Array-based translocation and rearrangement assays

• US 9,932,636 B2
• Filed: 06/26/2015
• Issued: 04/03/2018
• Est. Priority Date: 03/11/2008
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Sparks, Andrew, Shapero, Michael H., Fu, Glenn K., Jones, Keith W.
• Primary Examiner(s): Whisenant, Ethan C
• Application Number:
  US14/751,884
• Publication Number:
  US 20150292019A1
• Time in Patent Office: 1,012 Days
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2539/101 Subtraction analysis
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation

Abstract

Methods for detecting genomic rearrangements are provided. In one embodiment, methods are provided for the use of paired end tags from restriction fragments to detect genomic rearrangements. Sequences from the ends of the fragments are brought together to form ditags and the ditags are detected. Combinations of ditags are detected by an on-chip sequencing strategy that is described herein, using inosine for de novo sequencing of short segments of DNA. In another aspect, translocations are identified by using target specific capture and analysis of the captured products on a tiling array.

Claims

1. A method for analysis of genomic rearrangements in a sample from a genome, the method comprising:

digesting the sample with a selected restriction enzyme to obtain restriction fragments, with each restriction fragment having a first end tag including a predicted sequence of the genome and a second end tag including a predicted sequence of the genome, with the first end tag and the second end tag flanking a central portion;

generating a population of paired-end tags wherein the first end tag and the second end tag of each restriction fragment are directly coupled;

hybridizing the first end tags of the population of paired-end tags to an array having at least 100,000 different probes attached to a substrate; and

,

determining at least a partial sequence of the second end tags in the population of paired-end tags, wherein the presence of a first end tag from a first fragment and a second end tag from a second different fragment indicates a genomic rearrangement.

2. The method of claim 1 wherein the partial sequence is at least 5 bases.

3. The method of claim 1 wherein the partial sequence is 6 bases.

4. The method of claim 1 wherein the partial sequence is at least 6 bases.

5. The method of claim 1 wherein the first end tag and the second end tag are each between 10 and 20 bases in length.

6. The method of claim 1 wherein the first end tag and the second end tag are each between 18 and 27 bases in length.

7. The method of claim 1 wherein for each base to be sequenced in the second end tag the array includes a probe having a complement of the first end tag and between 0 and 5 inosines.

8. A method for detecting rearrangements in a genome, the method comprising:

(a) fragmenting a genomic sample with a restriction enzyme to obtain restriction fragments each having a first terminal sequence of the genome and a second terminal sequence of the genome, said first and second terminal sequences being immediately adjacent to the cleavage site of the restriction enzyme;

(b) generating a population of paired-end sequences wherein the first terminal sequence and the second terminal sequence are directly coupled;

(c) analyzing the first terminal sequences of the population of paired-end sequences by hybridization to an array having at least 100,000 different support-bound probes wherein each probe is perfectly complementary to a different first terminal sequence and determining at least 5 bases of the sequence adjacent to the first terminal sequence to identify a plurality of combinations of first and second terminal sequences present in the same fragment; and

(d) comparing the results of (c) to predetermined combinations of first and second terminal sequences, wherein the predetermined combinations correspond to an absence of rearrangements, and wherein the combinations from (c) that do not match the predetermined combinations are indicative of genomic rearrangements.

9. The method of claim 8 wherein the expected combinations used in step (d) are from a database of the first terminal sequence and the second terminal sequence combinations predicted from in silico digestion of a genome.