Genomics Flashcards
Genomics
Study of the genome (entire genetic material of an organism)
Structural Genomics
Study of gene structure
Cytological mapping
Banding pattern of stained chromosomes
G bands produced by Giemsa staining are rich in A:T regions (regions of compact chromatin)
Used to detect chromosomal translocations
FISH
Fluorescence in situ hybridization
Uses biotin bound probe detected with avidin bound to a fluorescent dye
Physical mapping
Arranges sequence features on a linear map
Provides location of DNA sequences on a chromosome
Contig Map
Set of overlapping genomic DNA clones ordered by restriction mapping
Presence of a particular STS or EST on a genomic fragments used to order clones to their position on a chromosome by comparing their position relative to other STS or ESTs
Sequence Tagged Sites (STS)
Short unique genomic sequences (200-500 bp), usually derived from whole genome sequencing
Expressed Sequence Tags (ESTs)
Short cDNA sequences
Genetic Mapping
Based on genetic markers that occur due to DNA polymorphisms
Relative positions of markers mapped by determining recombination frequencies in crossings or co-segregation in pedigrees
Restriction Fragment Polymorphisms (RFLP)
Occurs due to addition or deletion of RE sites
MInisatellite (Variable Number Tandem Repeates- VNTR)
Polymorphic locus of short (10-80 nucleotides) DNA sequences present as several tandem repeats of varied number
Microsatellite (Short Tandem Repeats- STR)
Same as VNTR but repeat units are shorter (~10 nucelotides)
Polymorphisms are due to varibale number or repeats between RE sites
Single Nucleotide Polymorphisms (SNPs)
Single base pair substitution within a reference sequence
Haplotypes
Set of SNPs on the same chromosome that are inherited together
Hapmap
Catalog of SNPs/haplotypes in a population that can be used for tracing evolutionary history or predicting disease susceptibility
Anchor Marker
DNA sequences that are mapped both genetically and physically
FISH can be used to link these to the cytological map
Positional Cloning
Identifying chromosomal position of a gene responsible for a disease by association (pedigree analysis) with mapped genetic markers (RFLP, STRs, SNPs) and then using mapping techniques (Contig assembly and screening) to clone the gene
Human Genome Project
Public funded Human Genome Organization (HUGO) and privately owned company (Celera) compete at mapping and sequencing human genome
HUGO Method
Created genetic maps
- Ordered contigs for each chromosome
- Sequenced each contig
Celera Method
Shotgun sequencing
- Randomly fragment genome
- Sequence each fragment
- Order fragments using a computer
Encode
Encyclopedia of DNA Elements
Comparative Genomics
Study of genome evolution and comparison of genomes of various organisms
Bioinformatics
Deduce structure/function of gene products
Create phylogentic trees based upon DNA sequence comparisons to study chromosomal and genome evolution
Functional Genomics
Study of gene function
Transcriptome
Entire set of mRNA transcripts in a biological sample
DNA Microarray
Measures gene expression on a large scale- shows which RNAs are expressed, and their abundance in a cell under specific set of conditions
Microarray contains many DNA porbes on a solid support
Labelled cDNA hybridized to microarray and bound cDNA analyzed using a fluorescence detector
Proteome
Entire set of proteins in a biological sample
Comparative proteomic studies can identify differences in protein expression between 2 biological samples
Interactome
Entire set of protein-protein interactions in a biological sample
Giemsa Staining:
• DNA dye that preferentially binds A-T regions (heterochromatic regions)
○ Produces dark “G bands” on chromosomes
Used to produce a karyotype
