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The first DNA chip with CE MARK DETECTION OF THE MOST FREQUENT FH MUTATIONS AND COPY NUMBER CHANGES OF THE LDLR GENE
What is LIPOchip? ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Biochip Chip/Array  : DNA fragments (15-60bp) printed (spotted) on a solid support (glass) in an ordered way
Size of one spot : 50-100 μm 60-75mm Biochip
MOLECULAR BASIS OF HYBRIDIZATION ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
MOLECULAR BASIS OF HYBRIDIZATION A T C G T A G C AMPLIFICATION (PCR) ( region of interest) FRAGMENTATION  DNAse:  random cuts Alkaline Phosphatase : 3´ ends free 5´ 5´ 3´ 3´ LABELLING  Biotin : Indirect labelling Patient DNA  (COMPLEMENTARITY) + HYBRIDIZATION  DNAchip  With oligos specific to the mutations
N M Homozygous donor Heterozygous   donor Technical base N N N M M M N N N
Experimental procedure DNA-chip design & printing Hybridization optimization SPECIFICATIONS Mutations/SNPs to be analyzed Image Capture and Software development GENOTYPE Oligonucleotide design Multiplex PCR design
Oligonucleotide design ,[object Object],[object Object],[object Object],Allele-Specific Oligonucleotides: TTTCTAGCAGG G GGAGGAGTTTG TTTCTAGCAGG C GGAGGAGTTTG 11nt wt mut 11nt
Oligonucleotide design ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Multiplex PCR Design M1 M2 M3 Exon 1 M4 M5 Exon 6
Multiplex PCR Design ,[object Object]
Multiplex PCR Design ,[object Object],A B C
Genotypes computing ,[object Object]
Detection of Copy Number Changes ,[object Object],[object Object],[object Object],[object Object],[object Object]
DAY1 DAY 2 OVERLAPPING PROCESSES 56 ul WORKFLOW 1  Amplification 7.5µl DNA   (20ng/µl) 2 Fragmentation 3 Labelling 4 Hybridization 5 Results  analysis 24 ul PCR mixes 1, 2 y 3 and 4 DNAse +  Alkaline Phosphatase TdT +  Biotin-ddUTP 2 hours 45 minutes 60 minutes 4 hours and 30 minutes
ESSENTIAL EQUIPMENT REQUIRED FOR PROCESSING 1. Thermocycler:  Applied Biosystem 9700 ,[object Object],[object Object]
ESSENTIAL EQUIPMENT REQUIRED FOR PROCESSING 2.-  Hybridization station:  Tecan  HS 4800™ Pro Hybridization Stations   ,[object Object],[object Object],[object Object]
3. Scanner:  Innoscan 710A (Innopsys) ,[object Object],[object Object],ESSENTIAL EQUIPMENT REQUIRED FOR PROCESSING
ESSENTIAL EQUIPMENT REQUIRED FOR PROCESSING 4. LIPOchip software:  result analysis and report

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LIPOChip

  • 1.  
  • 2. The first DNA chip with CE MARK DETECTION OF THE MOST FREQUENT FH MUTATIONS AND COPY NUMBER CHANGES OF THE LDLR GENE
  • 3.
  • 4. Biochip Chip/Array : DNA fragments (15-60bp) printed (spotted) on a solid support (glass) in an ordered way
  • 5. Size of one spot : 50-100 μm 60-75mm Biochip
  • 6.
  • 7. MOLECULAR BASIS OF HYBRIDIZATION A T C G T A G C AMPLIFICATION (PCR) ( region of interest) FRAGMENTATION DNAse: random cuts Alkaline Phosphatase : 3´ ends free 5´ 5´ 3´ 3´ LABELLING Biotin : Indirect labelling Patient DNA (COMPLEMENTARITY) + HYBRIDIZATION DNAchip With oligos specific to the mutations
  • 8. N M Homozygous donor Heterozygous donor Technical base N N N M M M N N N
  • 9. Experimental procedure DNA-chip design & printing Hybridization optimization SPECIFICATIONS Mutations/SNPs to be analyzed Image Capture and Software development GENOTYPE Oligonucleotide design Multiplex PCR design
  • 10.
  • 11.
  • 12. Multiplex PCR Design M1 M2 M3 Exon 1 M4 M5 Exon 6
  • 13.
  • 14.
  • 15.
  • 16.
  • 17. DAY1 DAY 2 OVERLAPPING PROCESSES 56 ul WORKFLOW 1 Amplification 7.5µl DNA (20ng/µl) 2 Fragmentation 3 Labelling 4 Hybridization 5 Results analysis 24 ul PCR mixes 1, 2 y 3 and 4 DNAse + Alkaline Phosphatase TdT + Biotin-ddUTP 2 hours 45 minutes 60 minutes 4 hours and 30 minutes
  • 18.
  • 19.
  • 20.
  • 21. ESSENTIAL EQUIPMENT REQUIRED FOR PROCESSING 4. LIPOchip software: result analysis and report