PPT-A Comprehensive Workflow for Microbial Genome Sequencing

From Swab to Publication Madison I Dunitz 1 David A Coil 1 Jenna M Lang 1 Guillaume Jospin 1 Aaron E Darling 2 Jonathan A Eisen 1 UC Davis Genome Center 1 University of California Davis . Venter et. al (2004). Presented by. Ken . Vittayarukskul. Steven S. White.. Context of the Problem . Evolutionary history is directly tied to microbial genetics. Little is known. Until recently, microbial diversity was measured by PCR amplification and sequencing of only ribosomal genes. Lenka Veselovská. Laboratory of Developmental Biology and Genomics . Next Generation Sequencing (NGS) . M. odern high-throughput DNA sequencing technologies. parallel, rapid . Decreasing price, time, workflow complexity, error rate. for Colorectal . Cancer. Ulrike (. Riki. ) Peters. Fred Hutchinson Cancer Research Center. University of Washington. Overview. Significance and rationale. . Current efforts on rare and less frequent variants. (very) large datasets. 5/24/18. Goals for the course. Understand how next-generation sequencing technologies are used in biomedical research. Learn how to use publicly available databases/websites to find specific information about genes. How we obtain the sequence of nucleotides of a species. …ACGTGACTGAGGACCGTG. CGACTGAGACTGACTGGGT. CTAGCTAGACTACGTTTTA. TATATATATACGTCGTCGT. ACTGATGACTAGATTACAG. ACTGATTTAGATACCTGAC. TGATTTTAAAAAAATATT…. tens of thousands of DNA bases in length Fugu is thedraft sequenced after human Its compact form and sim-sequence We now have in hand the basic gene-leveldescription of two vertebrates Comparing a Bas E. Dutilh. March 4. th. 2013. Protein function. Phenotypic. . function. E.g. . apoptosis. GO: . Biological. . process. Cellular. . function. E.g. . ribosome. GO: . Cellular. component. Molecular. Modified from Dan Russell. (Relevant) Trivia. How many base pairs (bp) are there in a human genome?. How many protein coding genes are in the Human genome. How much did it cost to sequence the first human genome?. Tim Graubert, MD. Division of Oncology, Stem Cell Biology Section. Washington University School of Medicine. Siteman Cancer Center. Genome Center at Washington University. Genome Center Leadership. Rick Wilson. “. User facility. providing high-throughput DNA sequencing & analysis in support of DOE missions in alternative . energy. , . carbon cycling . & . bioremediation. .”. Opened in 1999. ~240 UC Employees. Loren Hauser. Miriam Land. Yun-Juan Chang. Frank Larimer. Doug Hyatt. Cynthia Jeffries. NEB Educational Support. 2. http://www.neb.com/nebecomm/course_support.asp?. Why study Computational Biology. . . In the paper, researchers describe the final product of the Human Genome Project, which was the 13year effort to read the information encoded in the human chromosomes that reached its culmination i Whole genome sequencing of babies REASONS FOR USING WHOLE GENOME SEQUENCING IN BABIES There are a number of possible reasons for carrying out whole genome or exome sequencing Seeking a diagnosis for a for a rare disease Information for patients and family members Genomic Medicine Service What is your genome? Your genome is the information needed to build the human body and keep it healthy. It