In silico PCR

Computer-based tool for PCR experiments

1. IN SILICOPCR

2. THERE ARE THREE KINDS OF EXPERIMENTS
•IN VIVO EXPERIMENT
•IN VITRO EXPERIMENT
•IN SILICOEXPERIMENT

3. WHAT IS IN SILICOPCR?
•REFERS TO COMPUTATIONAL TOOLS USED TO CALCULATE
THEORETICAL PCRRESULTS USING A GIVEN SET OF PRIMERS
(PROBES) TO AMPLIFY DNA SEQUENCES FROM A SEQUENCED
GENOME.
•THESE TOOLS ARE USED TO OPTIMIZE THE DESIGN OF PRIMERS
FOR TARGET DNA OR CDNASEQUENCE. .

4. THE ADVANTAGES OF IN SILICOPCR
•THEDESIGNOFAPPROPRIATEPRIMERS.
•IDENTIFYTHELENGTHANDTHESEQUENCEOFTHEAMPLICON.
•IDENTIFYTHEEXACTLOCATIONOFTHEAMPLICONONTHE
GENOME.
•RECOGNIZEMULTIPLEAMPLICONSONTHEGENOME.

5. SOFTWARE AVAILABLE
•EPCRAT NATIONAL CENTER FOR
BIOTECHNOLOGY INFORMATION (NCBI).
•FAST PCRAPPLICATION
•UCSC GENOME BROWSER.

6. WHAT IS VARIANT?
•A VARIANT IS A CHANGE TO THE NUCLEOTIDE SEQUENCE AT A
PARTICULAR POSITION IN THE GENOME, COMPARED TO THE
REFERENCE GENOME ASSEMBLY.
•VARIANTS CAN OCCUR IN A CODING SEQUENCE REGION OR NON-
CODING SEQUENCE.

7. •A VARIANT CAN BE IDENTIFIED BASED ON ITS POSITION
IN THE GENOME OR IN SPECIFIC GENE.
•GENOMIC COORDINATE FOR A VARIANT:
Position on the genome

8. •THE SAME VARIANT ON CHROMOSOME 17 CAN ALSO BE
DESCRIBED RELATIVE TO ITS POSITION WITHIN A GENE.
•IN THIS CASE, THE PREVIOUS GENE LOCATED WITHIN
THE GENE TP53 CAN ALSO BE DESCRIBED AS:

9. NUCLEOTIDE POSITION WITHIN THE GENE

10. •ONCE THE NUCLEOTIDE POSITION THAT A VARIANT
OCCURS AT HAS BEEN IDENTIFIED, THE VARIANT CAN
BE NAMED
Description Example variant
A substitution of a C nucleotidefor a T nucleotide at
nucleotide 586 within a gene.
c.586C>T
A deletion of four nucleotide within a gene, from
position c.485, up to and including nucleotide c.488
c.485_488 del
A duplication of three nucleotideswithin a gene, from
position c.485, up to and including nucleotide c.487
c.482_484 dup
An insertion of three nucleotide within a gene (A,T,
and C) occurring directly after position c.300
c.300insATC

11. VARIANT ON THE PROTEIN LEVEL
Variant typeProtein changeNucleotidechange
Nonsense (premature
stop codon)
p.Arg196*c.586C>T
Frameshiftp.iLe162Thrfs*7c.485_488 del
In frame duplicationp.Arg196dupc.482_484 dup
Missense p.Tyr234Cysc.701A>C
silentp.Gln192=c.576G>A
inronicp.?c.560-5C>G
Premature stop 7 a apost the
deletion