Compositions and methods for detection of chromosomal aberrations with novel hybridization buffers

Patent metadata

Field	Value
Publication number	US-9297035-B2
Application number	US-99449509-A
Country	US
Kind code	B2
Filing date	May 27, 2009
Priority date	May 27, 2008
Publication date	Mar 29, 2016
Grant date	Mar 29, 2016

Abstract

The present invention provides compositions and methods for the detection of nucleic acid sequences associated with chromosomal aberrations. The invention may, for example, eliminate the use of or reduce the dependence on formamide in hybridization. Compositions for use in the invention include an aqueous composition comprising at least one nucleic acid sequence and at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences.

First claim

The invention claimed is:

1. A composition comprising:
(a) a first molecular probe that detects a nucleotide sequence associated with a chromosomal aberration,
(b) at least one polar aprotic solvent in an amount effective to denature double-stranded nucleotide sequences within a sample having a preserved cell morphology, and
(c) a hybridization solution,
wherein the nucleotide sequence is a marker for a chromosomal aberration,
wherein the polar aprotic solvent has lactone, sulfone, sulfite, nitrile, and/or carbonate functionality, and
wherein the polar aprotic solvent has a cyclic base structure.

2. The composition according to claim 1 , wherein the chromosomal aberration is aneuploidy, potential breakpoint, insertion, inversion, deletion, duplication, gene amplification, rearrangement, or translocation.

3. The composition according to claim 1 , wherein the chromosomal aberration is associated with a congenital genetic disorder, cancer, or infection.

4. The composition according to claim 3 , wherein the chromosomal aberration is associated with cancer.

5. The composition according to claim 4 , wherein the first molecular probe detects ALK, BCL2, BCL3, BCL6, BCL10, BCL12, BCR, CCND1, E2A, EGFR, ETV6, FIP1L1, HER2, IGH, IGK, IGL, MALT1, MLL (ALL-1, HTRX1, HRX), MYC (c-Myc), PAX5, PDGFRA, PDGFRB, SIL, TCF3 (E2A, ITF1), TCL1A, TCRAD, TCRB, TCRG, telomere, TLX1, TLX3 (HOX11L2, RNX), or TOP2A.

6. The composition according to claim 1 , wherein the first molecular probe detects a target for a non-hemaetological disease selected from the group consisting of: BASE, BRCA1, CCND1, CCNE1, DCD,E2F3, n-MYC/MYCN, COX-2/PTGS2, LRIG1, ER a, hTERT, MLN64/STARD3, PGR, SNAI1, SRC, TOP1, TUBB1, AIB1, DLC-1, EDD, Pip4k2b/5k, Sil, TBX2, c-Kit, VEGF, VCAM-1, Tie-1, Ts/TYMS, PSMA, PSA, PAP, P15, P16, BCL1, BCL2, MTOR, TIMP1, ESR1, PTEN, MDM2/CDK4, MET, C-MET, ERB1, FGFR1, IGF1R, NET, FGFR3, ABCB1, TMPRSS2, BRCA2, TOP2B, ERCC1, AKT1, AKT2, AKT3, HRAS, NRAS, RAF1, HER3, HER4, ENT1, RRM1, RRM2, RRM2B, PIK3CA, AURK4, AURKB, AURKC, MAPT/tau, TTBK1, TUBB, VEGFR, CCND3, CDK6, CDK2, CDC2, HDAC, ESR2, SCUBE2, BIRC5, FASN, DHFR, TP/ECGF1, TYMP, DPYD, TK1, HMGIC, ABCA2, ABCB11, ABCC1, ABCC2, ABCC3, ABCC4, ABCC5, ABCG2, MVP, ATP7A, ATP7B, SLC29A1, SLC28A1, SLC19A1, TUBB4, TUBA, MAP4, MAP7, STMN1, KIF5B, HSPA5, PSMD14, FPGS, GSTP1, GPX, GCLC, GGT2, MT, AKR1B1, HMGB1, HMGB2, XPA, XPD, MSH2, MLH1, PMS2, APEX1, MGMT, GLO1, RB1, GML, CDKN1A, CDKN2A, CDKN1B, ERBB2, KRAS2, ITGB1, JUN, FOS, NFKB1, TP53, TP73, BCL2L1, MCL1, BAX, BIRC4, TNFRSF6, CASP3, CASP8, HSPB1, MALAT1(alpha) t(11;19)(q11;q13.4), MHLB1 t(11;19)(q11;q13.4), COL1A1 t(17;22)(q22;q13), PDGFB t(17;22)(q22;q13), FKHR t(2;13) & t(1;13), ETV6 t(12;15)(p13;q25), NTRK3 t(12;15)(p13;q25), TLS/FUS t(12;16)(q13;p11), CHOP t(12;16)(q13;p11), EWS t(12;22)(q13;q12), EWS/FLI1 t(11;22)(q24;q12), and FLI1 t(11;22)(q24;q12).

7. The composition according to claim 1 , wherein the first molecular probe detects a target for a hemaetological disease selected from the group consisting of: ABL t(9;22)(q34;q11), PRDM16 del(1p36.32) del(21q22.12), RUNX1/AML1 del(1p36.32) del(21q22.12), CEP8, PDGFRB, NUP98, FGFR1, ASS, ETO t(8;21)(q22;q22), AML1 t(8;21)(q22;q22), CBFbeta inv(16)(p13q22) t(16;16)(p13;q22), MYH11 inv(16)(p13q22) t(16;16)(p13;q22), AF9 t(9;11), PML t(15;17)(q22;q21), PLZF t(11;17)(q23;q21), NuMA t(11;17)(q13;q21), NPM t(5;17)(q23;q12), RAR alpha t(15;17)(q22;q21) t(11;17)(q23;q21) t(11;17)(q13; q21) t(5;17)(q23;q21), EVI1 t(3;v)(q26;v), GR6 t(3;3)(q21;q26), RPN1 t(3;3) (q21;q26), DEK t(6;9), CAN t(6;9), MLF1 t(3;5)( . . . ;q23), FUS t(16;21), ERG t(16;21), NUP98 t(7;11), HOX9A t(7;11), MOZ/MYST3 t(8;16)(p11;p13), CBP t(8;16)(p11;p13), p300 t(8;22)(p11;q13), TIF2/GRIP-1/NCoA-2 inv(8)(p11q13), MKL1, PBX1 t(1;19)(q23;p13.3) +var., ABL t(9;22)(q34;q11), AF4/AFF1 t(4;11)(q21;q23), AML1/RUNX1 t(12;21)(p13;q22), IL3 t(5;14)(q31;q32), HLF t(17;19), IKZF1 del(7)(p12.2), CDKN2A/CDKN2B del(9)(p21.3), TAL1 1p32 aberrations, LMO2 t(11;14)(p13;q11)+var., LMO1 t(11;14)(p15;q11), HOX11 t(10;14)(q24;q11)+var., TAL2 t(7;9)(q34;q32), TAN1 t(7;9)(q34;q34), CEP12, ATM, D13S25, D13S319, TP53, P53, TNFAIP3 del(6)(q23.3-q24.1), CDK6 BCL1 t(11;14)(q13;q32)+var., IRF4 t(6;14)(p25;q32), C-MAF t(14;16)(q32;q23), FGFR3 t(4;14)(p16;q32), MUM2/3 t(1;14)(q21;q32), NPM t(2;5)(p23;q35), ASS, RB1, and ATM.

8. The composition according to claim 1 , wherein the first molecular probe detects a centromere selected from the group consisting of: CEP1, CEP2, CEP3, CEP4, CEP5, CEP6, CEP7, CEP8, CEP9, CEP10, CEP11, CEP12, CEP13, CEP14, CEP15, CEP16, CEP17, CEP18, CEP19, CEP20, CEP21, CEP22, CEP23, CEP X, and CEP Y.

9. The composition according to claim 4 , wherein the cancer is adrenocortical carcinoma, bladder cancer, brain cancer, burn cancer, breast cancer, cervical cancer, colorectal cancer, colon cancer, rectal cancer, endometrial cancer, esophageal cancer, kidney (renal) cancer, leukemia, liver cancer, lung cancer, gastric cancer, glioma, hematological cancer, head and neck cancer, melanoma, lymphoma, leukemia, non-Hodgkin lymphoma, ovarian cancer, pancreatic cancer, prostate cancer, retinoblastoma, sarcoma, skin cancer (nonmelanoma), testicular cancer, thyroid cancer, or uterine cancer.

10. The composition according to claim 9 , wherein the cancer is breast cancer and the first molecular probe detects HER2.

11. The composition according to claim 9 , wherein the cancer is colorectal cancer and the first molecular probe detects EGFR.

12. The composition according to claim 4 , wherein the cancer is a hematopoietic malignancy.

13. The composition according to claim 12 , wherein the first molecular probe detects a chromosomal aberration chosen from t(1;14) (q34;q11), t(1;19) (q23;p13), t(2;5), t(2;18) (q12;q21), t(2;8), t(4;11), t(4;11) (q21;q23), t(6;11) (q27;q23), t(7;22) (p22;q12), t(8;14), t(8;22), t(9;11) (p22;q23), t(9;22) (q34;q11), t(10;14) (q24;q11), t(11;14), t(11;14) (p13;q11), t(11;19) (q23;p13), t(14;18) (q23;q21), t(14;18), t(18;22) (q21;q11), and t(21;22) (q22;q12).

14. The composition according to claim 1 , further comprising a second molecular probe.

15. The composition according to claim 14 , wherein the second molecular probe detects a reference sequence.

16. The composition according to claim 15 , wherein the reference sequence is a centromere sequence.

17. The composition according to claim 16 , wherein the centromere sequence is selected from the group consisting of: CEP1, CEP2, CEP3, CEP4, CEP5, CEP6, CEP7, CEP8, CEP9, CEP10, CEP11, CEP12, CEP13, CEP14, CEP15, CEP16, CEP17, CEP18, CEP19, CEP20, CEP21, CEP22, CEP23, CEP X, and CEP Y.

18. The composition according to claim 14 , wherein the first molecular probe and the second molecular probe detect sequences flanking or within one or more potential breakpoints.

19. The composition according to claim 14 , further comprising a third molecular probe.

20. The composition according to claim 1 , wherein the first molecular probe is a DNA probe, a PNA probe, or an LNA probe.

21. The composition according to claim 14 , wherein the second molecular probe is a DNA probe, a PNA probe, or an LNA probe.

22. The composition according to claim 19 , wherein the third molecular probe is a DNA probe, a PNA probe, or an LNA probe.

23. The composition according to claim 1 , wherein the molecular probe further comprises a label.

24. The composition according to claim 23 , wherein the label is a chromophore, fluorophore, biotin, DIG

Assignees

• Matthiesen Steen Hauge
• Petersen Kenneth H
• Poulsen Tim Svenstrup
• Dako Denmark As

Inventors

• Matthiesen Steen Hauge
• Petersen Kenneth H
• Poulsen Tim Svenstrup

Classifications

• Y10T436/143333

  Saccharide [e.g., DNA, etc.] · CPC title

• C12Q1/6876 Primary

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C12Q1/6832 Primary

  Enhancement of hybridisation reaction · CPC title

• C12Q1/6841

  In situ hybridisation · CPC title

• C12Q2527/00

  Reactions demanding special reaction conditions · CPC title