Monitoring the quality of data in the clinical use of pathogen genomes

Dr Tom ConwayIBM Research Australia

Uses of Microbial Genomes: Public Health

Infected Food Microbiological Investigation

Cluster Analysis

Uses of Microbial Genomes: Clinical

Antibiotic Resistance Test

Detecting Resistance Genes

Current Practice Genomics Methods

Typical Genomics WorkflowSample Prep

SequencingSequence Data

AnalyticsReporting InterventionSequence Data

Measuring Sequence Quality

Using a Reference Sequence

alignment

Reference

Sequencesthat failed to align to reference

xx

xx x o

x oxo

xx

Sequence fragment

Sequence Data as Words

1: imped, and shivered, and glafed, and growled; and

2: wind was rushing was the sea; and that the smwll

3: nd broad impression of thk identity of things seem

(from Great Expectations with apologies to Charles Dickens)

Sequence Data as WordsGTGGGTTTTTATCGGCTGGCACATGTGTTGGGGTGGGT TTTATC GCTGGC CATGTG TGGGTT TTATCG CTGGCA ATGTGT GGGTTT TATCGG TGGCAC TGTGTT GGTTTT ATCGGC GGCACA GTGTTG GTTTTT TCGGCT GCACAT TGTTGG TTTTTA CGGCTG CACATG GTTGGG TTTTAT GGCTGG ACATGT

Accumulating Fragments: 10,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 20,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 50,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 100,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 200,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 500,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 1,000,000

# di

ffere

nt w

ords

word frequency

Accumulating Fragments: 1,000,000

# di

ffere

nt w

ords

word frequency

Differentiating True and False Words

# di

ffere

nt w

ords

word frequency

Estimated Genome Size

Isolate Number

Estim

ated

Gen

ome

Size

(Mbp

)

Isolate Number

True

Wor

d Fr

actio

n

True Word Fraction

Why This is Valuable

Quantifiable Robust

Efficient

Species Independent

ActionableInterpretable

The TeamTomConway

JeremyWazny

JustinBedo

MahtabMirmomeni

BenGoudey

KellyWyres

NatalieGunn

HannahHuckstep