temple genomics and analytics collaborative
Next generation sequencing (NGS) and bioinformatics are essential in driving the growth and impact of life sciences. Nowadays, even modest laboratories can engage problems that were unthinkable only a few years ago, provided that they have access to NGS data collection and analysis. The newly formed Department of Medical Genetics and Molecular Biochemistry and the Institute for Genomics and Evolutionary Medicine in the College of Science and Technology at Temple University have partnered to create the Temple Genomics and Analytics Collaborative (TGAC) to conduct state-of-the-art next generation DNA sequencing (NGS) and bioinformatics for life sciences, medical, and health disparities research at Temple University.
The TGAC supports research in a variety of areas, including the phylomedicine of human infectious diseases, genetics of common and inherited diseases, and genomics of cancer:
Genomics of Metabolic Diseases
Patients with extreme obesity have a prevalence of Type 2 Diabetes (T2D) of over 30%. Many patients undergoing Roux-en-Y gastric bypass (RYGB) surgery experience rapid resolution of insulin resistance and T2D within hours or days, well before weight loss and a corresponding reduction in fat mass have occurred. We are working to identify sets of differentially expressed hepatic genes that are associated with three main phenotypes, T2D prior to RYGB, early resolution of T2D following RYGB, and long-term remission of T2D following RYGB.
PI: Glenn Gerhard, Temple University Hospital
Phylomedicine of Malaria Parasites
We are developing genome tools and generating data on relationships, population structure and host-specific adaptations of the malaria parasites found in primates. Specifically, we are using genomic sequencing data from Plasmodium parasites isolated from macaques and orangutans to identify loci involved in adaptation and to investigate how and when these parasites have diverged from one another.
PI: Ananias Escalante, Department of Biology
Ovarian Transcriptomic Approach to Identify Callithrix Lineage-specific Genes Implicated in Poly-ovulation
We are applying an interspecific exomic approach to examine patterns of gene loss/gain and differential selection on ovary-related genes using genome sequencing data from 4 primate species (human, orangutan, marmoset, bushbaby) to identify genes involved in multiple gestations.
PI: L. Christie Rockwell, Department of Anthropology
Implications of sORFs in Cardiac Necrosis
Cellular necrosis underlies many human disease states such as ischemic injury, neurodegenerative diseases, and other adult onset diseases. This project focuses on using DNA sequence data from human and mouse to understand mitochondrial signaling and pathways involved in necrotic cell death.
PI: John Elrod, Department of Pharmacology’s Center for Translational Medicine
Computational Methods for Phylogenetics
The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probabilities of interior branches of the tree. If the bootstrap probability is high for most braches, the tree is considered to be reliable. We are currently developing new methods to evaluate the reliability of interior branches and to assess the impact of interior branch reliability on the reliability of the overall tree.
PI: Masatoshi Nei, Department of Biology
We are developing new computational methods and software tools for evolutionary bioinformatics analysis of tumor genomic variation. In particular, our new methods infer clonal diversity within tumor samples and reconstruct phylogenetic relationships among clones in order to better understand tumor progression and metastasis.
PI: Sayaka Miura, Department of Biology
Population Genomics of Sabatia angularis Using RAD-seq Data: Pilot Study of 12 individuals
The goal of this project is to determine the sampling scheme necessary for a landscape genomic study of the herbaceous plant Sabatia angularis using restriction-site associated DNA sequencing (RAD-seq). This pilot project is essential to the success of the entire study because little is known about the genome size, ploidy, or genetic diversity of S. angularis.
PI: Rachel Spigler, Department of Biology
Gestational Vaginal Microbiome and Spontaneous Preterm Birth
Early markers to identify pregnant women at high risk for spontaneous preterm birth (SPTB) have not been established, and preventive options are therefore limited. This project is focused on characterizing the vaginal microbiome to predict SPTB.
PI: Deborah B. Nelson, Department of Epidemiology and Biostatistics, Department of Obstetrics and Gynecology