"O uso da plataforma HPC na descoberta de doenças genéticas", presented on http://3whpc.lcca.usp.br

1. O uso da plataforma HPC na
descoberta de doenças genéticas
David Santos Marco Antonio. PhD
Profa. Maria Rita Passos Bueno
Laboratório de Genética do Desenvolvimento Humano
Departamento de Genética e Biologia Evolutiva
Instituto de Biociências - USP
Finding the variability that could
explain genetic disorders.

2. DNA : Chromosome : Genes
DNA: A T C G
Chromosomes:
1 – 22
X and/or Y
Mitochondrial

3. DNA : Chromosome : Genes

4. http://en.wikipedia.org/wiki/Human_genome
DNA : Chromosome : Genes

5. Human genetic variation in populations
• Genes on the same order
• Mapped using reference genome: hg19, GRCh38.
• Variability among relatives/populations.
• Susceptibility to diseases.
• Improvements.
Falar sobre populações
1000Genomes

6. Human genetic variation in populations
Haplogroups YMitochondrial DNA

7. Disorder Mutation Chromosome
22q11.2 deletion syndrome D 22q
Angelman syndrome DCP 15
Canavan disease 17p
Charcot–Marie–Tooth disease
Color blindness P X
Cri du chat D 5
Cystic fibrosis P 7q
Down syndrome C 21
Duchenne muscular dystrophy D Xp
Haemochromatosis P 6
Haemophilia P X
Klinefelter syndrome C X
Neurofibromatosis 17q/22q/?
Phenylketonuria P 12q
Polycystic kidney disease P 16 (PKD1) or 4 (PKD2)
Prader–Willi syndrome DC 15
Sickle-cell disease P 11p
Tay–Sachs disease P 15
Turner syndrome C X
 P – Point mutation: InDel.
 D – Deletion of gene.
 C – Whole chromosome
extra/missing.
 T – Nucleotide repeat disorders.
Human Genetic Diseases

8. Genomic Sequencing
• Terabytes of data/sequencing.
• Storage.
• Processing.
• Lots of RAM.
Ben Moore

9. Genomic Sequencing

10. Data Processing
STEPS
Alignment
Quality
Control
Quality
Control
Sequencing
Reference
Sorting
Remove
Errors
Realignment
Recalibration

11. Data Processing
STEPS
Alignment
Quality
Control
Quality
Control
Sequencing
Reference
Sorting
Remove
Errors
Realignment
RecalibrationVariant Calling

12. Data Processing
STEPS
Variant Calling
dbSNP
SIFT
PolyPhen OMIM
exac03
6500
Exomes1000
Genomes
Clinical
Relevant Data

13. High Computational Cost
• Storage.
• RAM.
• CPU.
• Reprocessing.
@SEQ_ID
GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
Fastq format

14. Research
• Authism
• Cranio-fascial development
• Richieri-Costa
• Down
Diseases Models
• Human
• Zebra fish
• Drosophila
• Microbiome

15. Acknowledgements
• LCCA
• Guys in LCCA
• Guys in LCCA
• Profa. Maria Rita Passos Bueno
• Laboratório de Genética do Desenvolvimento Humano
• Instituto de Biociências.
• USP