L14- genomics and genome projects Flashcards
Why sequence the genome?
Get genetic information available
How many base pairs in the human genome
3,000,000,000 base pair
How is genome sequence obtained?
Obtain organisms genomic DNA -> break DNA into small fragments -> obtain DNA sequence -> search for overlaps to reconstruct the genome sequence
Why do we use model organisms?
Small genome – “value for money”
Easy organisms to manipulate
Provide information on fundamental biological processes
Technology development
Useful for comparative genomics
Why do we use smaller organisms like E.coli?
Helps us understand pathogenisis
Why do we use single cell eukaryotes?
Easy to manipulate
Why do we use c.elegans?
Useful in developmental studies?
What is the limitation of using fragments of DNA to sequence the genome?
Unable to identify the chromosome the sequence belongs to
In how many days was the genome sequence of a causative bacteria that appeared in europe early summer 2011?
2 days
What were the outcomes of genome sequencing of a causative bacteria that appeared in europe early summer 2011?
1) Revealed an unidentified new strain of E. coli.
2) Insight into the antibiotic resistance characteristics.
3) Insight to why the bacteria was so virulent and also why it seemed to be targeting adults.
What were the outcomes of the human genome project
Comprehensive Genome Map
Technological Advancements
Scientific Discoveries
Collaborative Efforts
What are the main limitations of identifying genes within a genome?
How big is a valid open reading frame
Identification of RNA splice sites
How do we define how big is a valid open reading from?
Search for ATG and then stop codon but at a reasonable disatnce?
What length do we question validity of an open reading frame?
Around 50 codons (and less)
What are RNA splice sites?
Conserved sequences
How do we overcome RNA splice sites?
RNA analyses can help but depends on the expression of the gene
What are the other limitations of identifying genes within a genome ?
Incomplete Coverage
Genetic Variation
Functional Understanding
Why would incomplete coverage be a limitation?
some highly repetitive and structurally complex regions of the genome, such as centromeres
and telomeres. Major ‘gaps’ in 2003 sequencing data. Recent advancement in sequencing technology filled most gaps.
Why would genetic variation be a limitation?
Does not capture the full extent of human genetic
diversity.
Why would fundamental understanding be a limitation?
understanding the function of every gene and
regulatory element remains a significant challenge
Problems in gene identification are emphasised by genome analyses in __________
Saccharomyces cerevisiae
The S. cerevisiae is _____ the size of the human genome
0.001
In contrast to the human genome, genes are ______________ in the S. cerevisiae genome with
very little repetitive DNA
tightly packed
In contrast to the human genome, RNA alternative ____________ S. cerevisiae rarely occurs to complicate gene identification
alternative splicing
Simple genetics can be performed in S. cerevisiae to analyse ______________
potential gene function
list some advancements due to human genome project
Foundation for precision medicine – cancer treatment, Pharmacogenomics
Gene therapy
Genetic screening
Several open databases being accessible
Comparative genomics- widely popular
