“Omics” has become the new mantra in molecular research.

Armand Sanchez
Departamento de Genética Animal
“Omics” has become the new mantra
in molecular research.
• “Omics” technologies include genomics, transcriptomics,
proteomics, metabolomics...
• Genomics had revealed the static sequences of genes and
proteins and focus has now been shifted to their dynamic
functions and interactions.
• Transcriptomics, proteomics and metabolomics reveal the
biological function of the gene product.
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Secuenciación del genoma de especies domésticas
2004
2005
2009
2011 ?
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Cost of Sequencing
ABI 3730XL
454/GS Junior
HiSeq Illumina
ABI SOLiD
Pacific Biosciences
Cost of human genome (30x coverage)
Ion torrent (ABI)
$100.000 by late 2009
$30.000 by late 2010
$10.000 by late 2011
MiSeq (Illumina)
• Costs in samples; cost in analysis ?
• Whole-genome vs. whole-exome ?
Coste de (re)secuenciar un genoma de mamífero
1.000 $ / genoma
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Comparison of sequencing instruments, sorted by
cost/Mb, with expected performance by mid 2011
Glen T.C. Molecular Ecology Resources (2011) 11, 759–769.
Next Generation Genomics: World Map of High-throughput Sequencers
http://pathogenomics.bham.ac.uk/hts/
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Next Generation Genomics: World Map of High-throughput Sequencers
http://pathogenomics.bham.ac.uk/hts/
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NGS Applications
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Targeted resequencing (SNP, Indel, CNV)
De novo genome sequencing
Whole transcriptome seq
Small RNAseq
Epigenomics eg. ChIP seq
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TY
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X E
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G PL
M
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I
O
IT OM IPT
D
E E C CR
A
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RN G TH AN
N TR
I
S vs
A
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C OM
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I EN
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NGS sequencing “capture arrays”
Exon1
Exon2
Exon3
Exon4
Exon5
ADN Genomico
Lavar
Exon6
Fragmentar y
añadir adaptadores
hibridar
ADN a descartar
AND diana
Eluir
Sondas
Secuenciador
ADN
diana
NimbleGen Array
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Estudios de asociación a nivel genómico (GWAS)
Utilización de chips de
genotipado de SNPS
Actualmente capaces de
analizar hasta 5 millones
de SNPs en una muestra
“SNP
chips”
Infinium
Assay
GeneChip
Array
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BioMark™ (Fluidigm)
TaqMan assays
Each 96.96 Dynamic Array is capable of producing 9,216 real-time qPCR data
points using just 1/200th the amount of reagents.
OpenArray: Six plate format options are available (assays x samples):
64 x 48; 128 x 24; 192 x 16; 256 x 12; 1024 x 3; and 3072 x 1
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Illumina BeadStation
“Golden Gate Assay”
“Infinium Assay”
Illumina BeadXpress
“VeraCode Golden Gate”
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SelSweep. M. Groenen
Genetics in the the Petabyte Age…
• Petabyte: 106 Gigabytes
“The Petabyte Age: Sensors everywhere.
Infinite storage. Clouds of processors. Our
ability to capture, warehouse, and understand
massive amounts of data is changing science,
medicine, business, and technology. As our
collection of facts and figures grows, so will the
opportunity to find answers to fundamental
questions.
Because in the era of big data, more isn't
just more. More is different. ”
Chris Anderson 23.06.08
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IBM's DNA Transistor technology slows and controls DNA molecules as
they move through a nanopore in a silicon chip. The technology decode the
bases of the DNA as it passes through the chip. Technologies are centered
on semiconductor-based nanopores, "which have advantages over proteinbased nanopores in terms of control, robustness, scalability, and
manufacturability."
The method combines advances in physics, electronics, and
nanotechnology and eliminates the need for chemical reagents, a major
cost of sequencing, to read a genome.
La (r)evolución genómica en mejora animal
• Hoy: Paneles masivos para el genotipado de SNPs
• Futuro próximo: Secuenciación del genoma i del
transcriptoma en especies domésticas
HACIA UN CAMBIO DE PARADIGMA…
DNA seq + RNA seq
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