PPT-TB Genotyping and Whole Genome Sequencing in California

CTCA Educational Conference March 7 2017 Martin Cilnis MPH MS Tuberculosis Control Branch California Department of Public Health 1 Potential Uses of Genotyping Confirm or refute outbreaks. Mayo/UIUC Summer . C. ourse in Computational Biology. Session Outline. Genome sequencing. Schematic overview of genome assembly. (a) DNA is collected from the biological sample and sequenced. (b) The output from the sequencer consists of many billions of short, unordered DNA fragments from random positions in the genome. (c) The short fragments are compared with each other to discover how they overlap. (d) The overlap relationships are captured in a large assembly graph shown as nodes representing . 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; . Method to sequence longer regions. cut many times at random (. Shotgun. ). genomic segment. Get one or two reads from each segment. ~500 bp. ~500 bp. Reconstructing the Sequence . (Fragment Assembly). 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. Timetable for today. Time. Activity. 00:00. Introduction to the session. 00:10. Story cards . 00:20. Info cards. 00:30. Issue cards. 00:40. Discuss two key. issues. 00:45. Feedback your issues. What is DNA?. National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention. Division of Tuberculosis Elimination. Objectives. At . the end of the . presentation, participants . will be . able . to . Explain the basics of tuberculosis . 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. Whole Genome Sequencing for Epidemiologists – A Brief Introduction Joel R Sevinsky , PhD Microbial genomes Common isolate identification techniques using molecular biology Whole genome sequencing (WGS) TexPoint fonts used in EMF: . A. A. A. A. A. A. A. A. A. A. A. A. A. A. A. A. Lecture 1. Instructor:. David Tse. dntse@stanford.edu. The Genome. …ACGTGACTGAGGACCGTG. CGACTGAGACTGACTGGGT. CTAGCTAGACTACGTTTTA. Knowing how many genes determine a phenotype (Mendelian and/or QTL analysis), and where the genes are located (linkage mapping) is a first step in understanding the genetic basis of a phenotype . A . 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?. 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 for suspected cancer Information for patients and family members Genomic Medicine Service NHS What is your genome? Your genome is the information needed to build the human body and keep it health