DR. HANLEE P JI, M.D.
Osteopathic Medicine at Blake Wilbur Dr, Palo Alto, CA
License number
California A75926
Category
Osteopathic Medicine
Type
Hematology & Oncology
Address
Address
875 Blake Wilbur Dr, Palo Alto, CA 94305
Phone
(650) 498-6000
(650) 721-1503
(650) 721-1503
Organization information
See more information about HANLEE P JI at bizstanding.comHanlee P Ji MD
875 Blake Wilbur Dr, Palo Alto, CA 94304
Categories:
Oncology Physicians & Surgeons
Phone:
(650) 723-7621 (Phone)
Professional information
Targeted Sequencing Library Preparation By Genomic Dna Circularization
US Patent:
2012000, Jan 5, 2012
Filed:
Jun 30, 2011
Appl. No.:
13/174297
Inventors:
Samuel Myllykangas - Espoo, FI
Hanlee P. Ji - Stanford CA, US
Hanlee P. Ji - Stanford CA, US
International Classification:
C12Q 1/68
US Classification:
435 612, 435 61
Abstract:
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.
Capture Probe And Assay For Analysis Of Fragmented Nucleic Acids
US Patent:
2013012, May 16, 2013
Filed:
Nov 15, 2012
Appl. No.:
13/678355
Inventors:
The Board of Trustees of the Leland Stanford Junio - Palo Alto CA, US
Georges Natsoulis - Kensington CA, US
Hanlee P. Ji - Stanford CA, US
Georges Natsoulis - Kensington CA, US
Hanlee P. Ji - Stanford CA, US
Assignee:
The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA
International Classification:
C12Q 1/68
US Classification:
506 2, 506 16
Abstract:
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.
Direct Capture, Amplification And Sequencing Of Target Dna Using Immobilized Primers
US Patent:
2012015, Jun 21, 2012
Filed:
Sep 21, 2011
Appl. No.:
13/239226
Inventors:
Samuel Myllykangas - Espoo, FI
Jason Buenrostro - Redwood City CA, US
Hanlee P. Ji - Stanford CA, US
Jason Buenrostro - Redwood City CA, US
Hanlee P. Ji - Stanford CA, US
International Classification:
C40B 20/00, C40B 40/06, C12P 19/34
US Classification:
506 2, 435 912, 506 16
Abstract:
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.