Chromosome-specific staining to detect genetic rearrangements

a chromosome and gene technology, applied in the field of cytogenetics, can solve the problems of high complexity of nucleic acid probes useful for the detection of genetic rearrangements, and achieve the effect of improving analysis, rapid and highly sensitive detection of chromosomal abnormalities

Inactive Publication Date: 2008-09-09
RGT UNIV OF CALIFORNIA
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  • Abstract
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Benefits of technology

[0116]This invention still further provides methods and reagents for producing staining patterns in a patient who is afflicted with a disease associated genetic rearrangement, such as those associated with the BCR-ABL fusion in CML, wherein said staining patterns are predictive and / or indicative of the response of a patient to various therapeutic regimens, such as chemotherapy, radiation, surgery, and transplantation, such as bone marrow transplantation. Such staining patterns can be useful in monitoring the status of such a patient, preferably on a cell by cell basis, and can be predictive of a disease recurrence for a patient that is in remission. Computer assisted microscopic analysis can assist in the interpretation of staining patterns of this invention, and the invention provides for methods wherein computer assisted microscopic analysis is used in testing patient cells on a call by cell basis, for e.g., to search for residual disease in a patient.
[0121]The invention still further provides for high complexity nucleic acid probes which have been optimized for rapid, efficient and automated detection of genetic rearrangements.
[0129]The present invention addresses problems associated with karyotyping chromosomes, especially for diagnostic and dosimetric applications. In particular, the invention overcomes problems which arise because of the lack of stains that are sufficiently chromosome-specific by providing reagents comprising heterogeneous mixtures of nucleic acid fragments that can be hybridized to the target DNA and / or RNA, e.g., the target chromosomes, target subsets of chromosomes, or target regions of specific chromosomes. The staining technique of the invention opens up the possibility of rapid and highly sensitive detection of chromosomal abnormalities, particularly genetic rearrangements, in both metaphase and interphase cells using standard clinical and laboratory equipment and improved analysis using automated techniques. It has direct application in genetic screening, cancer diagnosis, and biological dosimetry.

Problems solved by technology

Such nucleic acid probes useful for the detection of genetic rearrangements are typically of high complexity.

Method used

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  • Chromosome-specific staining to detect genetic rearrangements
  • Chromosome-specific staining to detect genetic rearrangements
  • Chromosome-specific staining to detect genetic rearrangements

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case i

[0310] The complexity of the probe is about 50 kb to about 100 kb. (In this case the complexity may be approximately equal to L since the probability is that no repetitive sequences will typically occur with more than a few copies in such a number of bases). Using a standard hybridization mixture (as exemplified in Section VI.B, infra), the target can be hybridized with about 2 ng of labeled probe DNA in 10 ul of hybridization mix, corresponding to approximately 1 pg / ul per kb of specific sequences (as used in Section VI.B, infra). Suppose the hybridization is to a slide containing 104 cells (a typical number), and each cell has about 6 pg of DNA, (typical for mammals). Then in this model calculation, there is 3 pg of shared repetitive sequences per cell. Thus, for 104 cells there are 3×104 pg or 30 ng of shared sequences on the slide. Similarly, there is 104×0.5×105×6 / 3×109 pg=1 pg of target for the specific sequences. The probe contains 1 / 2×2 ng or 1 ng of shared sequences and 1 n...

case ii

[0312] As the size of the target region is increased, the complexity of the probe necessarily is increased, and the amount of DNA in the hybridization mix needs to be increased in order to have a sufficient concentration of each portion of specific sequence to hybridize. Also, if one desires to decrease the hybridization time of the procedure, the probe concentration must be increased. In these situations, the increase in probe concentration results in an increase in the amount of shared sequences in the hybridization mixture, which in turn increases the amount of hybridization that will occur to the shared sequences in the target area or areas, thereby reducing the contrast ratio.

[0313]With very high complexity probes spanning several entire chromosomes, L / G can approach 1. In order to stain such a portion of the genome within a reasonable time, for example, overnight, the concentration of labeled nucleic acid needs to be increased, for example, 200 ng in 10 ul of hybridization mix...

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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.

Description

RELATED APPLICATION[0001]This application is a divisional, of applicationa Reissue application of U.S. Ser. No. 08 / 477,316, filed Jun. 7, 1995, now U.S. Pat. No. 6,344,315, granted Feb. 5, 2002, which is a continuation of U.S. Ser. No. 08 / 312,914, filed Sep. 30, 1994, now abandoned;, which is a continuation of applicationU.S. Ser. No. 08 / 137,745, filed Oct. 19, 1993, now abandoned, which is a continuation of applicationU.S. Ser. No. 08 / 015,390, filed Feb. 8, 1993, now abandoned, which is a continuation of applicationU.S. Ser. No. 07 / 670,242, filed Mar. 15, 1991, now abandoned, which is a continuation-in-part of applicationU.S. Ser. No. 07 / 659,974, filed Feb. 22, 1991, now abandoned, which is a continuation-in-part of applicationU.S. Ser. No. 07 / 537,305, filed Jun. 12, 1990;, now abandoned, which is a continuation-in-part of applicationU.S. Ser. No. 07 / 497,098, filed Mar. 20, 1990, now abandoned, which is a continuation of applicationcontinuation-in-part of U.S. <?insert-end id="I...

Claims

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Application Information

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Patent Type & Authority Patents(United States)
IPC IPC(8): C12Q1/68C07H21/00
CPCC12Q1/6827C12Q1/6841C12Q1/6876C12Q1/6879C12Q1/6886C12Q2563/107C12Q2563/131C12Q2525/151
Inventor GRAY, JOE W.PINKEL, DANIELKALLIONIEMI, OLLI-PEKKAKALLIONIEMI, ANNESAKAMOTO, MASARU
Owner RGT UNIV OF CALIFORNIA
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