WO1997038083A2 - New member of the multiple-tumor aberrant growth gene family - Google Patents
New member of the multiple-tumor aberrant growth gene family Download PDFInfo
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- WO1997038083A2 WO1997038083A2 PCT/EP1997/001710 EP9701710W WO9738083A2 WO 1997038083 A2 WO1997038083 A2 WO 1997038083A2 EP 9701710 W EP9701710 W EP 9701710W WO 9738083 A2 WO9738083 A2 WO 9738083A2
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- gene
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- proliferative capacity
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Classifications
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
- A01K2217/00—Genetically modified animals
- A01K2217/05—Animals comprising random inserted nucleic acids (transgenic)
Definitions
- the present invention relates to the identification of a new translocation or fusion partner of members of the multi-tumor aberrant growth (MAG) gene family, the members of which are frequently associated with aberrant cell growth as found in a variety of both benign and malignant tumors.
- MAG multi-tumor aberrant growth
- the invention in particular relates to the identification of the PSAFP-1 gene as the broadly acting HMG (High Mobility Group) fusion partner involved in a number of tumors, including but not limited to the mesenchymal tumors hamartomas (e.g. breast and lung), lipo as, pleomorphic salivary gland adenomas, uterine leiomyomas, angio yxomas, fibroadenomas of the breast, polyps of the endometrium, atherosclerotic plaques, and other benign tumors as well as various malignant tumors, including but not limited to sarcomas (e.g. rhabdomyosarcoma, osteosarcoma) and carcinomas (e.g. of breast, lung, skin, thyroid) .
- the invention relates in particular to the use of the PSAFP-1 gene and its derivatives in diagnosis and therapy.
- chromosome 12ql3-ql5 was reported in pulmonary chondroid hamartoma [13, 14] .
- solid tumors with involvement of chromosome region 12ql3-ql5 have been published; e.g. tumors of the breast [15, 16] , diffuse astrocytomas [17] , and a giant-cell tumor of the bone [18] .
- Malignant tumor types with recurrent aberrations in 12ql3-ql5 include myxoid liposarcoma [19], soft tissue clear-cell sarcoma [20, 21, 22] , and a subgroup of rhabdomyosarcoma [23] .
- locus D12S8 was used as a starting point for chromosome walking.
- chromosomal breakpoints as present in a number of uterine leio yoma-derived cell lines are clustered within a 445 kb chromosomal segment which has been designated Uterine Leiomyoma Cluster Region on chromosome ____ (ULCR12) [24] .
- a 1.7 Mb region on chromosome 12 encompasses the chromosome 12 breakpoints of uterine leiomyoma-, lipoma-, and salivary gland adenoma- cells, with the breakpoint cluster regions of the various tumor types overlapping [25] .
- MAR Multiple Aberration Region
- Translocation partners may be used in therapy and diagnosis, like the MAG genes.
- the present invention now provides for this translocation partner gene or derivatives thereof in isolated form and its use in diagnostic and therapeutic applications .
- MAG gene(s) refers to genes associated with multiple aberrant cell growth. It has been found that the PSAFP-1 gene is not only the translocation partner of certain MAG genes but if affected by some kind of inactivating mutation may also induce aberrant growth. Therefore, by definition the term “MAG gene(s)” also includes the newly identified PSAFP-1 gene.
- wildtype cell is used to indicate the cell not harbouring an aberrant chromosome or to a cell having a physiological expression level of the relevant gene.
- Wildtype or normal chromosome refers to a non- aberrant chromosome .
- the present invention provides for various diagnostic and therapeutic applications that are based on the information that may be derived from the gene. This information encompasses its nucleotide sequence or the amino acid sequence of the gene product derived from the gene.
- the aberration in cell growth may be directly or indirectly caused by the physical breaks that occur in the gene or its vicinity, or by other types of mutations in the gene or its vicinity.
- the aberration in cell growth may be caused by non-physiological expression forms of the gene. These non-physiological expression forms may be caused by the break, or may be due to stimulus that deactivates the gene. At present the exact mechanism or origin of the aberrant cell growth is not yet unraveled. However, exact knowledge on this mechanism is not necessary to define methods of diagnosis or treatment.
- Diagnostic methods according to the invention are thus based on the fact that an aberration in a chromosome results in a detectable alteration in the chromosomes' appearance or biochemical behaviour.
- a translocation for example will result in a first part of the chromosome (and consequently of the MAG gene) having been substituted for another (second) part (further referred to as "first and second substitution parts") .
- the first part will often appear someplace else on another chromosome from which the second part originates.
- hybrids will be formed between the remaining parts of both (or in cases of triple translocations, even more) chromosomes and the substitution parts provided by their translocation partners.
- the transcript of a hybrid will still comprise the region provided by the remaining part of the gene/chromosome but will miss the region provided by the substitution part that has been translocated.
- the gene may be equally afflicted.
- Translocations are usually also cytogenetically detectable.
- the other aberrations are more difficult to find because they are often not visible on a cytogenetical level.
- the invention now provides possibilities for diagnosing all these types of chromosomal aberrations.
- translocations markers or probes based on the MAG gene for the remaining and substitution parts of a chromosome detect the remaining part on the original chromosome but the substitution part on another, the translocation partner.
- inversions For example, two probes will hybridise at a specific distance in the wildtype gene. This distance might however change due to an inversion. In situ such inversion may thus be visualized by labeling a set of suitable probes with the same or different detectable markers, such as fluorescent labels. Deletions and insertions may be detected in a similar manner.
- the above in situ applications can very advantageously be performed by using FISH techniques.
- the markers are e.g. two cosmids one of which comprises a first part of the PSAFP-1 gene, while the other comprises a second part.
- Both cosmids are labeled with different fluorescent markers, e.g. blue and yellow.
- the normal chromosome will show a combination of both labels, thus giving a green signal, while the translocation is visible as a blue signal on the remaining part of one chromosome (e.g. 12) while the yellow signal is found on another chromosome comprising the substitution part.
- the intensity of the signal on the normal chromosome will be 100%, while the signal on the aberrant chromosomes is 50%.
- one of the signals shifts from one place on the normal chromosome to another on the aberrant one.
- probes will then of course include at least one probe hybrising to a DNA sequence located 5' or 3 ' of the gene.
- Probes as used herein should be widely interpreted and include but are not limited to linear DNA or RNA strands, Yeast Artificial Chromosomes (YACs) , or circular DNA forms, such as plasmids, phages, cosmids etc.. These in situ methods may be used on metaphase and interphase chromosomes .
- various diagnostic techniques may be performed on a more biochemical level, for example based on alterations in the DNA, RNA or protein, or on changes in the physiological expression level of the gene.
- mutation detection can be performed using standard technologies for mutation detection (see Laboratory Protocols for Mutation Detection. Ulf Landegren, Oxford University Press, 1996, ISBN 0 19 857795 8.
- PCR SSCP, SSCP and heteroduplex analysis for example: PCR SSCP, SSCP and heteroduplex analysis, REF & ddF (restriction endonuclease and dideoxy fingerprinting) , DGGE, CDCE, LSSP-PCR, CCM, FAMA, EMC, MREC, SSO, PASA-PCR, solid-phase inisequencing, multiplex solid- phase fluorescent primer extension, OLA, LCR, UHG, DNA sequencing, FISH, PCR, RT-PCR, antibodies, PTT, MAMA, RED, Northern blotting, Southern blotting) .
- the invention may thus for example relate to a method of diagnosing cells having a non-physiological proliferative capacity, comprising the steps of taking a biopsy of the cells to be diagnosed, isolating a suitable PSAFP-1 gene-related macromolecule therefrom, and analysing the macromolecule thus obtained by comparison with a reference molecule originating from cells not showing a non-physiological proliferative capacity, preferably from the same individual.
- the PSAFP-1 gene-related macromolecule may thus be a DNA, an RNA or a protein.
- the invention comprises the steps of taking a biopsy of the cells to be diagnosed, extracting total RNA thereof, preparing a first strand cDNA of the mRNA species in the total RNA extract or poly-A-selected fraction (s) thereof, which cDNA comprises a suitable tail; performing a PCR using a PSAFP-1 gene specific primer and a tail-specific primer in order to amplify PSAFP-1 gene specific cDNA's; separating the PCR products on a gel to obtain a pattern of bands; evaluating the presence of aberrant bands by comparison to wildtype bands, preferably originating from the same individual.
- NASBA Nucleic Acid Sequence-Based Amplification
- the method comprises the steps of taking a biopsy of the cells to be diagnosed, isolating total protein therefrom, separating the total protein on a gel to obtain essentially individual bands, optionally transfering the bands to a Western blot, hybridising the bands thus obtained with antibodies directed against a part of the protein encoded by the remaining part of the PSAFP-1 gene and against a part of the protein encoded by the substitution part of the PSAFP-1 gene; visualising the antigen-antibody reactions and establishing the presence of aberrant bands by comparison with bands from wildtype proteins, preferably originating from the same individual .
- the method comprises taking a biopsy of the cells to be diagnosed; isolating total DNA therefrom; digesting the DNA with one or more so- called "rare cutter” restriction enzymes (typically “6- or more cutters”) ; separating the digest thus prepared on a gel to obtain a separation pattern; optionally transfering the separation pattern to a Southern blot; hybridising the separation pattern in the gel or on the blot with a set of probes under hybridising conditions; visualising the hybridisations and establishing the presence of aberrant bands by comparison to wildtype bands, preferably originating from the same individual. Changes in the expression level of the gene may be detected by measuring mRNA levels or protein levels by means of a suitable probe.
- Diagnostic methods based on abnormal expression levels of the gene may comprise the steps of taking a sample of the cells to be diagnosed; isolating mRNA therefrom; and establishing the presence and/or the (relative) quantity of mRNA transcribed from the MAG gene of interest in comparison to a control.
- Establishing the presence or (relative) quantity of the mRNA may be achieved by amplifying at least part of the mRNA of the MAG gene by means of RT-PCR or similar amplification techniques.
- the expression level may be established by determination of the presence or the amount of the gene product (e.g. protein) by means of for example monoclonal antibodies.
- the diagnostic methods of the invention may be used for diseases wherein cells having a non-physiological proliferative capacity are selected from the group consisting of benign tumors, such as the mesenchymal tumors hamartomas (e.g. breast and lung) , adipose tissue tumors (e.g. lipomas) , pleomorphic salivary gland adenomas, uterine leiomyomas, angiomyxomas, fibroadenomas of the breast, polyps of the endometrium, atherosclerotic plaques, and other benign tumors as well as various malignant tumors, including but not limited to sarcomas (e.g.
- rhabdomyosarcoma rhabdomyosarcoma, osteosarcoma
- carcinomas e.g. of breast, lung, skin, thyroid.
- the invention is not limited to the diagnosis and treatment of so-called benign and malignant solid tumors, but the principles thereof have been found to also apply to haematological malignancies like leukemias and lymphomas .
- Another aspect of the invention thus relates to the implementation of the identification of the defective PSAFP-l gene in therapy.
- the invention for example provides functional molecules of the PSAFP-l gene for use in the treatment of diseases involving cells having a non- physiological proliferative capacity by correcting the gene defect.
- the defect may thus be repaired by means of introducing wildtype PSAFP-l DNA into non-physiologically proliferating cells which in turn may result in a normalisation of the cell growth.
- the invention for example provides anti-sense molecules or expression inhibitors of the PSAFP-l gene for use in the treatment of diseases involving cells having a non- physiological proliferative capacity by modulating the expression of the gene.
- a non-physiological high expression may thus be normalised by means of antisense RNA that is either administered to the cell or expressed thereby and binds to the mRNA, or antibodies directed to the gene product, which in turn may result in a normalisation of the cell growth.
- the invention thus provides derivatives of the PSAFP-l gene and/or its immediate environment for use in diagnosis and the preparation of therapeutical compositions, wherein the derivatives are selected from the group consisting of sense and anti-sense cDNA or fragments thereof, transcripts of the gene or fragments thereof, antisense RNA, triple helix inducing molecule or other types of "transcription clamps", fragments of the gene or its complementary strand, proteins encoded by the gene or fragments thereof, protein nucleic acids (PNA) , antibodies directed to the gene, the cDNA, the transcript, the protein or the fragments thereof, as well as antibody fragments.
- the derivatives are selected from the group consisting of sense and anti-sense cDNA or fragments thereof, transcripts of the gene or fragments thereof, antisense RNA, triple helix inducing molecule or other types of "transcription clamps", fragments of the gene or its complementary strand, proteins encoded by the gene or fragments thereof, protein nucleic acids (PNA) , antibodies directed to
- RNA molecules may be used for therapeutic treatment according to the invention.
- An example of this type of molecule are ribozymes that destroy RNA molecules.
- the principles of the invention may also be used for producing a transgenic animal model for testing pharmaceuticals for treatment of PSAFP-l gene related malignant or benign tumors and atherosclerotic plaques.
- Fig. 1 The relevant sequence data are given in Fig. 1 in which:
- A. shows the total cDNA of the PSAFP-l gene, a human fusion partner gene of MHGI-C.
- the cDNA was isolated through RACE product pCH223 from a pleomorphic salivary gland adenoma. The start and stop codons are underlined;
- B. shows the derived amino acid sequence of the open reading frame
- C. shows the HMGI-C part (top) and PSAFP-l part
- D. shows the amino acid sequence of the PSAFP-l translocation part of the fusion product fused to the DNA binding domain 3 (DBD3) of HMGI-C.
- the YAC clones comprising the PSAFP-l gene are
- CEPH mark 1 YACs 145F7, 275A12, and 405C8 (spanning about 760 kb) .
- Fig. 2 shows the long range physical map encompassing the PSAFP-l gene. The isolation of the gene and the claimed diagnostic tests and therapeutic methods may all be reduced to practice by the skilled person while using standard techniques as for example disclosed in Laboratory Protocol for Mutation Detection. Ulf Landegren, Oxford University Press, 1996, ISBN 0 19 857795 8.
- PCR SSCP SSCP and heteroduplex analysis
- REF & ddF restriction endonuclease and dideoxy fingerprinting
- DGGE DGGE
- CDCE LSSP-PCR
- CCM FAMA
- EMC EMC
- MREC SSO
- PASA-PCR solid-phase minisequencing
- multiplex solid- phase fluorescent primer extension OLA, LCR, UHG
- DNA sequencing FISH
- PCR RT-PCR
- antibodies PTT, MAMA, RED, Northern blotting, Southern blotting.
- the universal amplification primer (UAP2; 95L736) CUA CUA CUA CUA CUA AAG GAT CCG TCG ACA TC was used as 'reverse primer 1 .
- the following HMGIC-specific 'forward primers' were used: (i; 94N1501) 5' -CTT CAG CCC AGG GAC AAC-3 ' (exon 1) , (ii; 94N701) 5' -CAA GAG GCA GAC CTA GGA-3' (exon 3) , or (iii; 94M1892) 5 ' -AAC AAT GCA ACT TTT AAT TAC TG-3 ' O'-UTR) .
- HMGIC-specific forward primers (nested primers as compared to those used in the first round) were used: (i; 94N1502) 5'-CAU CAU CAU CAU CGC CTC AGA AGA GAG GAC-3 ' (exon 4) , or (iii; 94M1908) 5' -CAU CAU CAU TTG ATC TGA TAA GCA AGA GTG GG-3 ' (3'-UTR) .
- CUA/CAU-tailing of the nested, specific primers allowed the use of the directional CloneAmp cloning system (GIBCO/BRL) .
- the PSAFP-l sequences contained stop codons in all three possible reading frames. In phase with the HMGIC reading frame, a small open reading frame was present coding for 31 amino acids. There was also a putative poly-adenylation signal (ATTAAA) in the ectopic sequences, upstream of the site where the oligo-d(T) -primed cDNA synthesis started. This could indicate that the ectopic sequences correspond to a transcribed gene sequence (the putative PSAFP-l gene) . This was confirmed by Northern blot analysis.
- CEPH mark 1 and 3 YAC libraries were screened with PCR probe pCH223, which corresponds to the ectopic sequences. This resulted in the isolation of three CEPH-A YAC clones (145A7, 275A12 and 405C8) and 13 mega-YAC clones (750F1, 752F4 , 752F5, 768A7, 768B7, 768D2, 775B3,
- FISH analysis of normal metaphase chromosomes using YAC clone 850A6 as molecular probe confirmed the localization of this YAC to 3pl4.
- cDNA clones corresponding to the chromosome 3-derived PSAFP-l sequences were isolated and the nucleotide sequence thereof established.
- a routine BLAST search by e-mail at blast@-ncbi.nlm.gov revealed that the PSAFP-l sequences fused to HMGIC sequences were identical to those of the human FHIT gene (fragile histidine triad gene) (Ohta et al., Cell 84, 587-597, 1996) .
- the FHIT gene was recently shown to span the chromosome 3pl4,2 fragile site and the renal carcinoma-associated t(3;8) translocation breakpoint (12) and encodes a dinucleoside S ⁇ S' ' '-? 1 , P 3 -triphosphate hydrolase.
- RT-PCR was used for detection of fusion transcripts involving PSAFP-l sequences.
- RT-PCR was carried out as described by Krizman and Berget (Nucleic Acids Res. 21, 5198-5202, 1993) . Briefly, cDNA was synthesized from 5 ⁇ g of total RNA. Reverse transcription was performed according to the first strand cDNA synthesis protocol from GIBCO/BRL using PSAFP-l-specific cDNA synthesis primer (96C2322) 5' TGC CTG TCT GAG CCT TTT AGG T 3' and HMGIC-specific cDNA synthesis primer (95C3362) 5' TAC AGC AGT TTT TCA CTA 3' . Specific primers used in the various experiments are given in the legend to Figure 3.
- PCR products were subcloned in a TA-cloning kit vector and subsequently used for sequencing.
- RT-PCR resulted in a product of 481 bp ( Figure 3A, lane 3) .
- the reciprocal PSAFP-1/HMGIC transcript was also expressed as indicated by the presence of a 686 bp RT-PCR product ( Figure 3A, lane 4) .
- PCR was performed using an HMGIC gene-specific primer (5 '-end) and a primer complementary to the attached short additional nucleotide stretch. An aliquot of the thus obtained PCR product was analyzed by gel electroforesis; fusion constructs were detected by comparing them with the background bands of normal cells of the same individual . Nucleotide sequence analysis of the products conclusively established and defined the differences between the PCR products of normal and tumor cells.
- Suitable molecules for use in diagnosis and therapy are antibodies directed against the PSAFP-l gene.
- Two approaches have been followed to develop them. Based upon the nucleotide sequence of the PSAFP-l cDNA, computer analysis was used to predict the location of antigenic determinants within the proteins. Synthetic peptides containing such determinants were prepared and rabbits were immunized with these.
- cDNA sequences can be expressed in appropriate pro- and eukaryotic expression systems and the polypeptides synthesized in this way can be purified and used for immunization of mice. Cell lines obtained upon transfection or electroporation of constructs of the PSAFP-l gene were helpful in characterizing the antibodies obtained.
- rabbit polyclonal antibodies directed against the PSAFP-l-encoded proteins use was made of the following two peptides:
- H-RPVERFHDLRPD 8-Multiple Antigen Peptide (MAP) and (H-HRNDSIYEELQKHDK) 8-MAP obtained from Research Genetics Inc., Huntsville, AL, USA.
- the polyclonal antibodies were made according to standard techniques.
- suitable antibodies were generated using hybrid proteins as antigens. These contained various portions of the PSAFP-l coding region fused in frame to GST (glutathione-S-transferase) . The antibodies that were obtained detected a
- FIGURE 3 A 3' -RACE analysis of total RNA from the pleomorphic adenoma CG592 (lane 1) .
- PCR products obtained in RT-PCR analysis of total RNA corresponding to a normal HMGIC transcript (lane 2; first round PCR, primers 31970-004 [5-CCC AGC CCT ATC ACC TCA-3'] and 32627-001 [5' -AAG ACC ATG GCA ATA CAG-3'] ; second round PCR, primers 31970-005 [5' -CTC ATC TCC CGA AAG GTG-3'] and 32627-001) , a HMGIC/PSAFP-1 fusion transcript (lane 3; first round PCR, primers 32627-002 [5 ' -ACT GGT TGG CAA TAG CTC TT-3'] and 31970-004; second round PCR, primers 32627-002 and 31970-005) , the reciprocal PSAFP-1/HMGIC
- Lane 6 contains the pGEM DNA markers (M) (Promega) , with sizes of 1,605, 1,198, 676, 517, 460, 396, and 350 bp.
- B Nucleotide sequence of the HMGIC/PSAFP-1 fusion transcript detected in tumor CG592. The first three HMGIC exons are fused to exons 9 and 10 of the PSAFP-l gene. The relative positions of the various exons are indicated by arrows above the sequence and those of primers used in nested RT-PCR and 3 ' -RACE reactions are indicated by arrows labelled with the primer number, both above and below the sequence. The stop codon in the HMGIC/PSAFP-1 fusion transcript is indicated by an asterisk.
- D Schematic representation of the genomic organization of the HMGIC and PSAFP-l genes showing the hybrid transcripts detected, with fusions occurring in intron 3 of the HMGIC gene and intron 8 of the PSAFP-l gene The relative positions of particular functional domains in the deducted proteins of both genes are linked to the encoding exons.
- Functional domains D1-D3, DNA binding domains; S: spacer domain; AD: acidic domain.
- Translocation t (12;22) (ql3 ;ql3) is a nonrandom rearrangement in clear cell sarcoma. Cancer Genet. Cytogenet. 64: 101-103.
- Gyapay, G. Morissette, J., Vignal, A., Dib, C, Fizames, C , Millasseau, P., Marc, S. , Bernardi, G., Lathrop, M. and Weissenbach, J. (1994) .
- Genomic sequence sampling a strategy for high resolution sequence-based physical mapping of complex genomes. Nature Genetics 7, 40-47 (1994) .
- HMGI high mobility group protein
- HMGI high mobility group protein
- Mitelman F (1994) Catalog of Chromosome Aberrations in Cancer. 4th ed. , New York, Wiley- Liss .
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WO1991009865A1 (en) * | 1989-12-22 | 1991-07-11 | The Trustees Of Columbia University In The City Of New York | Purified myeloblastin, nucleic acid molecule encoding same, and uses thereof |
WO1995025429A1 (en) * | 1994-03-18 | 1995-09-28 | Myriad Genetics, Inc. | Mts gene, mutations therein, and methods for diagnosing cancer using mts gene sequence |
-
1997
- 1997-04-04 EP EP97919321A patent/EP0927194A2/en not_active Withdrawn
- 1997-04-04 WO PCT/EP1997/001710 patent/WO1997038083A2/en not_active Application Discontinuation
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WO1991009865A1 (en) * | 1989-12-22 | 1991-07-11 | The Trustees Of Columbia University In The City Of New York | Purified myeloblastin, nucleic acid molecule encoding same, and uses thereof |
WO1995025429A1 (en) * | 1994-03-18 | 1995-09-28 | Myriad Genetics, Inc. | Mts gene, mutations therein, and methods for diagnosing cancer using mts gene sequence |
Non-Patent Citations (3)
Title |
---|
DAL CIN ET AL.: "Rearrangement of 12q14-15 in pulmonary chondroid hamartoma" GENES, CHROMOSOMES & CANCER, vol. 8, 1993, pages 131-133, XP002046941 cited in the application * |
OHTA ET AL.: "The FHIT gene, spanning the chromosome 3p14.2 fragile site and renal carcinoma-associated t(3;8) breakpoint, is abnormal in digestive tract cancers" CELL, vol. 84, 23 February 1996, pages 587-597, XP002046939 * |
SCHOENMAKERS ET AL.: "Physical mapping of chromosome 12q breakpoints in lipoma, pleomorphic salivary gland adenoma, uterine leiomyoma, and myxoid liposarcoma" GENOMICS, vol. 20, no. 2, 15 March 1994, pages 210-222, XP002046940 cited in the application * |
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