D A N L AW S O N

B R C 2 0 11 – A N N U A L M E E T I N G

U T S O U T H W E S T E R N M E D I C A L C E N T E R

D A L L A S , T X

2 6 - 2 7 S E P T E M B E R 2 0 11

Challenges and opportunities of new sequencing technologies

Challenges and opportunities of new sequencing technologies

Challenges

PATRIC ViPR/IRD

EuPathDB VectorBase

Challenges & Opportunities of Next Gen Sequencing

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Metagenomics

Population biologyData visualization

Comparative genomics

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Opportunities, Challenges, & Impact of Next Generation Sequencing Technologies: GSCID perspective

Matthew HennDirector of Viral Genomics, Broad Institute

Jennifer WortmanDirector Microbial Informatics, Broad Institute

Granger SuttonProfessor Informatics, JCVI

BRC Annual Mtng. 2011.09.26 Session #2: GSCID Perspectives on Next Gen. Tech.

Henn, Wortman, & Sutton

Large number of genomes @ low cost

Opportunity: large scale projects with comparative potential

Challenges: Analyses computationally intensive Standardized analyses & reference selection Draft quality versus finished quality Genotype vs. phenotype correlations Visualization across large datasets & groups of samples Patient confidentiality

Impacts: Pangenome construction Gene content/synteny analysis Phylogenetic reconstruction Time series analysis

BRC Annual Mtng. 2011.09.26 Session #2: GSCID Perspectives on Next Gen. Tech.

Henn, Wortman, & Sutton

Opportunity: unprecedented sensitivity and specificity to detect sequence polymorphisms and genes

Challenges: Integration of data from multiple technologies Read-based analysis

Computationally & storage intensive need good read mapping to reference dbs

Visualization (genome -> read) What data do you make available

Levels of availability/access Data processing/QC steps

Impacts: SNP calling Population Profiling (e.g. viral) Assembly & Haplotype Reconstruction Annotation

BRC Annual Mtng. 2011.09.26 Session #2: GSCID Perspectives on Next Gen. Tech.

Henn, Wortman, & Sutton

High Resolution Data from Multiple Platforms

Opportunity: Understanding community dynamics in health and disease, polymicrobial diseases

Challenge: Exploratory (you don’t know what is there) What data are important & need be compared (e.g. reads, assemblies, variatns, genes, etc.) Read-based based analysis Metadata standardization Visualization

Impacts: Sequence many organisms in parallel Profile community transcription Comprehensive identification of community members/functions

BRC Annual Mtng. 2011.09.26 Session #2: GSCID Perspectives on Next Gen. Tech.

Henn, Wortman, & Sutton

Microbial Community Profiling

Challenges & Opportunities of Next Gen Sequencing

Seq

uen

cin

g reference assembliesre-sequencing isolates/strains

RN

A-S

eq

Metagenomics

Population biologyData visualization

Comparative genomics

BRC focus

Sca

lab

ility

Arc

hiv

ing d

ata

Ass

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bly