Byoungsok Jung

US Patent:

20060042948, Mar 2, 2006

Filed:

Sep 2, 2004

Appl. No.:

10/932078

Inventors:

Juan Santiago - Fremont CA, US
Byoungsok Jung - Mountain View CA, US
Rajiv Bharadwaj - Mountain View CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

C07K 1/26
G01N 27/447

US Classification:

204450000, 204600000

Abstract:

A capillary electrophoresis device and separation protocol uses a hydraulic resistance-providing structure (HRPS) in the main separation channel to separate the divide the main separate channel into an upstream portion and a downstream portion. The HRPS may take the form of a porous plug, or a solid plug provided with at least one shallow channel. A sample separates and migrates through the porous structure or the shallow channel, upon application of a voltage difference between the upstream and downstream sides. Among other things, the HRPS helps reduce electrokinetic flow in the presence of conductivity gradients and facilitates robust, high-gradient on-chip field amplified sample stacking. The HRPS also enables the use of a pressure-injection scheme for the introduction of a high conductivity gradient in a separation channel and thereby avoids flow instabilities associated with high conductivity gradient electrokinetics. The approach also allows for the suppression of electroosmotic flow (EOF) and benefits from the associated minimization of sample dispersion caused by non-uniform EOF mobilities. An injection procedure employing a single pressure-flow high-conductivity buffer injection step followed by standard high voltage control of electrophoretic fluxes of sample, may be employed.

US Patent:

20110036718, Feb 17, 2011

Filed:

Aug 17, 2009

Appl. No.:

12/542215

Inventors:

Byoungsok Jung - San Jose CA, US
Kevin Ness - San Francisco CA, US
Klint A. Rose - Alviso CA, US

International Classification:

G01N 27/447

US Classification:

204549

Abstract:

According to one embodiment, a method includes co-feeding fluids comprising a leading electrolyte, a trailing electrolyte, and at least one of DNA and RNA to a channel, and applying an electric field to the fluids in a direction perpendicular to an axis of the channel for inducing transverse isotachophoresis. In another embodiment, a method includes co-feeding fluids to a channel. The fluids include a leading electrolyte, a trailing electrolyte, biological objects, at least one of DNA and RNA, and a spacer electrolyte having an electrophoretic mobility that is between an electrophoretic mobility of at least some of the biological objects and an electrophoretic mobility of the at least one of the DNA and the RNA. The method also includes applying an electric field to the fluids in a direction perpendicular to an axis of the channel for inducing transverse isotachophoresis. Other methods of isotachophoresis are disclosed in addition to these.

US Patent:

20120228141, Sep 13, 2012

Filed:

Mar 6, 2012

Appl. No.:

13/413161

Inventors:

Byoungsok Jung - San Jose CA, US
Klint A. Rose - Alviso CA, US
Maxim Shusteff - Oakland CA, US
Alexandre Persat - Palo Alto CA, US
Juan Santiago - Stanford CA, US

International Classification:

C25B 9/00
B01D 43/00

US Classification:

204456, 204600, 204606, 204450

Abstract:

The present invention provides a mechanism for separating or isolating charged particles under the influence of an electric field without metal electrodes being in direct contact with the sample solution. The metal electrodes normally in contact with the sample are replaced with high conductivity fluid electrodes situated parallel and adjacent to the sample. When the fluid electrodes transmit the electric field across the sample, particles within the sample migrate according to their electrophoretic mobility.

US Patent:

20130043170, Feb 21, 2013

Filed:

Aug 10, 2012

Appl. No.:

13/571640

Inventors:

Klint A. Rose - Alviso CA, US
Karl A. Fisher - Brentwood CA, US
Douglas A. Wajda - Urbana IL, US
Christopher Bailey - Pleasanton CA, US
Dietrich Dehlinger - Dublin CA, US
Maxim Shusteff - Oakland CA, US
Byoungsok Jung - Palo Alto CA, US
Kevin D. Ness - Pleasanton CA, US

International Classification:

B03B 5/60

US Classification:

209659

Abstract:

An ultrasonic microfluidic system includes a separation channel for conveying a sample fluid containing small particles and large particles, flowing substantially parallel, adjacent to a recovery fluid, with which it is in contact. An acoustic transducer produces an ultrasound standing wave, that generates a pressure field having at least one node of minimum pressure amplitude. An acoustic extension structure is located proximate to said separation channel for positioning said acoustic node off center in said acoustic area and concentrating the large particles in said recovery fluid stream.

US Patent:

8414754, Apr 9, 2013

Filed:

May 30, 2007

Appl. No.:

11/755449

Inventors:

Juan G. Santiago - Stanford CA, US
Byoungsok Jung - Stanford CA, US
Rajiv Bharadwaj - Mountain View CA, US
Tarun Kumar Khurana - Stanford CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

B01D 57/02
G01N 27/447
G01N 27/453

US Classification:

204549, 204645

Abstract:

Analysis of samples is facilitated. According to an example embodiment, an electrophoresis approach involves electrophoretically stacking and/or separating a sample or samples. An electrolyte and a mixture of one or more samples with another electrolyte are added to a microchannel or capillary. An electric field is applied to stack (and, in some applications, further separate) the one or more samples. Generally, the electric field and electrolyte are used to facilitate isotachophoretic (ITP) stacking. In some embodiments, a further electric field is applied and used with the electrolyte to facilitate subsequent capillary electrophoresis (CE).

US Patent:

20220301654, Sep 22, 2022

Filed:

Aug 28, 2020

Appl. No.:

17/638904

Inventors:

- Menlo Park CA, US
Anton VALOUEV - Palo Alto CA, US
David BURKHARDT - San Francisco CA, US
Nathan HUNKAPILLER - Belmont CA, US
Eric FUNG - Los Altos CA, US
Xiaoji CHEN - Newark CA, US
Byoungsok JUNG - Atherton CA, US

International Classification:

G16B 20/20
G16B 40/20
C12Q 1/6886
G16H 10/40
G16H 50/20
G16H 20/10

Abstract:

Methods and systems for determining a subject's likelihood of responding to a treatment by assessing the subject's cell-free DNA (cfDNA) sample include receiving sequence data gathered from sequencing the cfDNA sample, generating a feature matrix of values that correspond to synonymous and nonsynonymous mutations detected in the sequence data, and predicting, based on analysis of the feature matrix at a TMB prediction model, a tumor mutational burden (TMB) for a tissue of interest at the subject. The predicted TMB is evaluated to determine whether a set of criteria indicating a likely response to treatment is met. The set of criteria can include criterion(s) that are met when the predicted TMB is high, when the predicted TMB corresponds to a predicted tumoral heterogeneity indicative of homogeneous tissue, when the predicted TMB corresponds to a tumor fraction indicative of a positive responder, or any combination thereof.

US Patent:

20210108262, Apr 15, 2021

Filed:

Oct 21, 2020

Appl. No.:

17/076715

Inventors:

- San Diego CA, US
Byoungsok Jung - Atherton CA, US
Emrah Kostem - Redwood City CA, US
Alex Aravanis - San Mateo CA, US
Alex So - San Diego CA, US
Xuyu Cai - Natick MA, US
Zhihong Zhang - San Diego CA, US
Frank J. Steemers - Encinitas CA, US

International Classification:

C12Q 1/6869
G16B 30/00
C12Q 1/6806
C12N 15/10
C12Q 1/6855

Abstract:

The disclosed embodiments concern methods, apparatus, systems and computer program products for determining sequences of interest using unique molecular index (UMI) sequences that are uniquely associable with individual polynucleotide fragments, including sequences with low allele frequencies and long sequence length. In some implementations, the UMIs include both physical UMIs and virtual UMIs. In some implementations, the unique molecular index sequences include non-random sequences. System, apparatus, and computer program products are also provided for determining a sequence of interest implementing the methods disclosed.

US Patent:

20190185930, Jun 20, 2019

Filed:

Dec 20, 2018

Appl. No.:

16/228466

Inventors:

- Menlo Park CA, US
Nathan Hunkapiller - Belmont CA, US
Nicholas Eattock - Fremont CA, US
Byoungsok Jung - Atherton CA, US

International Classification:

C12Q 1/6874

Abstract:

Methods for preparing sequencing libraries from a DNA-containing test sample, as well as methods for correcting sequencing-derived errors in sequence reads, and methods for identifying rare variants in a test sample, are provided.