High-throughput Proteomics for Biomarker Discovery

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…

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Transcriptome Analysis of Clinical FFPE Samples

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…

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Detection of Rare Genomic Changes in Patients

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…

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Development of Next-Gen Human Transcriptome Array

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,…

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Evaluation of the Performance of RNA-Seq and Microarray

maqc

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…

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