Skip to main content
. 2014 Apr 3;9(4):e92820. doi: 10.1371/journal.pone.0092820

Table 1. Genotyping concordance between FFPE and Frozen tissues.

Case Frozen genotype FFPE genotype Karyotype
Chr Locus Copy Def Size Locus Copy Def Size
Case 1 2 2p16.1 1 Loss 0.7 MB 2p16.1 1 Loss 0.5 MB −2
2q33.2-34 2.3 Gain 7.2 MB 2q33.2-34 2.3 Gain 7.2 MB
2q35-37.3 3 Gain 24 MB 2q35 2.4 Gain 24 MB
5 5q13.2-14.3 1.3 Loss 18.4 MB 5q13.2-14.3 1.4 Loss 17 MB −5
5q21.1-22.1 1.4 Loss 12 MB 5q21.1-22.1 1.5 Loss 10.5 MB
5q33.3-35.1 1.3 Loss 12.4 MB 5q33.3-35.1 1.45 Loss 11.8 MB
7 7p14.3-14.1 1.3 Loss 6.5 MB 7p14.3-14.1 1.5 Loss 6.7 MB der(7)t(7;?)(p11.2;?)
7q11.22-22.1 4 Gain 27.8 MB 7q11.22-22.1 4 Gain 24.4 MB add(7)(q22) [8]
7q22.1-36.3 3 Gain 38.3 MB 7q22.1-36.3 3 Gain 33.5 MB der(7;16)(p10;q10)
8 8p23.3-11.21 1.3 Loss 42.6 MB 8p23.3-11.22 1.4 Loss 39.6 MB −8 [17]
10q23.1-25.1 1.3 Loss 21.7 MB 10q23.1-25.1 1.5 Loss 21.3 MB
11 11p15.3-15.1 1.5 Loss 10.1 MB 11p15.4-14.3 1.5 Loss 14.2 MB
11p14.2-11.2 2.5 Gain 22 MB 11p14.2-11.12 2.4 Gain 23.6 MB
13 13q33.3-34 1.3 Loss 6.6 MB 13q33.3-34 1.3 Loss 6.7 MB add(13)(q34) [15]
16 16p11.2-11.1 4 Gain 0.8 MB 16p11.2-11.1 3 Gain 1.2 MB
16p11.1-q21 1.3 Loss 30.4 MB 16p11.1-q22.1 1.5 Loss 33 MB −16
16q23.1 4 Gain 2.7 MB 16q23.1 4 Gain 2.6 MB
16q23.1-23.2 1.2 Loss 3.7 MB 16q23.1-23.2 1.2 Loss 3.7 MB
16q23.2-23.3 4 Gain 1.2 MB 16q23.2-23.3 4 Gain 1.2 MB
16q23.3-24.1 1.1 Loss 2.5 MB 16q23.3-24.1 1.1 Loss 2.5 MB
16q24.1 4 Gain 2.0 MB 16q24.1 4 Gain 2.0 MB
16q24.1-24.3 1.2 Loss 2.8 MB 16q24.1-24.3 1.2 Loss 2.8 MB
17 17p13.3-13.1 2.5 Gain 8.5 MB 17p13.3-13.1 2.5 Gain 8.7 MB −17
17p12-q11.2 3 Gain 14.5 MB 17p12-q11.2 2.7 Gain 16.7 MB
17q21.33-25.33 2.7 Gain 31.8 MB 17q21.33-25.32 2.7 Gain 32.2 MB
X Xp22.33-q28 2 NP 154.3 MB Xp22.33-q28 3 Gain 154.3 MB +X [6]
Case 2 1 1p36.33-36.21 1.4 Loss 16.7 MB 1p36.33-36.13 1.5 Loss 18.2 MB
1q21.2-q44 2.7 Gain 102 MB 1q21.2-q44 2.6 Gain 102 MB der(1)(qter>1q21::p36.3>qter)
2 2p25.3-11.2 2.8 Gain 89.1 MB 2p25.3-11.2 2.6 Gain 88.9 MB
6 6q21-27 1.2 Loss 58.9 MB 6q21-27 1.4 Loss 58.7 MB
17 17p13.3-11.2 1.3 Loss 16.9 MB 17p13.3-11.2 1.5 Loss 19.2 MB del(17)(p11.2)
17p11.2-q25.3 2.8 Gain 59.7 MB 17p11.2-q25.3 2.7 Gain 60.3 MB i(17)(q10)
18 18p11.32-q21.33 2.9 Gain 60.5 MB 18p11.32-q21.33 2.8 Gain 60.1 MB +der(18)(t(14;18)(q32;q21) [4]
22 22q11.22 1 Loss 0.9 MB 22q11.22 1 Loss 1.0 MB
X Xp22.33-q28 3 Gain 156 MB Xp22.33-q28 3 Gain 156 MB +X
Case 3 1 1q24.3-42.11 2.9 Gain 55.1 MB 1q24.3-42.11 2.7 Gain 52 MB +1, der (1)
5 5p15.33-q35.3 2.6 Gain 180.6 MB 5p15.33-q35.3 2.6 Gain 180.6 MB 5
8 8p23.3-21.3 1.4 Loss 22.8 MB 8p23.3-21.3 1.4 Loss 22.3 MB del(8)(p21p23)
9 9p24.1-23 2.5 Gain 4.7 MB 9p24.2-23 2.4 Gain 7.1 MB add(9)(p22)
10 10p15.3 1.4 Loss 0.8 MB 10p15.3 1.5 Loss 0.8 MB dic(1;10)(10qter>10p15::1p13>1q25::1q21>1q32::1q25>1qter)
10p15.1-11.21 2.5 Gain 31.6 MB 10p15.1-11.21 2.5 Gain 31 MB
14 14q32.33 1 Loss 0.7 MB q32.33 1 Loss 1.0 MB add(14)(q32)
18 18p11.32-q11.2 3 Gain 22 MB 18p11.32-q11.2 3 Gain 22 MB 18
18q11.2-23 4 Gain 55 MB 18q11.2-23 4 Gain 55 MB
19 19q13.2-13.43 2.7 Gain 18.1 MB 19q13.2-13.43 2.6 Gain 19.4 MB
X Xp22.33-q28 3 Gain 156 MB Xp22.33-q28 3 Gain 156 MB +X
Case 4 1 1p31.1 1.2 Loss 13.7 MB 1p31.1 1.4 Loss 13.2 MB 78–79,inc[cp5]*
1q23.3-32.1 2.3 Gain 31.4 MB 1q23.3-32.1 2.3 Gain 29.5 MB
1q42.2-44 1.2 Loss 17.2 MB 1q42.2-43 1.5 Loss 10 MB
2 2p25.3-24.3 2.7 Gain 13.3 MB 2p25.3-24.3 2.3 Gain 14.3 MB
2p24.3-16.3 1.5 Loss 34 MB 2p24.3-16.3 1.6 Loss 34.1 MB
3 3p26.3-q13.13 1.6 Loss 108.1 MB 3p25.1-12.2 1.7 Loss 66.2 MB
4 4p16.3-q24 1.6 Loss 106.6 MB 4p16.3-q24 1.6 Loss 104.6 MB
4q25-34.1 2.7 Gain 64.7 MB 4q25-34.1 2.5 Gain 65.5 MB
4q34.3-35.2 2.6 Gain 7.4 MB 4q34.3-35.2 2.5 Gain 9.3 MB
5 5p15.33-15.31 2.6 Gain 8.7 MB 5p15.33 3 Gain 0.7 MB
5q15-22 1.5 Loss 54.6 MB 5q23.3-33.1 1.6 Loss 22.5 MB
7 7p22.3-21.1 1.1 Loss 17.8 MB 7p22.3-21.1 1.4 Loss 17.3 MB
7q11.22-36.3 3 Gain 93.5 MB 7q11.22-36.3 2.8 Gain 93.6 MB
8 8p23.3-12 1.6 Loss 32.9 MB 8p23.3-12 1.6 Loss 30.9 MB
9 9p23.1-22.3 0.8 Loss 8.5 MB 9p23.1-22.3 1.2 Loss 8.1 MB
9p21.3-21.1 0.7 Loss 7 MB 9p21.3-21.1 1 Loss 6.9 MB
9p21.1 0.8 Loss 1 MB 9p21.1 1.3 Loss 1 MB
9p13.3 1 Loss 1.3 MB 9p13.3 1 Loss 1.3 MB
9p13.3-q21.33 0.9 Loss 54.9 MB 9p13.3-q21.33 1.3 Loss 53.2 MB
9q22.2-22.31 0.7 Loss 2.5 MB 9q22.2-22.31 1 Loss 2.4 MB
9q22.31-22.33 1.2 Loss 4.4 MB 9q22.31-22.33 ND NA NA
9q31.1-31.2 0.8 Loss 6.3 MB 9q31.1-31.2 1.1 Loss 5.6 MB
9q32-34.11 1 Loss 15.1 MB 9q32-34.11 1.3 Loss 17 MB
10 10p15.3-12.1 3 Gain 28.1 MB 10p15.3-12.1 2.8 Gain 28.4 MB
10p11.22 0.3 Loss 2.6 MB 10p11.22 0.7 Loss 3.6 MB
11 11q13.1-13,4 1.6 Loss 8.7 MB 11q13.1-13,4 1.7 Loss 7 MB
13 13q12.11-34 1.2 Loss 96.7 MB 13q12.11-34 1.3 Loss 96.7 MB
14 14p11.2 0.3 Loss 0.5 MB 14p11.2 0.7 Loss 0.6 MB
14q32.32 0.7 Loss 0.6 MB 14q32.32 1.2 Loss 0.6 MB
17 17p13.3-13.2 1.2 Loss 5.9 MB 17p13.3-13.2 1.5 Loss 5.8 MB
17p13.2-13.1 3 Gain 1.7 MB 17p13.2-13.1 3 Gain 0.9 MB
17p13.1-11.2 1.2 Loss 14.4 MB 17p13.1-11.2 1.3 Loss 13.4 MB
17q11.1-25.3 3.2 Gain 55.7 MB 17q11.1-25.3 2.9 Gain 54.2 MB
20 20q11.22-13.33 3.2 Gain 30.4 MB 20q11.22-13.33 2.7 Gain 31.1 MB
21 21q11.2-22.3 1.5 Loss 33.1 MB 21q21.2-22.3 1.7 Loss 23 MB
Case 5 10 10q22.3-24.32 1.4 Loss 21.7 MB 10q22.3-24.32 1.5 Loss 22.3 MB del(10)(q24q26)
13 13q14.13-22.1 1.5 Loss 28.4 MB 13q14.13-22.1 1.5 Loss 27.4 MB de(13)(q14q22)
Case 6 1 1p11.2-q21.2 2.6 Gain 27.4 MB 1p11.2-q21.2 2.5 Gain 33.3 MB
4 4p16.3-q36.2 1.4 Loss 190.9 MB 4p16.3-q36.2 1.6 Loss 188.2 MB −4
5 5p15.33-q11.2 3.2 Gain 58.8 MB 5p15.33-q11.2 2.5 Gain 57.5 MB +5, i(5)(p10)
6 6p25.3-21.1 3.1 Gain 45 MB 6p25.3-21.1 2.5 Gain 45.3 MB
6p12.3-q27 1.4 Loss 121 MB 6p12.3-q27 1.6 Loss 97 MB −6
7 7p22.3-14.1 2.7 Gain 41.9 MB 7p22.3-14.1 2.5 Gain 45.2 MB
13 13q31.1-34 3 Gain 35.8 MB 13q31.1-34 2.5 Gain 35.8 MB add(13)(q34)
18 18q21.11-21.33 3.2 Gain 28.4 MB 18q21.11-21.33 2.7 Gain 28.2 MB add18(q21)
18q21.33-23 1 Loss 17.5 MB 18q21.33-23 1.3 Loss 17.6 MB
20 20p13-q11.23 2.6 Gain 38.1 MB 20p13-q11.23 2.5 Gain 38.1 MB
Case 7 1 1p12-q44 2.4 Gain 128.8 MB 1p12-q44 2.4 Gain 128.2 MB +1,add(1)(p32)
2 2p25.3-16.1 1.6 Loss 58.6 MB 2p25.3-16.1 1.6 Loss 58.1 MB −2
2p16.1-14 3.5 Gain 8.7 MB 2p16.1-14 3 Gain 8.7 MB
3 3p14.1-13 3.9 Gain 7.6 MB 3p14.1-13 3.5 Gain 7.6 MB 3
3q25.2-26.1 1.7 Loss 8.3 MB 3q25.2-26.1 1.7 Loss 6.0 MB
4 4p16.3-q35.2 1.6 Loss 190.9 MB 4p16.3-q35.2 1.6 Loss 190.9 MB −4
6 6p26.3-11.2 2.4 Gain 58.3 MB 6p26.3-11.2 2.5 Gain 57.3 MB +6,i(6)(p10)
7 7p22.3-36.3 2.4 Gain 159 MB 7p22.3-36.3 2.4 Gain 159 MB 7
10 10p16.3-15.2 1.6 Loss 3.6 MB 10p16.3 1.7 Loss 1.8 MB dic(1;10)(q10;p13)
17 17p13.3-q11.1 1.6 Loss 25.6 MB 17p13.3-q11.1 1.6 Loss 25.9 MB i(17)(q10) i(17)(q10)
20 20p12.3-12.1 1.5 Loss 5.9 MB 20p12.3-12.1 1.6 Loss 5.9 MB −20
20q11.1-13.33 1.6 Loss 33.3 MB 20q11.1-13.33 1.6 Loss 33.1 MB
Case 8 1 1p36.33-12 1.6 Loss 96.7 MB 1p36.33-12 1.7 Loss 96.7 MB i(1)(q10)
1q12-44 2.5 Gain 102.3 MB 1q12-44 2.4 Gain 102.1 MB
2 2p25.3-25.2 1.7 Loss 6.3 MB 2p25.3-25.2 1.7 Loss 5.0 MB
2p21-13.3 2.4 Gain 22.1 MB 2p16.3-13.3 2.4 Gain 17.2 MB add(2)(p11.2)
2q23.1-37.3 2.4 Gain 44.3 MB 2q23.1-37.3 2.3 Gain 37.1 MB
3 3p26.3-12.1 1.7 Loss 86.1 MB 3p26.3-12.1 1.7 Loss 84.1 MB del(3)(p13p25)
4 4p16.3-q35.2 1.6 Loss 188.5 MB 4p16.3-q35.2 1.7 Loss 188.5 MB −4
6 6q25.2-27 2.8 Gain 17.3 MB 6q25.2-27 2.5 Gain 18.5 MB
7 7q21.11-36.3 2.5 Gain 78.3 MB 7q21.11-36.3 2.4 Gain 79.2 MB add(7)(q36)
8 8p23.3-q23.1 1.6 Loss 108.8 MB 8p23.3-q21.11 1.7 Loss 78 MB del(8)(q13q24)
9 9p24.3-q34.3 2.5 Gain 140.8 MB 9p24.3-q34.3 2.4 Gain 140.8 MB 9
10 10p15.3-q26.3 1.7 Loss 136.3 MB 10p15.3-q26.3 1.7 Loss 136.3 MB −10
11 11q12.1-13.5 1.7 Loss 19.2 MB 11q12.1-13.5 ND NA NA −11
15 15q11.2-26.3 1.7 Loss 79.6 MB 15q11.2-26.3 1.7 Loss 74 MB −15
18 18p11.32-q23 1.6 Loss 77.8 MB 18p11.31-q23 1.7 Loss 72.3 MB −18
X Xp22.33-21.2 1.5 Loss 30.1 MB Xp22.33-21.2 ND NA NA XXX
Xp21.2-q21.33 2.5 Gain 63 MB Xp21.2-q28 2.5 Gain 133 MB

NP-normal ploidy; ND-Not detected; NA-Not applicable; Def-copy number variation definition;

*-No analysis was reported due to low number of cells survived.