Genome Data Mining: One Linkage Score Per DNA Letter.
Uploaded by
Korkut VataGenome Data Mining: One Linkage Score Per DNA Letter.
Uploaded by
Korkut VataGenome-Data Mining
Basis:
Getting a statistical score for
every DNA position and for
every disease term to build a
keyword normalized database
for Artificial Intelligence to
work on.
Database Structure
n1 = ATGC---------------------------tt / Atherosclerosis, HER2-Positive Breast
Cancer,
n2 = ATGC---------------------------tt / Hyperlipidemia, Anemia, ……
n3 = ATGC--------------------------tc / Glioma, polydacly..
n4
. .
n= 1.000.000
----------------------------------------------------------.
Methodology
cttcacaagt(CATG)cgcgtcgtt
•
Search: A - 345.000
T - 250.000
0.007
0.006
seconds
seconds
G - 255.000 0.011 seconds
C - 350.000 0.009 seconds
Solution for:
Probe Specificity and DNA Redundancy
Probe Specificity:
cttcacaagt(CATG)cgcgtcgtt
A – 245.000
T – 175.000
G- 252.000
C- 218.000
DNA Redundancy:
+ 890.000 out of 1 million
If the sum (ATGC) > 1 million
then; Probe is specific for 890.000 samples
extend the probe on 5', 3' Sample size is 890.000 for the
particular probe and particular
untill; database
the sum (ATGC) < 1 million Correction factor %88
Solution for:
Probe Specificity and DNA Redundancy
Probe Specificity:
cttcacaagt(CATG)cgcgtcgtt
A – 245.000
T – 175.000
G- 252.000
C- 218.000
DNA Redundancy:
+ 890.000 out of 1 million
If the sum (ATGC) > 1 million
then; Probe is specific for 890.000 samples
extend the probe on 5', 3' Sample size is 890.000 for the
particular probe and particular
untill; database
the sum (ATGC) < 1 million Correction factor %88
Statistics for Every DNA Letter
•
--------2.345.789.156
•
1 cctggagcac ggaagattct t gcggacacaaatcgcaact gctaaataaa atttatttat
•
61 ttgagtgcac agccatgagt cttcacaagt(CATG)cgcgtcgtt atgcttgact tttaaccaaa
•
121 acacttcgat tgtttcgcgt agcaatagtc gcacaatttt tgaagctttc aaggagttcc
•
181 tggatttttg ggatatcggc aacgaagttt ctgcagagtc agcagttcgg gtctccagca
•
241 acggagcttt caacttgccg cagagttttg gcaacgaatc caacgaatat gcccacctgg
•
301 ctacgcctgt ggatccagcc tacggaggca acaacacgaa caacatgatg cagttcacga
•
361 acaatctgga aattttggcc aacaataatt ccgatggcaa taacaaaatt aatgcatgca
•
421 acaaattcgt ctgccacaag ggcactgatt ccgaggatga ctccacggag gtcgatatca
•
481 aggaggatat tccgaaaacg gtggaggtat cgggatcgga attgaccacg gaacccatgg
•
541 ccttcttgca gggattaaac tccgggaatc tgatgcagtt cagccagcaa tccgtgctgc
•
601 gcgaaatgat gctgcaggac attcagatcc aggcgaacac gctgcccaag ctagagaatc
•
2.346.478 ----------
•
DNA position 2,345.789.156 Position Identifier: “cttcacaagt(CATG)cgcgtcgtt”
Disease / Normal
Disease / Normal
A- 165.000 C- 143.000
T– 225.000 T – 281.000
G- 255.000 G- 263.000
Delta Change 25% > Treshold
C- 365.000 C - 382.000
After normalization with respect to disease term frequencies.
HotSpot Card:
For HER2 Positive Breast Cancer
Probe: cttcacaagt(CATG)cgcgtcgt,
DNA position # 2.345.789.156
Score : 27% Decrease in T content
Genome-DataMining
DNA position 2,345.789.91
DNA position 2,345.799.913
DNA position 2,945.534.915
DNA position 1,345.789.91
DNA position 2.128.867.985
HER2-Positive Breast Cancer
DNA position 1,345.789.913 A 2x increased risk
DNA position 2,345.799.913 C 3 x increased risk
DNA position 945.534.715 BRCA1(known) T 5 x increased
DNA position 1,345.789.91 T 1,5 increased risk
DNA position 2.128.867.985 G 3X decreased risk
•
N = 17.546 data points for
HER-2 Positive Breast Cancer
Risk Factors for HER-2 Positive Breast Cancer
•
Upload your genome data, search for:
•
“Her-2 positive Breast Cancer”
Search: “Her-2 positive Breast Cancer”
•
17.546 DNA letters are checked for 2 copies of
genome (maternal, fathernal) and combined
risk factor is displayed.
•
2.3 times higher risk.
Extent
For All Disease Terms and Disease Variants….
Problems Solved:
•
Repeat regions are recognized and correct positions within
multiple regions are identified.
Correction factors for database size are determined.
Result
•
A database for every disease term.
•
Enter = “HER2 Positive Breast Cancer”
•
Result = 8 x increased risk for individual XYZ
Based on 17.546 Hotspots on XYZ's Genome
ARTIFICIAL INTELLIGENCE, AI WORKING BASE
HotSpot Card:
For HER2 Positive Breast Cancer
Probe: cttcacaagt(CATG)cgcgtcgt,
DNA position # 2.345.789.156
Score : 27% Decrease in T content in Disease
~ 15.000 Disease Terms
~ 20.000 Hotspots / Disease Terms
~300.000.000 Data Points Above Treshold Values
Structural Mapping: promoter, exon, intron, -5', -3'
Pathway Mapping
Metabolismal Mapping
Phenotype Mapping
Literature Mapping
Restructuring Healthcare Globally
Medical Education will be reframed with a weight towards Data- Mining.
Surgery will be the main medical profession.
The 100$ Whole Genome Test will provide the best genetic and clinical diagnosis
for the next century.
All human characteristics will be known including emotional status and
tendencies to certain behaviours.
.
The global healthcare system will be runned by an international consortium.
LIMITS ?
No Limit
But
Big-Pharma Politics
International Collaboration
Against
Big-Pharma Politics
By
Korkut Vata
Scientist
Tolunay Gümüş
Actor
