Lab 1 Lab Organization Meeting KARCHIN LAB Outline

Lab 1: Lab Organization Meeting KARCHIN LAB

Outline 1. 2. 3. 4. 5. Lab overview Potential risks and benefits of using your own data Instructions on switching to another data source Obtaining publicly available data Introduction to Open. CRAVAT KARCHIN LAB

Lab Overview Lab content will be uploaded on Wednesday mornings (Eastern Standard Time) The lab instructor is Dr. Kymberleigh Pagel, a Research Scientist from the Institute for Computational Medicine. Office hours: Tuesdays at 3 pm EST on Zoom Or upon request, email kpagel 1@jhu. edu. The lab is designed for students to learn how to interpret human DNA variation, using the Open. CRAVAT tool suite https: //opencravat. org and other tools. Each student will work individually over the semester on a final class project. You will analyze either your own DNA or publicly available DNA. KARCHIN LAB

Potential risks and benefits of using your own data • Use of your personal genetic information in this class is not required. • You withdraw your use of your genetic data at any time. • Any genetic data that you share will be deleted on the last day of the class. • Obtaining your personal genetic data comes with risks. • You may find out that you or a family member are at risk for particular diseases. • The validity of most genetic associations in the general population remains uncertain. • You may learn unexpected genealogical features (familial relationships, ancestral or cultural origins). • You may not use any results from the class for any medical purpose prior to consultation with healthcare professional. • You are strongly encouraged to discuss your choice of analyzing your personal genetic data and its potential risks with your immediate family members. KARCHIN LAB

Obtaining publicly available data • DNA data can be found freely available online from: • Personal Genome Project (PGP) • Open. SNP • Genome in a bottle • Other sources are acceptable KARCHIN LAB

Open. CRAVAT – Find the impact of DNA variants • Open. CRAVAT annotates genes and genetic variants with their known characteristics • Installation on your local computer is an option, but not required (size >5 G) • Submitting annotation queries does not require computational expertise • For online use, go to run. opencravat. org • To install locally, go to https: //github. com/Karchin. Lab/opencravat/wiki/quickstart KARCHIN LAB

Final Project - Types of projects Phenotype-driven 1. 2. 3. 4. 5. Start with a phenotype of interest Gather a cohort of individuals Annotate all genetic variation in the cohort Find genetic variation in the cohort relevant to that phenotype Make methods and/or draw conclusions KARCHIN LAB

Common phenotypes for analysis in PGP • Asthma • Crohn's disease • Ulcerative colitis • Irritable bowel syndrome • Rheumatoid arthritis • Type II Diabetes • Coronary artery disease KARCHIN LAB • Long QT Syndrome • Hypertrophic cardiomyopathy • Glaucoma • Color blindness • Bipolar disorder • Celiac disease • Psoriasis • Breast cancer • Prostate cancer • Migraine • Lactose intolerance • Dyslexia • Autism • Osteoporosis • Kidney stones https: //my. pgp-hms. org/google_surveys

Final Project Proposal • Due in early March. • No more than 2 pages, 1 page is fine • Minimally must include: • • • Title Background paragraph One-sentence proposal Describe data and resources you will use High level roadmap of intended project References KARCHIN LAB