genomics and the use of next genera3on sequencing (ngs) techniques...

Genomics and the use of Next Genera3on Sequencing (NGS)

TechniquesIMBB2016

BecA-ILRIHub,NairobiMay9–20,2016

FrancescaStomeo

Genomics

The study of the structure, organization, function, evolution of genomes (including interactions with the environment)

Genomics before NGS

1900 1977

1980 1990

1994-98

1998

2000

Watson and Crick identify DNA (the double helix) as the Chemical basis of heredity

Human Genome Projects (HPG) begins-an international effort to map and sequence all the genes in the human genome

Sanger and Gilbert derive methods of sequencing DNA

Working Draft of the human genome sequencing complete

Human genome project completed 2003

Rediscovery of Mendel's laws helps establish the science of genetics

Methodsofsequencing

•  Sangerdideoxymethod(primerextension–termina@on)•  Maxam-Gilbertchemicalcleavedmethod(DNAlabelled,chemicallycleavedinsequence-dependentmanner.•  NextGenera@onSequencing(pyrosequencing,reversibledye-terminators,etc.)

•  SinglestrandedDNAtemplate•  AprimerforDNAsynthesis•  DNApolymerase•  Deoxynucleosidetriphosphates(normaldNTP)–extendsDNAstrand•  Dideoxynucleo@detriphosphates(ddNTP)–terminatessynthesis

Cost for sequencing genomes rapidly reduced

What is NGS?

NGS plaBorms

Illumina454

ABISOLiD

General steps of illumina NGS technologies

GenomicDNA/cDNA

GenomicDNA/cDNA

General steps of illumina NGS technologies

GenomicDNA/cDNA

Library

General steps of illumina NGS technologies

General steps of Illumina NGS technologies

Amplifica@onstep

GenomicDNA/cDNA

Library

IlluminaHiSeq2000

454GSFLX SOLiDv4

Readlength 700bp 2*100bp 50*2bpAccuracy 99.9% 98% 99.94%Outputdata 0.7GB 600GB 120GBCost/millionbases $10 $0.07 $0.13

Illumina technologies

Nextera DNANexteraXT smallgenomesTruSeq totalRNATruSeqStranded RNAribosomalRNAremoved

Scope of Sequencing

Metagenomics (viral/bacterial)

Compilation of complete genomes, metagenomes,

annotation and curation of metadata

(meta)genome sequencing

Extraction of important biological

information

Vaccine dvlpmt

Diagnostics

Global diseases surveillance

Drug dvlpmt

Improved Public health intervention

geographical mapping

sequence variation analysis

Primer, microarray

phylogenetic analysis

protein modeling Databases

Improved drug selection

discovery of new micro-

organisms and pathways

Environmental sustainability

From Sequence to impact

Diversity studies

A reference genome for common bean and genome-wide analysis of dual domestications Schmutz et. al 2014 Nature Genetics 46

Expression studies

ThedevelopmentaltranscriptomeofDrosophilamelanogaster

Sequencing ancient genomes

Miller,W.etal.Sequencingthenucleargenomeoftheex@nctwoollymammoth.Nature456,387–390(2008).

Biological Ques3on?

Thank youIMBB2016

BecA-ILRIHub,NairobiMay9–20,2016

FrancescaStomeo