Zhen Guo

US Patent:

7300755, Nov 27, 2007

Filed:

May 12, 2004

Appl. No.:

10/843985

Inventors:

Effie W. Petersdorf - Seattle WA, US
Zhen Guo - Bellevue WA, US
Leroy Hood - Seattle WA, US

Assignee:

Fred Hutchinson Cancer Research Center - Seattle WA
Institute for Systems Biology - Seattle WA

International Classification:

C12Q 1/68
C07H 21/02
C07H 21/04

US Classification:

435 6, 536 231, 536 243

Abstract:

The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e. g. , oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb). Separation of the haplotypes of large genomic DNA fragments allows for linkage analysis of other HLA alleles and polymorphisms, microsatellite, SNPs, and the like across a large span of the HLA region, including HLA-A, -B, -C, and HLA-DRB1 regions.

US Patent:

7615350, Nov 10, 2009

Filed:

Oct 19, 2007

Appl. No.:

11/874407

Inventors:

Effie W. Petersdorf - Seattle WA, US
Zhen Guo - Bellevue WA, US
Leroy Hood - Seattle WA, US

Assignee:

Fred Hutchinson Cancer Research Center - Seattle WA
Institute for Systems Biology - Seattle WA

International Classification:

C12Q 1/68
C07H 21/02
C07H 21/04

US Classification:

435 6, 536 231, 536 243

Abstract:

The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e. g. , oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb). Separation of the haplotypes of large genomic DNA fragments allows for linkage analysis of other HLA alleles and polymorphisms, microsatellite, SNPs, and the like across a large span of the HLA region, including HLA-A, -B, -C, and HLA-DRB1 regions.

US Patent:

7972791, Jul 5, 2011

Filed:

Sep 29, 2009

Appl. No.:

12/569044

Inventors:

Effie W. Petersdorf - Seattle WA, US
Zhen Guo - Bellevue WA, US
Leroy Hood - Seattle WA, US

Assignee:

Fred Hutchinson Cancer Research Center - Seattle WA
Institute for Systems Biology - Seattle WA

International Classification:

C12Q 1/68
C07H 21/02
C07H 21/04

US Classification:

435 6, 536 231, 536 243

Abstract:

The present invention provides a novel method for specifically isolating and separating large segments of genomic DNA that can subsequently be used to determine a genomic haplotype. The invention relies on using a solid phase having a flat surface arrayed with oligonucleotides designed to specifically hybridize to each particular haplotype of an individual sample, e. g. , oligonucleotides designed to specifically hybridize with each of the two HLA-B haplotypes, HLA-A, HLA-C, HLA-DR, HLA-DQ, and the like. The genomic DNA is contacted and hybridized to the arrayed oligonucleotides to form a genomic DNA/oligonucleotide complex. The excess genomic DNA is washed away and the haplotype separated genomic DNA is denatured from the oligonucleotide probe and collected. The method of the present invention allows for the separation of genomic DNA fragments of between approximately 2 to about 4 megabases (Mb). Separation of the haplotypes of large genomic DNA fragments allows for linkage analysis of other HLA alleles and polymorphisms, microsatellite, SNPs, and the like across a large span of the HLA region, including HLA-A, -B, -C, and HLA-DRB1 regions.

US Patent:

20080187912, Aug 7, 2008

Filed:

Sep 7, 2006

Appl. No.:

11/517956

Inventors:

Effie W. Petersdorf - Seattle WA, US
Zhen Guo - Bellevue WA, US
John A. Hansen - Mercer Island WA, US
Leroy Hood - Seattle WA, US

Assignee:

Fred Hutchinson Cancer Research Center - Seattle WA
The University of Washington Office of Technology Transfer - Seattle WA

International Classification:

C12Q 1/68

US Classification:

435 6

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.

US Patent:

20090099035, Apr 16, 2009

Filed:

Nov 25, 2008

Appl. No.:

12/277511

Inventors:

Effie W. Petersdorf - Seattle WA, US
Zhen Guo - Bellevue WA, US
John A. Hansen - Mercer Island WA, US
Leroy Hood - Seattle WA, US

Assignee:

Fred Hutchinson Cancer Research Center - Seattle WA
The University of Washington - Seattle WA

International Classification:

C40B 30/04
C40B 40/08
C40B 50/18

US Classification:

506 9, 506 17, 506 32

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.

US Patent:

62809482, Aug 28, 2001

Filed:

Sep 3, 1999

Appl. No.:

9/380786

Inventors:

Richard A. Guilfoyle - Germantown MD
Zhen Guo - Bellevue WA

Assignee:

Wisconsin Alumni Research Foundation - Madison WI

International Classification:

C12Q 168
C12Q 170
C12P 1934
C07H 2104

US Classification:

435 6

Abstract:

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known. Profiling methods and other methods for characterizing polynucleotides are presented.

US Patent:

62289993, May 8, 2001

Filed:

May 7, 1999

Appl. No.:

9/307392

Inventors:

Richard A. Guilfoyle - Madison WI
Zhen Guo - Bellevue WA

Assignee:

Wisconsin Alumni Research Foundation - Madison WI

International Classification:

C07H 2100

US Classification:

536 221

Abstract:

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.

US Patent:

59940689, Nov 30, 1999

Filed:

Mar 11, 1997

Appl. No.:

8/815448

Inventors:

Richard A. Guilfoyle - Madison WI
Zhen Guo - Bellevue WA

Assignee:

Wisconsin Alumni Research Foundation - Madison WI

International Classification:

C12Q 168

US Classification:

435 6

Abstract:

A restriction site indexing method for selectively amplifying any fragment generated by a Class II restriction enzyme includes adaptors specific to fragment ends containing adaptor indexing sequences complementary to fragment indexing sequences near the termini of fragments generated by Class II enzyme cleavage. A method for combinatorial indexing facilitates amplification of restriction fragments whose sequence is not known.