Table 2.
Summary of V6 oligo array hybridization
| No. clones |
Min. size (Mb) |
Ave. log2 ratio |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Case no. | Abnormality | Region | Change | BAC | Oligo | BAC | Oligo | BAC | Oligo | Concordant |
| BAC V5 vs. Oligo V6 | ||||||||||
| B5-1 | dup(22)(q11.2) | 22q11.2 | Gain | 1 | 1 | 0.17 | 0.17 | 0.377 | 0.408 | Yes |
| B5-2 | Familial CNV | 19q13.4 | Gain | 2 | 2 | 0.91 | 0.91 | 0.261 | 0.439 | Yes |
| B5-3 | Familial CNV | 11q24.3 | Gain | 1 | 1 | 0.19 | 0.19 | 0.420 | 0.519 | Yes |
| ins(13;14)a | 13:q21.31 | Loss | 0 | 1b | NA | 0.13 | NA | −0.950 | Addb | |
| 14:q23.1-q23.3 | Gain | 1 | 2b | ~0.1 | 3.07 | 0.324 | 0.570 | Yes | ||
| B5-4 | Trisomy 21 | 21 | Gain | 13 of 16c | 19b | WC | WC | 0.408 | 0.537 | Yes |
| B5-6 | iso(18p) | 18p | Gain | 18 | 18 | 14.14 | 14.14 | 0.639 | 0.966 | Yes |
| B5-7 | der(4)t(4;8) | 4p16 | Loss | 10 | 10 | 3.39 | 3.39 | −0.289 | −0.755 | Yes |
| 8p23 | Gain | 4c | 6b | 6.45 | 6.45 | 0.219 | 0.578 | Yes | ||
| B5-8 | PWS/AS del | 15q11.2-q12 | Loss | 8b | 7 | 3.95 | 3.95 | −0.498 | −0.893 | Yes |
| B5-9 | del(2)(q14q21)d | 2q21.1-q21.3 | Loss | 1 | 3b | 0.17 | 6.97 | −0.571 | −1.029 | Yes |
| B5-10 | WBS del | 7q11.23 | Loss | 9 | 6b | 1.08 | 0.99 | −0.318 | −0.849 | Yes |
| Familial CNV | 7q36.1 | Gain | 1 | 1 | 0.14 | 0.14 | 0.318 | 0.527 | Yes | |
| B5-11 | mar(8) | 8p11.2-q11.2 | Gain | 4 | 4 | 7.46 | 7.46 | 0.424 | 0.734 | Yes |
| B5-12 | STS dup | Xp22.31 | Gain | 3 | 3 | 0.85 | 0.85 | 0.415 | 0.601 | Yes |
| B5-13 | der(6)t(6;10) | 6q27 | Loss | 1 | 4b | 0.13 | 1.58 | −0.455 | −0.861 | Yes |
| 10q24.31-q26.3 | Gain | 16 | 23b | 31.26 | 32.57 | 0.392 | 0.516 | Yes | ||
| B5-14 | WHS del | 4p16.3-p16.2 | Loss | 12 | 12 | 4.84 | 4.84 | −0.604 | −0.774 | Yes |
| B5-15 | der(13)t(1;13) | 1p36.33-p36.32 | Gain | 7 | 4 | 3.22 | 3.22 | 0.340 | 0.432 | Yes |
| 13q34 | Loss | 10 | 10 | 9.20 | 9.20 | −0.562 | −0.910 | Yes | ||
| B5-16 | del(5)(p15.32p14.2)d | 5p15.31-p14.3 | Loss | 2 | 4b | 1.18 | 10.89 | −0.525 | −0.966 | Yes |
| B5-17 | mos +13 | 13 | Gain | 20 | 47b,c | WC | WC | 0.074 | 0.114 | Yes |
| BAC V6 vs. Oligo V6 | ||||||||||
| B6-1 | mos 45,X/46,XX | X | Loss | 119 | 111b | WC | WC | −0.056 | −0.092 | Yes |
| B6-2 | Familial CNV | 7p22.2 | Gain | 1 | 1 | 0.18 | 0.18 | 0.388 | 0.540 | Yes |
| B6-6 | del(12)(q13.2q13.3)d | 12q13.3 | Loss | 1 | 1 | 0.13 | 0.13 | −0.477 | −0.952 | Yes |
| B6-9 | Possible CNV | 18q23 | Gain | 1 | 1 | 0.20 | 0.20 | 0.279 | 0.388 | Yes |
| B6-18 | dup(22)(q11.2) | 22q11.2 | Gain | 1 | 1 | 0.17 | 0.17 | 0.452 | 0.429 | Yes |
| B6-21 | dup(8)(p23.3p23.2) | 8p23.3 | Gain | 3 | 3 | 3.47 | 3.47 | 0.355 | 0.607 | Yes |
| Parallel clinical validation | ||||||||||
| C5 | dup(X)(p11.23p11.22) | Xp11.23-p11.22 | Gain | 4 | 4 | 5.22 | 5.22 | 0.133e | 0.533 | Yes? |
| C15 | Familial CNV | 5q23.1 | Gain | 1 | 1 | 0.15 | 0.15 | 0.223 | 0.222 | Yes |
| C17 | Familial CNV | 16p13.3 | Gain | 1 | 1 | 0.16 | 0.16 | 0.273 | 0.271 | Yes |
| C21 | PMD del | Xq22.2 | Loss | 3 | 3 | 0.76 | 0.76 | −0.226 | −0.801 | Yes |
| C28 | STS dup | Xp22.31 | Gain | 3 | 3 | 0.85 | 0.85 | 0.504 | 0.747 | Yes |
| C34 | WBS del | 7q11.23 | Loss | 8 | 6b | 1.08 | 0.99 | −0.364 | −0.594 | Yes |
| C35 | ins(6;X) | 6q25 | Loss | 3 | 3 | 3.69 | 3.69 | −0.428 | −0.923 | Yes |
| Xq28 | Gain | 4 | 4 | 1.13 | 1.13 | 0.404 | 0.808 | Yes | ||
| C37 | Possible CNV | 18:q11.1 | Gain | (1) | 1 | NA | 0.051 | −0.011f | 0.203 | Addg |
| C40 | 47,XXX | X | Gain | 104 of 119c | 110b | WC | WC | 0.194 | 0.508 | Yes |
| C38 | del(9)(q33.3q34.1) | 9q33.3-q34.1 | Gain | 2 | 2 | 1.64 | 1.64 | 0.263 | 0.267 | Yes |
| C42 | Familial CNV | 15q13.3 | Gain | 1 | 1 | 0.22 | 0.22 | 0.320 | 0.485 | Yes |
| C45 | dup(1)(q42.3) | 1q42.3 | Gain | 2 | 2 | 0.83 | 0.83 | 0.322 | 0.512 | Yes |
| C47 | Familial CNV | 7q22.1 | Loss | 1 | 1 | NA | 0.047 | −0.147e | −0.468 | Yesg |
| C48 | PWS/AS BP1-BP2 | 15q11.2 | Loss | 2 | 2 | 0.30 | 0.30 | −0.309 | −0.681 | Yes |
| C50 | del(6)(q25.2q25.3) | 6q25.2-q25.3 | Loss | 4 | 4 | 5.20 | 5.20 | −0.385 | −0.813 | Yes |
| C57 | Familial CNV | 6q11.1c | Loss | (1) | 1 | NA | 0.015 | −0.071f | −0.528 | Addg |
| C60 | mos inv dup(15) | 15q11.2-q13.3 | Gain | 4 of 10c | 9b | 8.88 | 8.88 | 0.706 | 1.336 | Yes |
| C63 | Familial CNV | 13q31.3 | Loss | 1 | 1 | 0.17 | 0.17 | −0.320 | −0.850 | Yes |
a
FISH analysis showed abnormality.
b
Change in no. of clones on array.
c
Not all BACs show gain.
d
Chromosome analysis showed larger abnormality.
e
BAC not at threshold.
f
Not detected by BAC array.
g
Partial gain or loss on oligo array.
Add, additional findings; WC, whole chromosome.