Genome analysis in practice Flashcards
(10 cards)
1
Q
What are the DNA based detection methods used for?
A
- Detection of point mutations
- Detection of sub-microscopic duplications and deletions
- Rapid detection of aneuploidies (increase/decrease in the number of chromosomes)
2
Q
What are methods used to detect point mutations?
A
- DNA sequencing by Sanger sequencing (1 gene at a time) or next generation sequencing (many/all genes)
- Allele specific PCR - analyses only the specific known point mutations
3
Q
What are the methods of detecting sub-microscopic duplications and deletions?
A
- MLPA, targets a group of specific known positions (chromosomal loci) where there might be a deletion - very targeted
- Chromosomal micro-array (CMA), genome wide, uses a large number of single nucleotide polymorphisms
4
Q
What is caused by trisomy 18?
A
Edward syndrome
5
Q
What is caused by trisomy 13?
A
Patau syndrome
6
Q
What are the methods of detecting aneuploidies?
A
Quantitative fluorescent PCR, gives signals for each number of chromosome
7
Q
What are the chromosome based analysis methods?
A
- karyotyping
- FISH (Fluorescence In-Situ Hybridisation)- uses a specific DNA probe that binds to one location on a chromosome (need to know the location on chromosome where the gene may be missing)
8
Q
Describe Sanger sequencing
A
- Older method
- Analyses one (or a few) genes at a time
- fluorescent dideoxynucleotide sequencing
9
Q
What does next generation sequencing allow for?
A
Analysis of a single gene, several genes, exome or the entire genome
10
Q
Describe the illumina method
A
- Next generation sequencing
- hundreds of millions of DNA fragments sequenced at once
- On a flow cell
- A computer is then used to identify the variants compared to the reference sequence
- Produces a variant call format (VCF) file
- The variants are filtered to exclude those that are just common variants (polymorphisms)
