DNA variants in DNA: genotyping and NGS Flashcards
(25 cards)
What is the purpose of DNA variant analysis?
Clinical genetics, pharmacogenetics, genetic mapping, genome wide association studies (GWAS), identification
DNA variant analysis helps in understanding genetic diseases and their treatments.
What is the difference between a mutation and a polymorphism?
A mutation is a change in the DNA sequence that can lead to disease, while a polymorphism is a variation that is common in the population and generally does not cause disease.
What does DNA sequencing determine?
The exact sequence of nucleotides within a DNA molecule.
What are alternative methods of DNA variant analysis?
Sequencing of microbiomes for analysis of disease mechanisms and epidemiology.
When was the first human genome sequenced?
Between 1990 and 2003.
What was the cost of the Human Genome Project?
$2.7 billion.
What is the current cost of whole genome sequencing (WGS) offered by private companies?
Less than $300.
What is whole exome sequencing (WES)?
A method that sequences all the protein-coding regions in a genome.
What does NGS stand for?
Next Generation Sequencing.
What is the common strategy in next-generation sequencing technologies?
To fragment the DNA into small overlapping fragments and piece the overall sequence back together.
What is read depth in DNA sequencing?
The number of times a base is read in different fragments.
Name two types of next-generation sequencing technologies.
- Illumina (Solexa) sequencing
- Ion torrent: Proton / PGM sequencing
What is clonal amplification in DNA sequencing?
The process where DNA fragments are amplified to create many copies of a single DNA fragment.
How does Illumina NGS sequencing work?
Nucleotides are added one at a time, each being fluorescently labeled, and an image is taken after each addition to determine the base.
What is the principle of Ion Torrent sequencing?
The release of H+ ions during the addition of a dNTP to a DNA strand is detected by changes in pH.
What is the advantage of long-read single molecule sequencing?
It resolves mapping issues with repetitive elements and discriminates paralogous sequences.
What does High Resolution Melt Point (HRM) Analysis do?
Discriminates DNA sequences based on nucleotide composition, length, GC content, and strand complementarity.
What is the function of allele-specific oligonucleotide (ASO) hybridization?
To detect specific alleles by hybridizing a specific oligonucleotide to the target DNA.
What are microarrays used for?
To analyze thousands of variants by hybridizing sample DNA to oligonucleotides.
What does the Amplification Refractory Mutation System (ARMS) do?
Uses allele-specific primers to amplify only the target mutation.
What is the purpose of the Taqman assay?
To detect specific SNPs using fluorescent probes.
What are simple sequence length polymorphisms (SSLPs)?
Repetitive DNA sequences made up of multiple copies of a simple repeating unit.
How is STR genotyping performed?
By amplifying STR loci using primers, followed by size fractionation using gel or capillary electrophoresis.
What is the utility of multiplex PCR of STRs?
Used in human identification and diagnostics.
