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. 1 Secuenciación del genoma de especies domésticas 2004 2005 2009 2011 ? 2 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 3 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/ 4 Next Generation Genomics: World Map of High-throughput Sequencers http://pathogenomics.bham.ac.uk/hts/ 5 NGS Applications • • • • • Targeted resequencing (SNP, Indel, CNV) De novo genome sequencing Whole transcriptome seq Small RNAseq Epigenomics eg. ChIP seq 6 TY I X E E G PL M N I O IT OM IPT D E E C CR A S RN G TH AN N TR I S vs A E E R C OM N I EN G 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 7 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 8 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 9 Illumina BeadStation “Golden Gate Assay” “Infinium Assay” Illumina BeadXpress “VeraCode Golden Gate” 10 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 11 12 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 13