Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

Kolquist, Kathryn A; Schultz, Roger A; Slovak, Marilyn L; McDaniel, Lisa D; Brown, Theresa C; Tubbs, Raymond R; Cook, James R; Theil, Karl S; Cawich, Victoria; Valentin, Caitlin; Minier, Sara; Neill, Nicholas J; Byerly, Steve; Morton, S Annie; Sahoo, Trilochan; Ballif, Blake C; Shaffer, Lisa G

doi:10.1186/1755-8166-4-25

Molecular Cytogenetics

Table 1 Thirty-four samples validated on an oligonucleotide array designed for detection of aberrations in leukemia and lymphoma*

From: Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis

Case	Karyotype	FISH		Concordant array results	Discordant array results	New findings by microarray
1	NA	LSI D13S319 96% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal		13q14.2q14.3(47,613,553-50,628,718) × 1	NA	22q11.23(22,674,846-22,723,991) × 0
2	NA	LSI D13S319 77% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal		13q14.2q14.3(47,123,245-50,443,082) × 1	NA	NA
3	NA	LSI D13S319 81% loss (34% mono, 47% bi), LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal		13q13.3q14.3(36,736,548-51,816,512) × 1, 13q14.3(49,315,855-50,237,971) × 0	NA	15q11.2(19,129,891-19,224,501) × 3, 18p11.32q23(123,388-76,100,854) × 3, 22q11.23(22,674,846-22,723,991) × 0
4	NA	LSI D13S319 42% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal		13q14.13q14.3(45,945,097-50,339,992) × 1	NA	NA
5	NA	LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 92% trisomy, LSI p53 normal		12p13.33q24.33(60,861-132,267,241) × 3	NA	NA
6	NA	LSI D13S319 97% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 74% trisomy, LSI p53 normal		12p13.33q24.33(60,861-132,267,241) × 3, 13q14.3(49,074,574-50,628,718) × 1	NA	19p13.3q13.43(220,598-63,782,017) × 3
7	NA	LSI D13S319 91% loss, LSI 13q34 normal, LSI ATM 89% loss, CEP 12 normal, LSI p53 normal		11q13.4q24.3(72,459,008-130,030,128) × 1, 13q14.11q21.1(43,421,790-53,019,141) × 1	NA	2p25.3p11.2(44,198-89,912,901) × 3
8	NA	LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 63% trisomy, LSI p53 normal		12p13.33q24.33(60,861-132,267,241) × 3	NA	NA
9	NA	LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 63% trisomy, LSI p53 normal		12p13.33q24.33(60,861-132,267,241) × 3	NA	NA
10	NA	LSI D13S319 92% loss, LSI 13q34 12% loss, LSI ATM normal, CEP 12 normal, LSI p53 normal		13q14.3(49,407,720-50,523,594) × 0~1	Array did not detect 13q34 deletion seen in 12% of cells by FISH	12q24.12(110,684,027-110,768,579) × 3
11	NA		LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal	NA	NA	1p31.3(64,811,810-68,404,781) × 3, 1q21.3q23.1(151,852,847-155,280,574) × 3, 2p16.1p15(59,245,962-62,672,016) × 3, 5q35.2q35.3(174,945,789-178,610,160) × 3, 11p15.4p15.3(7,907,684-11,413,676) × 3, 12p13.33p13.31(2,409,808-5,956,328) × 3, 16q24.1q24.2(82,968,178-86,062,471) × 3, 17q22q23.2(53,582,801-57,412,725) × 3, 18q21.32q22.1(57,089,022-60,760,895) × 3
12	NA		LSI D13S319 45% loss, LSI 13q34 normal, LSI ATM 47%, CEP 12 normal, LSI p53 normal	11q14.1q24.3(79,218,490-128,057,190) × 1, 13q14.11q21.33(43,525,071-71,879,067) × 1	NA	Yp11.31q12(2,706,656-57,735,230) × 0
13	NA		LSI D13S319 93% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal	13q14.3(49,457,877-50,339,992) × 0	NA	NA
14	NA		LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 71% trisomy, LSI p53 normal	12p13.33q24.33(60,861-132,267,241) × 3	NA	14q24.1q32.33 (68,329,913-105,393,508) × 1, 22q11.23(22,674,846-22,723,991) × 0
15	NA		LSI D13S319 89% loss, LSI 13q34 normal, LSI ATM 98% loss, CEP 12 normal, LSI p53 normal	11q14.3q23.2(88,551,231-114,026,260) × 1, 13q14.2q14.3(47,463,489-51,926,538) × 1	NA	2p16.1p14(56,499,065-66,570,230) × 3, 4p16.3p15.1(45,627-29,325,651) × 1, 5q33.2q35.3(152,262,081-180,619,169) × 3, 7q31.32q36.3(123,057,209-158,821,424) × 3
16	NA		LSI D13S319 40% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal	13q14.2q14.3(47,691,117-50,339,992) × 1	NA	1q32.1(203,529,401-204,498,513) × 1, 12p13.33q24.33(60,861-132,267,241) × 2~3
17	NA		LSI D13S319 92% loss, LSI 13q34 normal, LSI ATM 11% loss, CEP 12 90% trisomy, LSI p53 normal	12p13.33q24.33(60,861-132,267,241) × 3, 13q13.3q21.1(37,240,922-55,410,522) × 1	Array did not detect deletion of 11q22.3 seen in 11% of cells by FISH	5p15.32p15.31(5,388,368-6,879,401) × 1, 10q21.1q21.3(58,227,677-67,149,424) × 1, 10q23.31q23.33(90,215,922-95,066,500) × 1, 11q22.1q22.2(101,471,877-101,736,881) × 1, Yp11.32q12(1-57,735,230) × 0,
18	NA		LSI D13S319 70% loss, LSI 13q34 normal, LSI ATM 58% loss, CEP 12 normal, LSI p53 normal	11q14.1q25(78,733,283-131,062,293) × 1, 13q14.2q14.3(48,739,670-50,554,228) × 1	NA	NA
19	NA		LSI D13S319 96% loss, LSI 13q34 normal, LSI ATM 98% loss, CEP 12 normal, LSI p53 normal	11q14.3q23.3 (91,814,326-116,080,874) × 1, 13q14.2q14.3(48,774,702-50,765,417) × 1	NA	2p25.3p14(44,198-66,539,084) × 3, 2p14p11.2(66,729,955-88,771,193) × 2~3, 4q32.3q35.2(166,094,098-191,152,793) × 1, 6q16.3q27(102,816,244-170,736,131) × 1~2, 7p22.1p11.2(6,480,544-55,435,373) × 2~3, 8q23.1q24.3(107,914,570-146,263,042) × 3, 11p15.1p14.3(21,533,469-22,367,835) × 1, 11p14.3(22,398,459-24,320,961) × 3, 13q13.3(37,240,922-38,696,855) × 1, 13q14.11q14.12(43,995,777-5,551,120) × 3, 13q14.3q21.1(50,795,724-52,401,010) × 3, 13q21.1q21.2(55,083,523-58,084,123) × 3, 13q21.2(59,114,933-59,262,005) × 3, 13q21.31q21.32(63,478,713-65,130,349) × 3, 13q21.33q34(67,650,203-114,103,644) × 3, 19p13.3(220,598-546,817) × 1, 21q22.3(42,101,144-46,915,771) × 2~3
20	NA		LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 66% trisomy, LSI p53 62% loss	12p13.33q24.33(60,861-132,267,241) × 3, 17p13.3p11.1 (49,128-22,116,415) × 1	NA	22q11.23(22,674,846-22,731,268) × 0~1, Yp11.2q11.23(8,292,949-26,636,748) × 0
21	NA		LSI D13S319 92% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal	13q14.2q14.3(46,444,224-50,554,228) × 1	NA	NA
22	NA		LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 35% trisomy, LSI p53 normal	12p13.33q24.33 (60,861-132,267,241) × 3	NA	NA
23	NA		LSI D13S319 29% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal	13q14.3(49,604,393-49,730,034) × 1	NA	NA
24	NA		LSI D13S319 88% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 normal	13q14.2q14.3(46,444,224-50,554,228) × 1	NA	NA
25	44~46,X,X,add(1)(p36.1),i(6)(p10),del(8)(p21p23),add(12)(p11.2),- 13, del(14)(q12q32),-15, add(17)(p11.2),+2-6mar[cp11]/46,XX[9]		LSI D13S319 34% loss, LSI p53 49% loss	13q14.2q14.3(47,524,866-50,523,594) × 1, 17p13.3p13.1(49,128-8,581,862) × 1	Array did not detect del(14)(q12q32) seen on karyotype; -15 shows complexity on array	3p21.31(47,218,579-49,437,299) × 1, 5q35.1q35.3(168,342,673-180,619,169) × 3, 6p21.33p12.1(31,649,559-55,535,574) × 1, 7p22.3p15.3(130,978-21,156,763) × 3, 8p23.3p12(177,781-34,695,588) × 1, 8q24.13q24.3(126,709,259-145,344,434) × 3, 15q11.2q13.3(20,372,901-31,359,613) × 3, 15q13.3q15.1(31,388,923-39,994,112) × 1, 15q15.1q21.1(40,049,653-43,331,117) × 3, 15q21.1q22.2(43,385,070-58,614,700) × 1, 15q22.2q26.3(58,646,551-100,217,531) × 3
26	47,XY,+12[cp7]/46,XY[13]		LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 77.5% trisomy, LSI p53 normal	12p13.33q24.33(60,861-132,267,241) × 3	NA	7q34(141,693,456-141,719,136) × 1, 14q22.2(53,498,118-53,858,816) × 3
27	46,XY,del(11)(q13q23)[5]/47,idem,+12[8]/46,XY[7]		LSI D13S319 67% loss, LSI ATM 93% loss, CEP 12 15% trisomy	11q13.5q23.3(76,383,882-117,091,784) × 1, 12p13.33q24.33(1-132,349,534) × 3, 13q14.2q14.3(47,172,707-50,586,402) × 1~2	NA	NA
28	47,XY,+12[6]/46,XY[14]		LSI D13S319 normal, LSI 13q34 normal, LSI ATM normal, CEP 12 61% trisomy, LSI p53 normal	12p13.33q24.33(60,861-132,267,241) × 3	NA	NA
29	45,XY,del(13)(q21q34),-17[3]/46,XY,del(17)(p11.2)[3]/46,XY[14]		LSI D13S319 normal, LSI ATM normal, CEP 12 normal, LSI p53 45% loss	17p13.3p11.2(49,128-21,376,245) × 1	Array and FISH did not detect del(13)(q21q34) seen in 3/20 cells by karyotype	NA
30	47,XY,+ 12[4]/47,idem,del(11)(q13q23)[4]/46,XY[8]		LSI D13S319 normal, LSI 13q34 normal, LSI ATM 10.5% loss, CEP 12 85% trisomy, LSI p53 normal	12p13.33q24.33(60,861-132,267,241) × 3	Array did not detect 11q22.3 deletion seen in 10.5% of cells by FISH and in 4/16 cells by karyotype	13q12.2(27,492,830-27,493,700) × 3, 22q11.23(22,674,846-22,731,268) × 0
31	44~46,XY,del(6)(q15q23)[6]/42~44, idem,-3,-4,add(4)(p14),-8,add(10)(q22),del(13)(q12q22),add(17)(p11.2)[cp14]		NA	3p26.3p25.2(88,832-11,601,487) × 1, 3p24.3p21.31(21,821,826-45,382,789) × 1, 3p21.2p14.2(51,631,148-59,828,728) × 1, 3p11.2q21.3(88,616,646-129,821,181) × 1, 3q21.3q25.1(130,955,610-152,751,429) × 1, 4p16.3p14(45,627-39,064,794) × 1, 4p14p12(40,689,654-48,288,082) × 1, 6q14.1q24.3(83,060,798-147,519,394) × 1, 8p23.3p21.3(1-21,077,797) × 1, 8p21.1q12.1(27,859,739-56,426,895) × 1, 8q12.1q13.1(58,060,709-66,596,062) × 1, 8q21.13q22.1(81,697,427-96,822,423) × 1, 8q22.3q24.13(103,345,568-125,046,236) × 1, 8q24.21q24.3(130,132,793-141,102,164) × 1, 13q14.12q34(45,300,002-114,103,644) × 1	NA	10q24.1q25.2(99,015,708-114,057,326) × 1, 11q22.1q23.3(101,560,685-116,463,713) × 1, 16p13.3p13.2(35,819-8,125,327) × 1, 16p13.13p13.12(12,434,601-14,674,345) × 1, 16q21(57,250,542-61,322,202) × 1, 17p13.3p11.2(49,128-21,376,245) × 1, 18q12.3(38,266,239-38,764,068) × 1, 20p13p12.2(517,864-11,841,120) × 1; Array clarified a deletion on 13q to include LAMP1
32	45~46,XX,del(17)(p11.2p13),-20, +mar[cp16]/45~46,idem,add(3)(q25)[3]/46,XY[3]		LSI D13S319 72% loss, LSI 13q34 normal, LSI ATM normal, CEP 12 normal, LSI p53 79.5% loss	13q14.3(49,378,768-50,262,893) × 1, 17p13.3p11.2(49,128-21,247,183) × 1, 20p13p12.1(1,981,763-15,398,390) × 1, 20p11.21(23,271,365-25,666,747) × 1, 20q11.21q11.22(30,436,259-32,563,890) × 1	NA	3p21.31(46,911,912-49,973,212) × 1, 17q21.1q21.31(35,551,063-37,865,072) × 1
33	45,XY,-4, add(17)(p13)[1]/44,idem,add(13)(p12),add(14)(q32),- 15, del(20)(q11.2q13.3)[16]/46,XY[3]		NA	4p16.3p14(45,627-38,504,396) × 1, 4p13q22.3(41,631,408-96,524,997) × 1, 15q11.2q15.1(19,129,891-38,918,282) × 1, 15q21.2q22.2(49,131,112-57,212,181) × 1	del(20)(q11.2q13.3) not detected by aCGH	11q22.3q23.2(106,821,962-113,825,965) × 1, 13q12.11(19,508,097-20,625,750) × 1, 17p13.3(49,128-2,779,693) × 1, 17p13.1p11.2(9,888,292-18,868,118) × 1, 17p11.2(19,082,873-20,794,597) × 1, 22q11.23(22,674,846-22,723,991) × 0
34	45,X,-Y[7]/46,XY,add(8)(p11.2),add(11)(q13)[4]/46,XY[9]		LSI D13S319 62.5% loss, LSI 13q34 normal, LSI ATM 31% loss, CEP 12 normal, LSI p53 normal	11q13.4q25(72,590,406-134,425,038) × 1, 13q14.2q14.3(47,588,669-50,414,293) × 1	-Y not detected by aCGH	7p22.3p12.2(130,978-49,815,456) × 3, 8p23.3p12(1-33,376,370) × 1, 22q12.2q13.33(30,406,286-49,519,766) × 3

aCGH, array-based comparative genomic hybridization; NA, not applicable.
*Rearrangements at the immunoglobulin loci were excluded except for α T-cell receptor loci (13q14.2) and β T-cell receptor loci (7q34) since they can recombine in malignant B cells [19].

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