04 - DLA Flashcards
(21 cards)
What are deletions that are too small to be seen by G banding?
Microdeletions
- G banding has low resolution
What is the Philadelphia chromosome?
9;22 translocation, a chunk of chromosome 22 got stuck onto chromosome 9
- Chronic myeloid leukamia
Two types of FISH analysis?
Locus specific and SKY
Locus specific?
Must have an idea of what you are looking for
- Hybridizes to a specific locus on a chromosome
SKY
Chromosome painting
- Uses whole chromosome specific probes to paint each chromosome
- Looks at the entire genome
DiGeorge Syndrome (22q11.2 Deletion Syndrome)
Curious DiGeorge - Immunodeficiencies (CANE)
- Micro-deletion on the q arm on chromosome 22 (TuTu)
- FISH, technique to diagnose
- failure to develop the 3rd and 4th pharyngeal pouches
- Thymic aplasia – 3rd pharyngeal pouch develops into the thymus (Thyme)
- parathyroid dysplasia/decreased PTH – 3rd and 4th pharynegeal pouch develop into the parathyroid gland
- Decreased T-cells (mature in the thymus) and calcium (PTH signals the need for calcium)
- abnormal facies
Velocardiofacial syndrome
22q11.2 deletion syndrome
- Cleft palate
- abnormal facies
DG too - truncus arteriosus (elephant trunk)
DG too - tetralogy of Fallot (tetric floor)
-
Chromosome painting
Better for major chromosome rearrangements and not small deletions
Microarray CGH
Can see microdeletions at a very high resolution
- can map the location of genomic duplications and deletions between DNA samples (compares)
Is the philadelphia chromosome found with Microarray CGH?
No it is not found because the 9;22 has no loss or gain but it is found with G-band, Locus specific FISH and SKY (painting chromosome)
What is the first tier test?
Microarray CGH
SNP array
You can very quickly make a genomic map (easily see if someone is hetero or homo)
What is cDNA?
mRNA is very unstable so to get around that you use a reverse transcriptase to turn the mRNA back into cDNA
What is used to detect triple repeat expansion?
PCR
Base pairs for G band, FISH, Micro Array CGH, ASO
G band - >5Mb
FISH - 100-500Kb
Microarray - 30 Kb
ASO - 15b
What test would you use to diagnosis someone with huntingtons disease?
Triple repeat expansion disorder of CAG
- use PCR
What does a FAST FISH test rely on?
Interphase stage cells
What is SNP Chip?
Test that is trying to discover polymorphisms in a population
What is cDNA Microarray measuring?
Gene expression
What does NGS rely on?
Massively parallel production of sequencing
- Doing multiple runs of the same sequence. Getting a ton of bases of a sequence
What is Sanger sequence?
NGS - single primer and a single run of sequence. You only get around 500 bases of sequence
