Lecture 25

Question 1

basic premise that guided the development of the analytical algorithms at CMH

Answer 1

• develops variety of analytic tools for sequence analysis making it usable for time sensitive medical decision making, for example in the NICU
• ->Algorithms
• each baby has several 100,000 SNPs
• each baby has a unique clinical presentation
• CMH algorithm takes the combination of entries in the medical record and Id’s potential associations with known genetic variants
• these genes then become primary targets- essentially weighting them statistically
• dramatically improves the speed and reliability of genetic testing

Question 2

Bioinformatics

Answer 2

an interdisciplinary field that develops methods for understanding complex biological data.
- as an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, and engineering to study and process biological data.

• the study, inventions, and implementation of structures and algorithms to improve communication, understanding and management of medical information

Question 3

common uses of bioinformatics?

Answer 3

• ID of candidate genes and nucleotides (SNPs)

- tries to understand the organizational principles (patterns) within nucleic acid and protein sequences

Question 4

Genbank/EMBL/DDBJ, Medline, SwissProt, PDB

Answer 4

database interfaces

Question 5

BLAST, FASTA

Answer 5

sequence alignment

Question 6

Clustal, MultAlin, DiAlign

Answer 6

multiple sequence alignment

Question 7

Genscan, GenomeScan, GeneMark, GRAIL

Answer 7

gene finding

Question 8

pfam, BLOCKS, ProDom

Answer 8

protein domain analysis and identification

- look for patterns within strings of nucleotides that may help to understand the function

Question 9

Gibbs sampler, AlignACE, MEME

Answer 9

pattern identification/characterzation

Question 10

PredictProtein, SwissModeler

Answer 10

protein folding prediction

Question 11

HUGO

Answer 11

“human Genome Organisation

- the international organisation of scientists involved in human genetics

Question 12

GEO

Answer 12

Gene Expression Omnibus

• a public functional genomics data repository supporting MIAME-compliant data submissions
• Array- and sequence-based data are accepted.
• tools are provided to help users query and download experiments and curated gene expression profiles

Question 13

GeneCards

Answer 13

a searchable, integrate database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted human genes

Question 14

Partek

Answer 14

• informatic analysis
• menu driven
• a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signal from noisy data

Question 15

Ingenuity

Answer 15

• informatic analysis
• an all-in-one, web-based software application that enables you to analyze, expression, microRNA, and SNP microarrays, metabolomics, proteomics, and RNA-seq experiments
• allows assessment at multiple levels of integration with easy access to the primary data that supports relationships

Question 16

OMIM

Answer 16

Online Mendelian Inheritance in Man
0 a continuously updates catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship.
- as of July 2015 appox. 8,062 of the over 23,000 entries represented phenotypes, the rest represented genes, many of which were related to known phenotypes

Question 17

TCGA

Answer 17

The Cancer Genome Atlas
- research program supported by national Cancer Institute and NHGRI at NIH
- researchers will ID the genomic changes in more than 30 different types of human cancer
- help us understand what turns a normal cell into a cancer cell by comparing DNA from normal and cancer tissue
learned already:
- are certain areas of the genome commonly affected in several types of cancer
specific changes - also called signature- allow us to tell one type of cancer from another

Question 18

COSMIC

Answer 18

the catalogue of somatic mutations in cancer
- world’s largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer
- in the UK
also includes drug sensitivity

Question 19

UCSC Genome Browser on Human

Answer 19

site contains the reference sequence and working draft assemblies for a large collection of genomes.
- it also provides portals to ENCODE data at UCSC and to the Neandertal project

Question 20

ENCODE Project

Answer 20

ENCyclopedia of DNA Elements
- national human genome research institute (NHGRI) launched a public research consortium named ENCODE in Sept 2003
- carry out a project to ID all functional elements in the human genome sequence
objective is to map all regulatory features in the human genome in all tissues and cell types

Question 21

GWAS

Answer 21

Genome-Wide association studies
- have ID’d many noncoding variants associated with common diseases and traits
using the ENCODE database, Maurano et al. showed that these variants are concentrated in regulatory DNA and 88% active during fetal development and are enriched in variants associated with gestational exposure-related phenotypes

Question 22

Gene Expression Omnibus

Answer 22

a public functional genomics database of array and sequence-based expression prfiles