Computation For Technology Development

Description The ability to reliably, robustly, and reproducibly detect quantitative protein abundance from biofluids and tissues of patients would have many applications in both research and clinical medicine. SGTC enjoys a long-standing collaboration with the laboratory of Richard Smith (Pacific Northwest National Laboratory), one of the leading groups developing the liquid-chromatography mass spectrometry (LC-MS) approach […]

We collaborated with biotech companies such as Ion Torrent and developed some of the original base calling algorithms for NGS platforms. For inquires, please contact wzxiao at stanford.edu

Introduction Glue Grant Human Transcriptome Array (GG-H) is a collaboration result between Stanford Genome Technology Center, Wing Wong’s lab at Stanford, Affymetrix Inc and the Inflammation and Host Response to Injury program (“Glue Grant”). The array has been comprehsively designed to interrogate various apects of the transcriptome, incuding gene expression, alternative splicing, detection of coding SNPs and non-coding transcription. With

Chromosome abnormalities, including losses and gains of entire chromosomes, alterations of chromosome arms, focal amplifications and deletions, and rearrangements, are common characteristics of cancer genome. Detection of such alterations in an early stage provides an opportunity of cancer prevention. We are studying tumor-derived chromosomal alterations, as well as single base mutations through the analysis of

Introduction Clinical genomic studies often require profiling of the human transcriptome from a large number of patients. These RNA samples are typically from small amount of tissues or blood and often partially degraded from clinical archives of formalin-fixed, paraffin-embedded (FFPE) specimens, which present challenges for transcriptome analysis. For example, while RNA-seq can simultaneously discover new

Project Summary In clinical medicine and in most research on physiology and patho-physiology, it has been a traditional concept to use the total amount or the concentration of certain substances (proteins or substrates) in a special compartment of the body of a living organism to represent the metabolism or health condition of the host. With

Project Summary We propose and test a method for the absolute quantitation of RNA molecules in RNA-Seq gene expression studies. Prior to any PCR amplification, cDNA fragments are generated and randomly labeled with a diverse set of “stochastic labels” comprising of nucleic acid barcodes. After amplification and sequencing, the number of stochastic labels observed for

Project Summary RNA-Seq has been recently developed for transcriptome studies, including the discovery and quantification of genes, exons and isoforms, alternative splicing and differential expression. We participated in the MAQC-III/SEQC consortium led by FDA (Leming Shi, PI), to conduct a dedicated multi-site multi-platform experiment with several built-in ground truths to evaluate the performance of this technology. The consortium systematically analyzed the data to establish best

Project Summary  The evolution of a cancer system consisting of cancer clones and normal cells is a complex and dynamic process with multiple interacting factors including clonal expansion, somatic mutation, and sequential selection. As a typical example, in patients with chronic lymphocytic leukemia (CLL), a monoclonal population of transformed B cells expands to dominate the