Oligonucleotide arrays for high resolution HLA typing

• US 20080187912A1
• Filed: 09/07/2006
• Published: 08/07/2008
• Est. Priority Date: 06/17/1999
• Status: Abandoned Application

• Current Assignee: Fred Hutchinson Cancer Research Center (Fred Hutchinson Cancer Research Center|Argus Genetics|Mars), University of Washington
• Original Assignee: Fred Hutchinson Cancer Research Center (Fred Hutchinson Cancer Research Center|Argus Genetics|Mars), University of Washington
• Inventors: Hood, Leroy, Petersdorf, Effie W., Guo, Zhen, Hansen, John A.
• Application Number:
  US11/517,956
• Publication Number:
  US 20080187912A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Arrays of HLA Class I oligonucleotide probes on a solid support are provided, wherein the probes are sufficient to represent at least 80% of the known polymorphisms in exons 2 and 3 of the HLA Class I locus.

Claims

1. A method of HLA-B tissue typing, said method comprising:

(a) amplifying exons 2 and 3 from a genomic sample of tissue using labeled primers and an asymmetric PCR method to form a labeled, single-stranded DNA sample;

(b) contacting said labeled, single-stranded DNA sample with 4 an array of HLA-B oligonucleotide probes under hybridization conditions; and

(c) detecting hybridization for said DNA sample and assigning an HLA-B allele type by analysis of said hybridization.

2. A method in accordance with claim 1, wherein said HLA-B oligonucleotide probes are attached to one or more solid supports selected from the group consisting of plates, slides, capillaries, spheres, particles, gels and films.

3. A method in accordance with claim 1, wherein said HLA-B oligonucleotide probes are HLA-B exon 2 and exon 3 oligonucleotide probes.

4. A method in accordance with claim 1, wherein the HLA-B oligonucleotide probes each have from 17 to 23 nucleotides.

5. A method in accordance with claim 2, wherein the HLA-B oligonucleotide probes are present on said solid support at a surface density of from about 250 to about 450 angstrom²/molecule.

6. A method in accordance with claim 1, wherein the HLA-B oligonucleotide probes are present on said solid support at a surface density of from about 325 to about 375 angstrom²/molecule.

7. A method in accordance with claim 1, wherein said array is on a glass slide or plate.

8. A method in accordance with claim 1, wherein said array is on beads.