NGC17 Talk @ Xilinx - June 8, 2017

1. Hardware accelera*on of gene*c variant caller
NOMICA
Lorenzo Di Tucci, Giulia Guidi, Chiara Crippa, Sara Notargiacomo, Marco D. Santambrogio
Xilinx - 8th June 2017

2. 2
MOTIVATION
Improving the diagnosis of genetic
diseases by reducing the required time
and the misdiagnosis cases

3. 3
MOTIVATION
Many human diseases have a
gene3c component
By iden*fying causal variants
specific treatments may be
recommended
Large scale databases of known
variants are used for comparison
Even modestly complex
algorithm would require
prohibi3vely long 3me to
complete
ACCELERATION OF THE VARIANT CALLING

4. 4
FASTQ VCF
DNA is extracted from a blood sample of the individual and
loaded on to a sequencing machine
GATK Best
Practice
• Data
Pre-processing
• Variant
Discovery
• Callset
Refinement
VARIANT
CALLING
Sequencing

5. 5
VARIANTS
Germline variants
(inherited)
Soma3c variants
(cancer)
Human Gene3c
Disorders
cys3c fibrosis
Personalized
medicine
response to drug treatment
Parent Children Environmental
factors
Individual

6. 6
WORKFLOWS
Germline variants Soma3c variants
The heart of the computation
is the Pair HMM

7. 7
PAIRHMM
Pairwise alignment of each read against
each candidate haplotype
The likelihood of each read-haplotype
pairing is calculated
Computationally intensive
Insert
I
Delete
D
Match
M
aii
aim
ami
amm
adm
amd
add

8. 8
PROFILING
Stage Time Runtime %
Assembly 2,598s 13%
Pair-HMM 14,225s 70%
Transversal + Genotyping 3,379s 17%
Biological sample - NA12878 80xWGS - Mauricio et al. of Broad Ins*tute

9. 9
DATA &
ANALYSIS
1000Genomes
Texas Cancer
Research Biobank
Catalogue of human
variations and
genotype data
Genomic data from
tumor and normal
matched pair specimens
Hardware implementation

10. Thanks for your aWen*on!
Lorenzo Di Tucci, Giulia Guidi, Chiara Crippa, Sara Notargiacomo, Marco D. Santambrogio
{giulia.guidi, chiara2.crippa}@mail.polimi.it
{lorenzo.ditucci, sara.notargiacomo, marco.santambrogio}@polimi.it
NOMICA