
Sequencing Detection |
Implied Fetal Fraction |
||
|---|---|---|---|---|---|---|---|---|---|
| 12-Plex | Deeper | From CNV | From Chr Y | ||||||
| 1470 | 47,XY,+idic(9)(pter→q21.1::q21.1→pter) | ∼42 | karyotype | 12 + 2 | dup9: 1–72,100 | yes | not done | 7.5% (15.1%)b | 9.7% |
| 8048 | 47,XX,+del(9)(q11) | ∼42 | karyotype | 27 + 1 | dup9: 1-71,200 | yes | not done | 31.8% | – |
| 7851 | 47,XY,+der(22)t(9;22)(p13;q11.2)mat | chr9: ∼42 | karyotype | 11 + 6 | dup9: 1–72,600 | yes | not done | 7.2% | 6.8% |
| chr22: ∼3 | dup22: 17,300–21,000 | no | 8.2% | ||||||
| 5216 | 46,XX,del(13)(q22) | ∼40 | karyotype | 11 + 5 | del13: 83,600–115,000 | no | yes | 4.6% | – |
| 12317 | 46,XX,del(4)(p15.2) | ∼26 | karyotype | 24 + 2 | del4: 1–25,200 | yes | not done | 11.7% | – |
| 2092 | 46,XX,der(4)ins(14;4)(q13:q25q21.3)mat | chr4: ∼25 | karyotype | 11 + 5 | del4: 85,900–109,500 | yes | not done | 13.8% | – |
| 10853 | 46,XY,del(2)(p23p25.1) | ∼25 | karyotype | 24 + 1 | del2: 11,000–28,400 | yes | not done | 16.8% | 18% |
| 11660 | 46,XX,der(7)t(4;7)(p15.3;q34)pat | chr4: ∼17 | karyotype | 13 + 2 | dup4: 1–16,800 | yes | not done | 8.2% | – |
| chr7: ∼20 | chr7 not detected | no | |||||||
| R-01071 | 46,XY,del(4)(p15.32) | ∼18 | karyotype | 21 + 0 | del4: 1–15,600 | no | yes | 4.6% | 5.3% |
| 13122 | 46,XX,dup(21)(q21.2q22.2) | ∼16 | karyotype | 20 + 0 | dup21: 25,800–41,400 | yes | not done | 9.2% | – |
| 21 | 46,XX,del(5)(p15.1)dn | ∼15 | karyotype | 14 + 0 | del5: 1–15,500 | yes | not done | 19.2% | – |
| 12279 | 46,XY,del(18)(p11.1).arr 18p11.32p11.21(149,080–14,007,190)×1 | 13.8 | karyotype and microarray | 18 + 2 | del18: 1–18,700 | yes | not done | 7.8% | 7.7% |
| dup18: 18,700–78,000 | 9.0% | ||||||||
| R-01025 | 46,XX,del(9)(p23)dn.ish del(9)(34H2−,RP11-165F24−) | ∼13 | karyotype and FISH | 17 + 3 | del9: 1–16,800 | yes | not done | 11.9% | – |
| 12344 | arr 15q26.1q26.3(91,836,928–102,481,320)×1 | 11 | microarray | 28 + 4 | dup15: 34,400–90,100 | yes | not done | 14.8% | 15.8% |
| del15: 90,100–102,300 | |||||||||
| 1144 | 46,XX,der(18)t(12:18)(p13.1;q23)pat | chr12: ∼12 | karyotype | 17 + 1 | dup12: 1–9,400 | yes | not done | 8.8% | – |
| chr18: ∼5 | del18: 72,300–78,000 | 8.0% | |||||||
| 10855 | 46,XX,del(1)(q41q42) | ∼12 | karyotype | 13 + 2 | not detected | no | no | – | – |
| R-00940 | 46,XX,der(7)(pter→q36.1::?q36.1→q36.1::p21→pter)dn.ish der(7)?dup(7)(q36.1→q36.1)(RP11-4340++)del(7)(q36.3→qter)(RP11-6903−,c3K23−)dup(7)(p21→pter)(c109A6+) | ∼10 | karyotype and FISH | 12 + 5 | dup7: 1–16,500 | yes | not done | 7.7% | – |
| del7: 152,700–159,100 | 11.5% | ||||||||
| 9639 | 46,XY,del(6)(p25) | ∼7 | karyotype | 21 + 2 | del6: 1–7,400 | yes | not done | 15.8% | 20% |
| R-01716 | 46,XX,add(6)(p25).ish del(6)(p25.3p25.3)(CTB-62I11−,RP11-118B18−).arr[hg18] 6p25.3p25.1(77,025–5,820,602)×1 | 5.7 | karyotype, FISH, and microarray | 21 + 0 | del6: 1–6,400 | yes | not done | 17.3% | – |
| R-00875 | 46,XX,del(5)(p15.33)dn.ish del(5)(p15.33)(c84C11−,RP11-348B13−,RP11-129I19−,RP11-473F9+,RP11-259D10+) | ∼4.5 | karyotype and FISH | 17 + 3 | del5: 1–10,500 | yes | not done | 9.7% | – |
| 10256 | 46,XY,ish del(8)(q24.3q24.3)(RP11-65A5−).arr 8q24.3(140,186,782–144,969,635)×1 dn | 4.8 | karyotype and microarray | 13 + 2 | del8: 140,300–145,100 | no | yes | 9.8% | 9.2% |
| 11600 | 46,XX dup within 17p12 | ∼1.5 | karyotype and QF-PCR | 11 + 2 | dup17: 14,600–16,000 | no | yes | 10.2% | – |
| 8383 | 46,XY,dup(17)(p11.2p11.2).arr 17p11.2(16,637,872-20,294,010)×3 | 3.7 | karyotype and microarray | 22 + 0 | dup17: 16,900–20,800 | no | yes | 7.0% | 5.8% |
| 11590 | 46,XX dup within 17p12 inherited from the mother | ∼1.5 | karyotype and QF-PCR | 11 + 0 | dup17: 14,200–15,900 | yes | not done | – | – |
| 612 | 46,XX dup within 17p12 inherited from the mother | ∼1.5 | karyotype and QF-PCR | 12 + 6 | dup17: 14,200–15,900 | yes | not done | – | – |
| R-00983 | 46,XY.ish del(22)(q11.2q11.2)(RP11-1057H19−) | <3 | karyotype and FISH | 21 + 0 | not detected | no | no | – | 2.5% |
| R-01012 | 46,XX.ish del(22)(q11.2q11.2)(RP11-1057H19−) | <3 | karyotype and FISH | 20 + 4 | del22: 18,600–22,000 | no | yes | 8.2% | – |
| 12295 | 46,XX,del(22)(q11.2q11.2) | <3 | karyotype and BACs-on- Beads | 12 + 6 | del22: 19,100–23,300 | no | yes | 9.6% | – |
| 6876 | 46,XY.mlpa 22q11.2(P290)×3 inherited from the mother | <3 | karyotype and MLPA | 14 + 1 | dup22: 19,100–22,000 | yes | not done | – | 18% |
| 13067 | 46,XY,del(22)(q11.2q11.2) | <3 | karyotype | 28 + 1 | del22: 19,200–22,000 | no | yes | 23.8% | 23.5% |
| 2493 | 46,XY.ish del(22)(q11.2q11.2)(TUPLE1−)dn | <3 | karyotype and FISH | 22 + 2 | del22: 19,200–22,000 | no | yes | 13.4% | 17.3% |
Abbreviations are as follows: BAC, bacterial artificial chromosome; Chr, chromosome; CNV, copy-number variant; FISH, fluorescence in situ hybridization; MLPA, multiplex ligation-dependent probe amplification; and QF-PCR, quantitative fluorescence PCR.
a
The ∼ symbols mean that we can only provide an upper limit for the size estimate because of the limits of karyotyping.
b
This sample has an extra isodicentric chromosome 9; therefore, there are four total fetal copies of the region 9pter→9q21.1, and the fetal-fraction measurement is based on this. In parentheses is given the fetal-fraction measurement if only three copies of this region are present in the fetus.