Zhang Lab
Detecting Genetic Abnormalities
Associate Professor, UNMC Department of Pathology, Microbiology and Immunology
Director, Clinical Molecular Bioinformatics, Division of Diagnostic Molecular Pathology and Human Genetics
Most of our lab's research is focused on detection of large-scale genetic abnormalities in lymphoid malignancies using next generation sequencing.
Dr. Zhang has designed several pipelines for multiple lymphoma projects, including mutation detection, gene expression analysis, fusion gene detection, T-cell clonality assessment, and DNA copy number analysis in various sample types such as frozen fresh tissue samples, FFPE tissue samples, or cell-free DNA.
Next generation sequencing, also known as high throughput sequencing or massively parallel sequencing, has dramatically changed the way scientists extract genetic information from biological systems. The technology helps us to develop great insight into the abnormalities affecting the genome, transcriptome and epigenome through DNA sequencing of genomic DNA, cDNA and bisulfite treated DNA with cheaper cost.
Next generation sequencing allows us to discover point mutations, as well as structural alterations such as indels, inversion and translocations that contribute to diseases. Sequencing of the transcriptome provides us the capability to identify changes of gene expression, alternative splicing, gene fusions, mutations and non-coding RNA species. Sequencing after Bisulfite treatment can be used to determine the global cytosine methylation status of DNA.
In the follicular lymphoma project, Dr. Zhang developed a mutational analysis pipeline that is able to confidently identify somatic mutations without paired normal control DNA. By using the pipeline, we have successfully detected genes more frequently mutated in transformed follicular lymphoma cases. The recurrently mutated genes are often involved in epigenetic regulation, the JAK-STAT or the NF-κB pathway, immune surveillance, and cell cycle regulation, or are transcription factors involved in B-cell development.
She has also designed several pipelines for the T-cell lymphoma project. The pipelines involved use WES, whole genome sequencing, and amplicon sequencing data to detect somatic mutation and use whole transcriptome sequencing to identify novel gene fusions and differential gene expression.
Dr. Zhang’s goal is to develop analysis methods for the research laboratory and employ them in the clinical laboratory setting.