Genomics Flashcards
Lesson 6
What has been the trend with cost of sequencing 1 human genome over the years?
It has dropped dramatically from $100,000,000 in 2001 to around $1,000 in 2021, with a massive drop-off in 2007-2010
What is high throughput sequencing?
It is qualitative and quantitative
How are assays used in sequencing?
Numerous assays that harness the quantitative power of sequencing technologies are used to understand genome function
Genomics
the study of whole sets of genes, their products, and their interactions
Bioinformatics
the application of computational methods to the storage and analysis of biological data
Gene annotation
the process of identifying all protein-coding genes in a genome sequence and ultimately their functions
What are some centralized resources for analyzing genome sequences?
NCBI, GenBank (database of sequences), BLAST (allows searching GenBank - the google of genomics)
Is all of our DNA necessary
No, most of the DNA in our genomes in junk!!!
What are the different types of variation of different genomes?
Single Nucleotide Polymorphisms (SNPs)
various types of chromosomal structural rearrangements (deletions, transversions etc)
Copy number variants (CNVs)
Repetitive DNA
What is a Single Nucleotide Polymorphism (SNP)
a substitution of a single nucleotide that occurs at a specific position in the genome; NOT a mutation (substitutions occur at an appreciable degree within a population)
What is Minor Allele Frequency (MAF)
the frequency at which the least common allele occurs in a given population
Common variants (MAF > 5%)
Rare variants (MAF < 1%)
What is Copy Number Variants (CNVs)?
Loci where some individuals have one or multiple copies of a particular gene or genetic region, rather than the standard two copies
Caused by duplications and deletions
Like SNPs, may or may not have phenotypes or cause disease
Where does CNVs stem from?
Many CNVs stem from segmental duplications (large blocks of 10,000 to 300,000 bp that have been copied to another region of the genome)
CNVs vs SNPs
Total number: 38000 vs 14 million
Size: 100-3000 bp vs 1 bp
Type: deletions, duplication, complex vs transition, transversion,
Effects on genes: gene dosage, interruption vs missense, nonsense, frameshift
Percentage of reference genome covered: 30% vs 1%
What are the four categories of repetitive DNA?
Short tandem repeats: Duplications of sample sets of DNA bases (1-5 bp)
Tandem repeats: Duplications found at the centromeres and telomeres of chromosomes that are 100-200bp long
Interspersed Repeats- DNA transposons and retrotransposons
Segmental Duplications
What are the phenotypic effects of simple and tandem repeats?
STR and TR containing genes are directly involved in the generation of phenotypic variation (liquid yeast example)
What are transposable elements?
segments of DNA that can move within the genome of a cell by means of a DNA or RNA intermediate
What do DNA transposons do?
move through DNA intermediate; “copy and paste” or “cut and paste”
What does retrotransposons do?
move through an RNA intermediate, always “copy and paste”, most abundant
How does transposable elements impact the genome size
TE activity can dramatically increase genome size
How are TEs a source of phenotypic variation
Insertion of Gret1 retrotransposon resulted in the loss of color of grapes (from purple to green)
Rearrangement of retrotransposon led to the revertant, colored grapes (from green to red)
How is sequencing and comparisons of genomes made possible?
Through advances in genomics and bioinformatics
What percent of human genes are conserved in other organisms?
Around 50%
How does genomes vary?
Varies in size, number of genes, and gene density
bacteria have smaller genomes (1-6 Mb) compared to eukaryotic genomes (12-670,000 Mb)
