Lecture 39

Question 1

Basics of OMIM (Online Mendelian Inheritance in Man)

Answer 1

Continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship

Question 2

Basics of GEO (Gene Expression Omnibus)

Answer 2

Public functional genomics database of array and sequenced-based expression profiles

Question 3

Basics of TCGA (The Cancer Genome Atlas)

Answer 3

TCGA researchers will identify the genomic changes in more than 30 different types of human cancer; will help us understand what turns a normal cell into a cancer cell by comparing DNA from normal and cancer tissue

Question 4

Basics of ENCODE (Encyclopedia of DNA Elements)

Answer 4

Used to identify all functional elements in the human genome sequence; map all regulatory features in the human genome in all tissues and cell types

Question 5

Basics of eMERGE (The Electronic Medical Records and Genomics Network)

Answer 5

Tasked with developing methods and best practices for utilization of the electronic medical record (EMR) as a tool for genomic research

Question 6

Basics of ClinGen (Clinical Genome Resource)

Answer 6

NIH-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research

Question 7

Define biomedical informatics

Answer 7

Study, invention, and implementation of structures and algorithms to improve communication, understanding, and management of medical information

Question 8

Basics of HUGO (Human Genome Organization)

Answer 8

International organization of scientists involved in human genetics

Question 9

Basics of GeneCards

Answer 9

Searchable, integrated database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted human genes

Question 10

Basics of Partek

Answer 10

Comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signals from noisy data

Question 11

Basics of Ingenuity

Answer 11

Enables you to analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays; metabolomics, proteomics, and RNA-Seq experiments

Question 12

What does BCL2 do? Will be a question!!!!

Answer 12

Oncogene that causes lymphomas/leukemias (myeloid lymphoma)

Question 13

Basics of COSMIC (Catalogue of Somatic Mutations In Cancer)

Answer 13

World’s largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer

Question 14

Basics of UCSC Genome Browser of the Human Genome Assembly

Answer 14

Provides access to many other genomes; contains reference sequence and working draft assemblies for a large collection of genomes

Question 15

Basics of SPHINX (Sequence and Phenotype Integration Exchange)

Answer 15

Web-based tool for exploring data for hypothesis generation, especially around drug response implications of genetic variation across the eMERGE PGx cohort

Question 16

What are Phenome-wide association studies (PheWAS)?

Answer 16

Analyze many phenotypes compared to a single genetic variant (or other attribute)

Question 17

Define big data analytics

Answer 17

Process of examining large and varied data sets (big data) to uncover hidden patterns, unknown correlations, market trends, customer preferences, and other useful information that can help organizations make more-informed business decisions