Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

Abstract

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

1. A method of staining targeted interphase chromosomal material based upon a nucleic acid segment employing a unique sequence high complexity nucleic acid probe of greater than about 50,000 bases, wherein said targeted chromosomal material is a genetic rearrangement associated with at least one chromosome in humans, said method comprising employing said chromosomal material and a unique sequence high complexity nucleic acid probe of greater than about 50,000 bases in in situ hybridization, wherein the chromosomal material is present in a morphologically identifiable cell nucleus; allowing said probe to bind to said targeted chromosomal material; and detecting said bound probe, wherein bound probe is indicative of the presence of target chromosomal material. 
     
     
       2. A method of staining targeted interphase chromosomal material based upon a nucleic acid segment employing a unique sequence high complexity nucleic acid probe of greater than about 40 kb, wherein said targeted chromosomal material is a genetic rearrangement associated with at least one chromosome in humans, said method comprising contacting said chromosomal material with a unique sequence high complexity nucleic acid probe of greater than about 40 kb, wherein the chromosomal material is present in a morphologically identifiable cell nucleus; allowing said probe to bind to said targeted chromosomal material; and detecting said bound probe, wherein bound probe is indicative of the presence of target chromosomal material. 
     
     
       3. A method of staining targeted interphase chromosomal material based upon a nucleic acid segment employing a unique sequence high complexity nucleic acid probe of greater than about 50,000 bases, wherein said targeted interphase chromosomal material is a genetic rearrangement associated with at least one chromosome in humans, said method comprising contacting said interphase chromosomal material with a unique sequence high complexity nucleic acid probe of greater than about 50,000 bases, wherein the chromosomal material is present in a morphologically identifiable cell nucleus; allowing said probe to bind to said targeted interphase chromosomal material; and detecting said bound probe, wherein bound probe is indicative of the presence of target interphase chromosomal material. 
     
     
       4. The method of  claim 2 , wherein the genetic rearrangement is a translocation or an inversion. 
     
     
       5. The method of  claim 2 , wherein the unique sequence high complexity nucleic acid probe is labeled. 
     
     
       6. The method of  claim 5 , wherein said labeled unique sequence high complexity nucleic acid probe comprises fragments complementary to a single chromosome, fragments complementary to a subregion of a single chromosome, fragments complementary to a genome or fragments complementary to a subregion of a genome. 
     
     
       7. The method of  claim 2 , wherein the interphase chromosomal material is interphase chromosomal DNA. 
     
     
       8. The method of  claim 3 , wherein the genetic rearrangement is a translocation or an inversion. 
     
     
       9. The method of  claim 3 , wherein the unique sequence high complexity nucleic acid probe is labeled. 
     
     
       10. The method of  claim 9 , wherein said labeled unique sequence high complexity nucleic acid probe comprises fragments complementary to a single chromosome, fragments complementary to a subregion of a single chromosome, fragments complementary to a genome or fragments complementary to a subregion of a genome. 
     
     
       11. The method of  claim 3 , wherein the interphase chromosomal material is interphase chromosomal DNA. 
     
     
       12. The method of  claim 2 , wherein complexity of the unique sequence high complexity nucleic acid probe is greater than about 100,000 bases. 
     
     
       13. The method of  claim 3 , wherein complexity of the unique sequence high complexity nucleic acid probe is greater than about 100,000 bases.