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Multiplex (+/-) stranded arrays and assays for detecting chromosomal abnormalities associated with cancer and other diseases

A chromosome and array technology, applied in the field of multi-strand arrays, can solve problems such as non-existence of translocations, missed opportunities to detect translocations, and incomplete characterization of translocations

Inactive Publication Date: 2012-08-08
SIGNATURE GENOMICS LAB
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In many cases, existing techniques detect irrelevant ends rather than ends that contribute to cancer or other disease phenotypes
Moreover, existing techniques may lead to incorrect conclusions that translocations do not exist due to incomplete characterization of translocations or missed opportunities to detect translocations

Method used

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  • Multiplex (+/-) stranded arrays and assays for detecting chromosomal abnormalities associated with cancer and other diseases
  • Multiplex (+/-) stranded arrays and assays for detecting chromosomal abnormalities associated with cancer and other diseases
  • Multiplex (+/-) stranded arrays and assays for detecting chromosomal abnormalities associated with cancer and other diseases

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0264] Exemplary (+ / -) CGH method

[0265] figure 1 An overview of the (+ / -) chain array CGH program is shown. The CGH procedure compares a patient genomic DNA sample 100 with a control genomic DNA sample 102 . In this case, the samples compete for the hybridization targets (oligonucleotides) arrayed on the (+ / -) strand CGH microarray 104 . (+ / -) strand CGH microarray 104 includes positive (+) strand oligonucleotide probes 106 and negative (-) strand oligonucleotide probes 108 . Amplification primers 110 and 110' (e.g., the same primers) are added to patient genomic DNA sample 100 and control genomic DNA sample 102 for carefully moderated amplification 112, e.g., linear amplification, to generate , that is, probes for regions where balanced translocations are likely to occur. The primers extend selected chromosomal regions by approximately 10,000 to 20,000 bases each, thereby providing a rich mixture of positive (+) and negative (-) strand DNA hybridization probes represen...

Embodiment 2

[0285] Exemplary (+ / -) CGH Microarrays

[0286] figure 2 Schematically shows in more detail figure 1 Multiplex (+ / -) strand CGH microarrays in 104 . The plus (+) and minus (-) strand oligonucleotides making up the hybridization targets on the array can be arranged in any suitable order or pattern. See, e.g., U.S. Patent Application No. 11 / 057,088, to Shaffer et al., entitled "Method and Apparatuses for Achieving Precision Diagnoses," the contents of which are incorporated by reference incorporated into this article. The (+ / -) strand CGH microarray 104 may be a chimeric density DNA microarray. Each (+ / -) strand CGH microarray 104 is typically both a whole genome array and a custom targeted array. As a gene-wide array, the (+ / -) strand CGH microarray 104 can detect DNA copy number changes that may occur genome-wide. As a custom targeting array, the (+ / -) strand CGH microarray 104 specifically targets loci in many regions of diagnostic interest. The (+ / -) strand CGH micro...

Embodiment 3

[0292] Exemplary Hardware Environment for Implementing (+ / -) CGH Microarrays

[0293] figure 1 Most of the steps in the exemplary processes shown in can be performed directly or indirectly in a computing environment. That is, amplification 112, labeling 122, and quality control 132 are typically computer-controlled, computer-assisted, or computer-monitored. Scanning, analysis, display and reporting of results in array CGH are also mediated by computer equipment.

[0294] image 3 An exemplary computing environment and components of a (+ / -) chain array CGH system are shown. An exemplary hardware component is a microarray scanner 300, as image 3 A placeholder in , typically representing a molecular diagnostic device. Microarray scanner 300 may include a computing device and / or may be communicatively coupled to computing device 302 . The set-up shown is relatively rudimentary compared to the set-up of an actual clinical diagnostic laboratory, but shows some examples betwee...

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Abstract

Multiplex (+ / -) stranded analyses, such as array comparative genomic hybridization (aCGH), are provided for detecting chromosomal rearrangements associated with cancer and other diseases. For example, an illustrative multiplex array for CGH includes discrete plus (+) strand and minus (-) strand DNA probes, complementary to each other but separable on the CGH array. The minus (-) strand DNA probes recover diagnostic information lost to conventional microarrays, since many genes transcribe from the minus (-) strand. In an illustrative system, patient and control DNA samples are prepared for CGH by amplification and labeling using comprehensive primers that generate both plus (+) strands and minus (-) strands of DNA in the samples. The breakpoints of a translocated chromosome may be detected on a multiplex microarray by DNA probes of one polarity, while DNA copy number changes associated with the translocation region may be detected by corresponding DNA probes of the complementary polarity. Related methods for identifying translocation partner genes are also provided.

Description

[0001] Related Applications Cited [0002] The priority basis of this patent application is U.S. Provisional Patent Application No. 61 / 246,077, the applicant of which is McDaniel et al. ", the filing date is September 25, 2009. The entire content of this provisional application is incorporated herein by reference. [0003] Sequence Listing Statement [0004] The Sequence Listing related to this application is provided in text format in lieu of a paper copy and is hereby incorporated by reference into this specification. The name of the text file containing the sequence listing is 220058_412_SEQUENCE_LISTING.txt. The text file size is 131KB, completed on September 27, 2010, and submitted electronically through EFS-Web at the same time as this manual. field of invention [0005] The present invention generally relates to multiple (+ / -) strand arrays, such as (+ / -) strand comparative genomic hybridization arrays, and their use in detecting chromosomal abnormalities, such as d...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68
CPCC12Q1/6827C12Q2565/519C12Q2565/513C12Q2539/101
Inventor 利萨·麦克丹尼尔布莱克·巴立夫罗杰·舒尔茨布赖斯·台布斯巴塞姆·贝贾尼利萨·沙福尔
Owner SIGNATURE GENOMICS LAB
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