Hanlee P Ji

20120157322, Jun 21, 2012

Sep 21, 2011

13/239226

Samuel Myllykangas - Espoo, FI
Jason Buenrostro - Redwood City CA, US
Hanlee P. Ji - Stanford CA, US

C40B 20/00
C40B 40/06
C12P 19/34

506 2, 435 912, 506 16

Certain embodiments provide a method for capturing a genomic fragment. The method may comprise: obtaining a substrate comprising a first population of surface-bound oligonucleotides and a second population of surface-bound oligonucleotides; hybridizing a first member of the first population of surface-bound oligonucleotides to a selection oligonucleotide comprising a region that hybridizes with the first member and a region that contains a genomic sequence; extending the first member of the first population of surface-bound oligonucleotides to produce a support-bound selection primer that comprises a sequence that is complementary to the genomic sequence; hybridizing the support-bound selection primer to a nucleic acid fragment comprising the genomic sequence; extending the support-bound selection primer to produce an extension product that contains a sequence that flanks the genomic sequence, e.g., in a genome; and amplifying the extension product on the substrate.

20130123117, May 16, 2013

Nov 15, 2012

13/678355

The Board of Trustees of the Leland Stanford Junio - Palo Alto CA, US
Georges Natsoulis - Kensington CA, US
Hanlee P. Ji - Stanford CA, US

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

C12Q 1/68

506 2, 506 16

Disclosed is an efficient and scalable method for targeted resequencing and variant identification of nucleic acids such as genomic DNA found in single stranded, fragmented form, such as in a clinical sample of formalin-fixed, paraffin-embedded (FFPE) tissue. The method uses a large number of capture probes mixed with the sample in the presence of a 5′ to 3′ exonuclease, a 3′ to 5′ exonuclease, a ligase, and a universal amplification oligonucleotide that hybridizes to the various capture probes. The nucleases act on ssDNA, not dsDNA. A single stranded circle is formed by the ligase, and is then amplified to produce a population (library) of double stranded linear DNA molecules that are suitable for sequencing. It is shown that the library produces a high degree of fidelity to the original sample, and predictable base changes are shown.

20120003657, Jan 5, 2012

Jun 30, 2011

13/174297

Samuel Myllykangas - Espoo, FI
Hanlee P. Ji - Stanford CA, US

C12Q 1/68

435 612, 435 61

Certain embodiments provide a method of sequencing that comprises: a) contacting, under hybridization conditions, a target genomic fragment with: i. a vector oligonucleotide comprising a binding site for a sequencing primer; and ii. a splint oligonucleotide that hybridizes to the vector oligonucleotide and to the nucleotide sequences at the ends of a target genomic fragment, to produce a circular nucleic acid; b) contacting the circular nucleic acid with a ligase, thereby ligating the ends of the vector oligonucleotide to the ends of the target genomic fragment to produce a circular DNA molecule; c) separating the circular DNA molecule from the splint oligonucleotide; and d) sequencing the target genomic fragment of the circular DNA molecule using the first sequencing primer.

20220316015, Oct 6, 2022

Dec 17, 2020

17/634223

- Stanford CA, US
Hanlee P. Ji - Stanford CA, US

C12Q 1/6886
C12N 15/10
C12Q 1/6869

A method for determining if a tumor has a mutation in a microsatellite is provided. In some embodiments, the method may comprise: (a) isolating genomic DNA from a tumor sample and a non-tumor sample from the same patient to produce: i. a sample of tumor DNA and ii. a sample of non-tumor DNA, respectively, (b) without pre-amplifying the tumor or non-tumor DNA, sequencing a plurality of microsatellite loci from both the tumor and non-tumor DNA using OS-seq to provide sequence reads, wherein the sequenced microsatellite loci comprise mononucleotide, dinucleotide, trinucleotide and tetranucleotide microsatellites loci, and (c) comparing the results.

20210048426, Feb 18, 2021

Apr 2, 2020

16/838882

- Stanford CA, US
Henrik H.J. PERSSON - Stanford CA, US
Billy Tsz Cheong LAU - Stanford CA, US
Hanlee P. JI - Stanford CA, US
Robert W. DUTTON - Stanford CA, US
Yang LIU - Stanford CA, US
Ronald W. DAVIS - Stanford CA, US

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

G01N 33/487
C12Q 1/6869
C12Q 1/6825
G01N 27/447

The present disclosure provides a sensor including a pore and an applied electric field that is capable of detecting analytes such as nucleic acids. In accordance with various embodiments, the sensor comprises a fluidic chamber having electrically opposing portions with a membrane between, the membrane providing a pore suitable for the passage of an electrolyte between the electrically opposing portions of the fluidic chamber, and having at least one charged analyte tethered in proximity to the pore, a first circuit configured to apply an electric field capable of passing the electrolyte through the pore and pulling the at least one charged analyte into the pore, and a second circuit configured to measure a signal indicative of the charge of the at least one charged analyte. Also provided are methods for using the sensor, for example, to sequence a nucleic acid molecule.

20190024141, Jan 24, 2019

Aug 7, 2018

16/057670

- Stanford CA, US
Jason D. Buenrostro - Redwood City CA, US
Hanlee P. Ji - Stanford CA, US

C12Q 1/6806
C12Q 1/6837
C12Q 1/6853
C12Q 1/6874
C12Q 1/6869

Certain embodiments provide a method for capturing a genomic fragment. The method may comprise: obtaining a substrate comprising a first population of surface-bound oligonucleotides and a second population of surface-bound oligonucleotides; hybridizing a first member of the first population of surface-bound oligonucleotides to a selection oligonucleotide comprising a region that hybridizes with the first member and a region that contains a genomic sequence; extending the first member of the first population of surface-bound oligonucleotides to produce a support-bound selection primer that comprises a sequence that is complementary to the genomic sequence; hybridizing the support-bound selection primer to a nucleic acid fragment comprising the genomic sequence; extending the support-bound selection primer to produce an extension product that contains a sequence that flanks the genomic sequence, e.g., in a genome; and amplifying the extension product on the substrate.

20180100145, Apr 12, 2018

Apr 13, 2016

15/560136

- Stanford CA, US
Hanlee P. Ji - Stanford CA, US

C12N 15/10
C12Q 1/6806
C12Q 1/6855

A population of nucleic acid adaptors is provided. In some embodiments, the population contains at least 50,000 different molecular barcode sequences, where the barcode sequences are double-stranded and at least 90% of the barcode sequences have an edit distance of at least 2. In certain cases, the adaptor may have an end in which the top and bottom strands are not complementary (i.e., may be in the form of a Y-adaptor). In some embodiments and depending on the how the adaptor is going to be employed, the other end of the adaptor may have a ligatable end or may be a transposon end sequence.

20170097332, Apr 6, 2017

Dec 16, 2016

15/382364

- Stanford CA, US
Henrik H.J. PERSSON - Stanford CA, US
Billy Tsz Cheong LAU - Stanford CA, US
Hanlee P. JI - Stanford CA, US
Robert W. DUTTON - Stanford CA, US
Yang LIU - Stanford CA, US
Ronald W. DAVIS - Stanford CA, US

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

G01N 33/487
C12Q 1/68
G01N 27/447

The present disclosure provides a sensor including a pore and an applied electric field that is capable of detecting analytes such as nucleic acids. In accordance with various embodiments, the sensor comprises a fluidic chamber having electrically opposing portions with a membrane between, the membrane providing a pore suitable for the passage of an electrolyte between the electrically opposing portions of the fluidic chamber, and having at least one charged analyte tethered in proximity to the pore, a first circuit configured to apply an electric field capable of passing the electrolyte through the pore and pulling the at least one charged analyte into the pore, and a second circuit configured to measure a signal indicative of the charge of the at least one charged analyte. Also provided are methods for using the sensor, for example, to sequence a nucleic acid molecule.