cancer genome sequencing, cancer genome analysis, cancer genetics, mutations, targeted therapies, tumor sequencing, inherited cancer, personalized medicine
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Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine | dna-discovery.stanford.edu Reviews
https://dna-discovery.stanford.edu
cancer genome sequencing, cancer genome analysis, cancer genetics, mutations, targeted therapies, tumor sequencing, inherited cancer, personalized medicine
dna-discovery.stanford.edu
Personal Cancer Genome Initiative - Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine
http://dna-discovery.stanford.edu/initiatives/personal-cancer-genome-initiative.html
Ji Research Group –. In The Division of Oncology. Personal Cancer Genome Initiative. Novel DNA Sequencing Technology Development. New Approaches in Computational and Statistical Analysis. Our research program is focused on:. Development of novel approaches for analyzing cancer genomes. Discovery and validation of genetic signatures portending prognosis and therapeutic prediction for individuals with cancer. The genetic analysis of complete cancer genome sequences derived from inherited cancer. How you ca...
Software - Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine
http://dna-discovery.stanford.edu/software
Ji Research Group –. In The Division of Oncology. A standalone algorithm for ultrasensitive rare single nucleotide variant detection using next-generation sequencing. The RVD program takes BAM files of deep sequencing reads in as input. Using a Beta-Binomial model, the algorithm estimates the error rate at each base position in the reference sequence. User Guide and Downloads ». User Guide and Downloads ». SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community&#...
People - Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine
http://dna-discovery.stanford.edu/people
Ji Research Group –. In The Division of Oncology. Director, Ji Research Group. Associate Professor - Division of Oncology, Stanford University School of Medicine, Dept. of Medicine. Senior Associate Director - Stanford Genome Technology Center. Raquo; email [genomics ji]. MD/PhD. Oncological Science. Director of Cancer Genomics, Intermountain Healthcare. Director of Translational Cancer Research in Ji Group / Intermountain Healthcare Cancer Initiative. Raquo; email [lnadauld]. Raquo; email [nandor].
Completed Projects - Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine
http://dna-discovery.stanford.edu/projects/completed-projects
Ji Research Group –. In The Division of Oncology. Raquo; Targeted Genomic Circularization for Identifying Genetic Variants. A major focus of our research group has been developing numerous approaches to enable mutation discovery from any given region of the human genome. We were one of the first groups to demonstrate the integration of a novel molecular assay with next generation sequencing technology for the discovery of somatic mutations and germline polymorphisms. Read More ». What impedes the success...
Publications - Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine
http://dna-discovery.stanford.edu/publications
Ji Research Group –. In The Division of Oncology. Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer; Lincoln D Nadauld, Sarah Garcia, Georges Natsoulis, John M Bell, Laura Miotke, Erik S Hopmans, Hanlee P Ji et al,; Genome Biology, August 2014; 15:428. [ Genome Biology. Detecting mutations in mixed sample sequencing data using empirical Bayes; Muralidharan O, Natsoulis G, Bell J, Ji HP, Zhang N; Annals of Applied Statistics, 2013; 6(3), 1047-10...
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Stanford OligoGenome - Statistics
http://oligogenome.stanford.edu/faq_statistics
Stanford Human Oligo Genome Project. Ji Research Group - Stanford Genome Technology Center. View in UCSC Browser. The Human OligoGenome Resource. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. Human genome build: 37.1. DbSNP build id: 131. Whole Genome In Silico. Total Number of Oligos. 2,160,412,134. 1,977,714,818. 1,759,938,713. 1,938,321,961. 2,852,444,206. Percent of Genome Covered. Percent of Oligos with U0 1. Percent of Oligos with P 0. Percent of CCDS Covered.
Stanford OligoExome - Annotations
http://oligoexome.stanford.edu/v8faq/annotations
Stanford Human Oligo Exome Project. Ji Research Group - Stanford Genome Technology Center. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. Table S5: Novel SNVs. Table S8: Capture Oligos. Human genome build: 36.3. DbSNP build id: 129. Stanford Genome Technology Center. Oligos are annotated (in annotation codes and other annotations fields) as follows:. Both 20b segments at the end of the oligo have 1 perfect match within the genome AND match in opposite orientation AND at.
Publications - Genome Portal - Ji Research Group - Stanford University
http://genomeportal.stanford.edu/publications.html
Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. The Human OligoGenome Resource. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis. The Human OligoGenome Resource. Stanford Genome Tech Center.
Stanford OligoExome - Table S5
http://oligoexome.stanford.edu/v8faq/table_s5
Stanford Human Oligo Exome Project. Ji Research Group - Stanford Genome Technology Center. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. Table S5: Novel SNVs. Table S8: Capture Oligos. Human genome build: 36.3. DbSNP build id: 129. Stanford Genome Technology Center. Table S5: Novel SNVs. Capture assay 3 -replicate 1. Capture assay 3 -replicate 1. Capture assay 3 -replicate 1. Capture assay 3 -replicate 1. Capture assay 3 -replicate 1. Capture assay 3 -replicate 1. Captu...
Stanford OligoExome - Forgot
http://oligoexome.stanford.edu/forgot
Stanford Human Oligo Exome Project. Ji Research Group - Stanford Genome Technology Center. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. Table S5: Novel SNVs. Table S8: Capture Oligos. Human genome build: 36.3. DbSNP build id: 129. Stanford Genome Technology Center. Request link to reset password. Stanford Genome Tech Center. Website provided by the Ji Research Group. School of Medicine and Genome Technology Center at Stanford University. National Institutes of Health.
Stanford OligoExome - Figure S1
http://oligoexome.stanford.edu/v8faq/figure_s1
Stanford Human Oligo Exome Project. Ji Research Group - Stanford Genome Technology Center. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. Table S5: Novel SNVs. Table S8: Capture Oligos. Human genome build: 36.3. DbSNP build id: 129. Stanford Genome Technology Center. Stanford Genome Tech Center. Website provided by the Ji Research Group. School of Medicine and Genome Technology Center at Stanford University. National Institutes of Health. Doris Duke Charitable Foundation.
About - Genome Portal - Ji Research Group - Stanford University
http://genomeportal.stanford.edu/about.html
Systematic genomic identification of colorectal cancer genes delineating advanced from early clinical stage and metastasis. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. The Human OligoGenome Resource. A Flexible Approach for Highly Multiplexed Candidate Gene Targeted Resequencing. What is Genome Portal? We encourage you to explore our projects! The websites are developed and maintained by members of Ji Research Group, part of Stanford Genome Technology Center.
Cancer Genome Atlas Analysis of Colorectal Cancer - Ji Research Group - Stanford University
http://genomeportal.stanford.edu/tcga-crc
Stanford - Cancer Genome Atlas Analysis of Colorectal Cancer. Systematic identification of colorectal cancer genes delineating clinical stage and metastasis. We compiled multiple genomic data types (mutations, copy number alterations, gene expression and methylation status) as well as clinical meta-data from The Cancer Genome Atlas (TCGA). Our analysis of multiple genomic features identifies a number of colorectal cancer genes associated with advanced clinical stage disease and metastasis.
The Stanford-Cancer Genome Atlas Portal
http://genomeportal.stanford.edu/pan-tcga
The Cancer Genome Atlas Clinical Explorer: An Interface for Identifying Clinical Genomic Driver Associations. What Genes are associated with a Clinical Parameter of your interest? These genes are identified by Elastic-net analysis. Check if Gene/Protein/miR of your interest is associated with Clinical Parameters. Query For Outcome Summary. What Cancer Type are you interested in? HNSC-Head and Neck squamous cell carcinoma. KICH-Chromophobe renal cell carcinoma. KIRC-Kidney renal clear cell carcinoma.
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Ji Research Group, DNA Discovery - Oncology - Stanford University School of Medicine
Ji Research Group –. In The Division of Oncology. DNA Discovery - Integrating Genomics and Genetics into Clinical Oncology Medicine. Raquo; Research focused on accelerating and enabling personalized cancer medicine to patients. Raquo; Novel next generation sequencing technology development for translational and clinical research in cancer genetics and oncology. Raquo; Current translational genomic projects as a joint effort between the Stanford Cancer Institute and the Stanford Genome Technology Center.
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