Lecture 25 Flashcards
basic premise that guided the development of the analytical algorithms at CMH
- 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
Bioinformatics
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
common uses of bioinformatics?
- ID of candidate genes and nucleotides (SNPs)
- tries to understand the organizational principles (patterns) within nucleic acid and protein sequences
Genbank/EMBL/DDBJ, Medline, SwissProt, PDB
database interfaces
BLAST, FASTA
sequence alignment
Clustal, MultAlin, DiAlign
multiple sequence alignment
Genscan, GenomeScan, GeneMark, GRAIL
gene finding
pfam, BLOCKS, ProDom
protein domain analysis and identification
- look for patterns within strings of nucleotides that may help to understand the function
Gibbs sampler, AlignACE, MEME
pattern identification/characterzation
PredictProtein, SwissModeler
protein folding prediction
HUGO
“human Genome Organisation
- the international organisation of scientists involved in human genetics
GEO
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
GeneCards
a searchable, integrate database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted human genes
Partek
- informatic analysis
- menu driven
- a comprehensive suite of advanced statistics and interactive data visualization specifically designed to reliably extract biological signal from noisy data
Ingenuity
- 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
OMIM
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
TCGA
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
COSMIC
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
UCSC Genome Browser on Human
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
ENCODE Project
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
GWAS
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
Gene Expression Omnibus
a public functional genomics database of array and sequence-based expression prfiles
