molecular diagnostics - hemepathreview
TRANSCRIPT
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Molecular Diagnostics
(a brief review)
Amanda Peterson
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Overview
• DNA basics and mutations
• Southern Blot
• Northern Blot
• Western Blot
• PCR
• FISH
• DNA Microarray
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DNA
• DNA A=T G≡C
• More stable than RNA
• Denaturing depends on G C content
– Denaturing temperature (Tm)
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Mutations
• Any change
• Silent- No change in protein
• Missense- change in protein
• Nonsense- truncation
• Splice- change in site = intron not removed
• Frame Shift- altered reading frame (+/- 1 or 2 bp)
• Unstable trinucleotide repeats
• Chromosomal translocations
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Restriction Enzymes
• Cut at specific sequences in DNA
• Can be anywhere from 4-8 bp in
length
• Usually cut palindromes
for example: racecar
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RFLP (restriction fragment
length polymorphisms)
Restriction enzymes recognize a specific “code”
Mutations result in a loss of recognition of that code
resulting in a different sized fragment of DNA that
can be identified on a gel
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Limitations
• most human genetic diseases are
more varied than the single mutation
• diseases which result from several
mutant genes working together to
produce the disease phenotype
• genetic diseases for which no gene
has yet been discovered
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Southern Blot (DNA)
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Limitations
• Abundant High quality DNA needed
• Labor intensive
• Requires fresh or frozen tissue
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Northern Blot (RNA)
• method for determining transcript
size
• for detecting alternatively spliced
transcripts.
• Same as Southern Blot except the
probe is to a specific RNA sequence
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Limitations
• RNAase!!!
• Less sensitive than RT-PCR
• Can only detect one probe at a time
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DNA Amplification
• PCR-
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DNA Amplification
• RT-PCR: reverse transcription
– RNA to DNA (cDNA)
• Multiplex PCR: 2 different targets
• Nested PCR
• Real Time PCR: simultaneous
amplification and detection
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PCR Testing for F V Leiden:
Results on Capillary Electrophoresis
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FISH
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FISH
• Can detect translocations, gene
amplifications and deletions
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Microdeletion Syndromes Diagnosable with FISH
• Cri-du-Chat
• Steroid Sulfatase Deficiency
• DiGeorge Syndrome
• Kallman Syndrome
• Williams Syndrome
• Prader-Willi/Angelman Syndrome
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Detection of bcr/abl mutation by FISH
The chromosomes can be seen in blue. Probes for bcr and abl are normally
separated as red spot and green spot. A bcr/abl mutation is seen as a yellow
spot (upper left) when the red probe and the green probe are located next
to each other.
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(CISH) Chromogenic In-situ
Hybridization
• Similar to FISH
• enzymatic reactions under the
brightfield microscope on formalin-
fixed, paraffin-embedded (FFPE)
tissues.
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DNA Microarrays
• Genome wide evaluation
• Gene expression profiling
• Genes from 1 sample compared to
another (patient and control)
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DNA Microarray
http://plasticdog.cheme.columbia.edu/undergraduate_research/projects/sahil_mehta_project/work.htm
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DNA Microarray
http://radio.weblogs.com/0105910/images/ecoli_dna.jpg
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References
• Kjeldsberg, C. Practical Diagnosis
of Hematologic Disorders
• Mais, D. Quick Compendium Clinical
Pathology