Kandaswamy Kizhsevur Vijayan

US Patent:

20110171634, Jul 14, 2011

Filed:

Jun 30, 2009

Appl. No.:

13/001697

Inventors:

Ming Xiao - Huntingdon Valley PA, US
Parikshit A. Deshpande - Princeton NJ, US
Han Cao - Philadelphia PA, US
Michael Austin - Philadelphia PA, US
Kandaswamy Vijayan - San Diego CA, US
Alexey Y. Sharonov - Hamden CT, US
Michael Boyce-Jacino - Titusville NJ, US

Assignee:

Bionanomatrix, Inc. - Philadelphia PA

International Classification:

C12Q 1/68
C07H 1/00
G01N 33/53
C07K 1/107
C12N 9/96
G01N 30/96
B82Y 15/00

US Classification:

435 61, 536 2532, 436501, 530322, 530395, 435188, 5303911, 422 69, 977762, 977774, 977902, 977896

Abstract:

Provided are methods and devices for single-molecule genomic analysis. In one embodiment, the methods entail processing a double-stranded nucleic acid and characterizing said nucleic acid. These methods are useful in, e.g., determining structural variations and copy number variations between individuals.

US Patent:

20130116153, May 9, 2013

Filed:

Oct 26, 2012

Appl. No.:

13/661524

Inventors:

Kevin L. Gunderson - Encinitas CA, US
Shengrong Lin - Fremont CA, US
Maria Candelaria Rogert Bacigalupo - Cardiff by the Sea CA, US
Kandaswamy Vijayan - San Diego CA, US
Bala Murali Venkatesan - San Diego CA, US
James Tsay - San Diego CA, US
John M. Beierle - Laguna Niguel CA, US
Lorenzo Berti - San Diego CA, US
Sang Ryul Park - San Diego CA, US

Assignee:

ILLUMINA, INC. - San Diego CA

International Classification:

B01J 19/00

US Classification:

506 16, 506 30, 506 26

Abstract:

A microarray is designed capture one or more molecules of interest at each of a plurality of sites on a substrate. The sites comprise base pads, such as polymer base pads, that promote the attachment of the molecules at the sites. The microarray may be made by one or more patterning techniques to create a layout of base pads in a desired pattern. Further, the microarrays may include features to encourage clonality at the sites.

US Patent:

20130338042, Dec 19, 2013

Filed:

Mar 1, 2013

Appl. No.:

13/783043

Inventors:

Jonathan Mark Boutell - Essex, GB
Kathryn M. Stephens - Poway CA, US
Mostafa Ronaghi - San Diego CA, US
Kevin Gunderson - Encinitas CA, US
Bala Murali Venkatesan - San Diego CA, US
M. Shane Bowen - La Jolla CA, US
Kandaswamy Vijayan - San Diego CA, US

Assignee:

ILLUMINA, INC. - San Diego CA

International Classification:

B01J 19/00

US Classification:

506 26

Abstract:

A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

US Patent:

20220298553, Sep 22, 2022

Filed:

Dec 29, 2021

Appl. No.:

17/564592

Inventors:

- San Diego CA, US
Devon CAYER - Del Mar CA, US
Richard LECOULTRE - San Diego CA, US
Joseph ROKICKI - San Diego CA, US
Kerry WILSON - La Jolla CA, US
Eugene TU - San Diego CA, US
Kandaswamy VIJAYAN - San Diego CA, US

Assignee:

Omniome, Inc. - San Diego CA

International Classification:

C12Q 1/6816
C12Q 1/6869
C12Q 1/6874
C12Q 1/6827

Abstract:

Method of identifying a cognate nucleotide (i.e., the “next correct nucleotide”) for a primed template nucleic acid molecule. In some embodiments, an ordered or random array of primed target nucleic acids characterized by different cognate nucleotides can be evaluated using a single imaging step to identify different cognate nucleotides for a collection of different primed template nucleic acid molecules. An optional incorporation step can follow the identifying step. A polymerase different from the ones used in the binding and examination steps can be used to incorporate a nucleotide, such as a reversible terminator nucleotide, preliminary to identification of the next cognate nucleotide.

US Patent:

20220243261, Aug 4, 2022

Filed:

Jan 13, 2022

Appl. No.:

17/575279

Inventors:

- San Diego CA, US
Jonathan Mark Boutell - Nr Saffron Walden, GB
Kathryn M. Stephens - Poway CA, US
Mostafa Ronaghi - San Diego CA, US
Kevin L. Gunderson - Encinitas CA, US
Bala Murali Venkatesan - San Diego CA, US
M. Shane Bowen - La Jolla CA, US
Kandaswamy Vijayan - San Diego CA, US

Assignee:

Illumina, Inc. - San Diego CA

International Classification:

C12Q 1/6848
B01J 19/00
C12Q 1/6844
C12Q 1/6874

Abstract:

A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.

US Patent:

20220203357, Jun 30, 2022

Filed:

Mar 18, 2022

Appl. No.:

17/699001

Inventors:

- San Diego CA, US
Jesse Lu - San Diego CA, US
Alex Price - San Diego CA, US
Pengyu Yang - San Diego CA, US
Kandaswamy Vijayan - San Diego CA, US

International Classification:

B01L 3/00
C12M 1/32

Abstract:

Disclosed is an assay device comprising a high density of wells aligned thereon.

US Patent:

20210340612, Nov 4, 2021

Filed:

Mar 3, 2021

Appl. No.:

17/190894

Inventors:

- San Diego CA, US
Joseph ROKICKI - San Diego CA, US
Keunho AHN - San Diego CA, US
Brittany Ann ROHRMAN - San Diego CA, US
Michael NGUYEN - San Diego CA, US
Kandaswamy VIJAYAN - San Diego CA, US

Assignee:

Omniome, Inc. - San Diego CA

International Classification:

C12Q 1/6869
C12Q 1/6806
C07H 21/02
C07H 99/00
C07H 21/04
C12Q 1/6874

Abstract:

Method and composition for identifying cognate nucleotides in a Sequencing By Binding™ procedure, wherein one or more labeled nucleotides are detected in ternary complexes but never incorporated. Labeled nucleotides can be incorporable nucleotides that contact preformed blocked primed template nucleic acids. Alternatively, labeled nucleotides are labeled non-incorporable nucleotides. Labeled nucleotides, including labeled non-incorporable nucleotides, can be detected in ternary complexes in the same reaction mixture that incorporates a reversible terminator nucleotide to create a blocked primed template nucleic acid. Detection of ternary complexes can take place in the presence of a catalytic metal ion.

US Patent:

20210108258, Apr 15, 2021

Filed:

Dec 7, 2020

Appl. No.:

17/113180

Inventors:

- San Diego CA, US
Kevin L. Gunderson - Encinitas CA, US
Shengrong Lin - Fremont CA, US
Maria Candelaria Rogert Bacigalupo - Cardiff by the Sea CA, US
Kandaswamy Vijayan - San Diego CA, US
Bala Murali Venkatesan - San Francisco CA, US
James Tsay - San Diego CA, US
John M. Beierle - Carlsbad CA, US
Lorenzo Berti - San Diego CA, US
Sang Ryul Park - San Diego CA, US

International Classification:

C12Q 1/6844
C40B 50/18
C12Q 1/686
B01J 19/00

Abstract:

A method includes forming a patterned substrate including a plurality of base pads, using a nano-imprint lithography process. A capture substance is attached to each of the plurality of base pads, optionally through a linker, the capture substance being adapted to promote capture of a target molecule.