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

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Dr. Tom Conway discusses monitoring the quality of pathogen genome data used in public health and clinical settings. Typical genomics workflows involve sample preparation, sequencing, and analyzing sequence data. Sequence quality is measured by aligning to reference sequences and identifying mismatches. As more sequence fragments accumulate, the number of distinct words increases until reaching an asymptote, and word frequency distributions become more informative. Comparing true and false word counts derived from sequences can estimate genome size and true word fraction for quality control. This quantifiable, efficient, and interpretable approach is valuable for clinical and public health applications across species.

Healthcare

Monitoring the quality of
data in the clinical use of
pathogen genomes
Dr Tom Conway
IBM 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 Workflow
Sample Prep
Sequencing
Sequence Data
Analytics
Reporting InterventionSequence Data

Using a Reference Sequence
alignment
Reference
Sequences
that failed to
align to
reference
x
x
x
x x o
x o
xo
x
x
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 Words
GTGGGTTTTTATCGGCTGGCACATGTGTTGGG
GTGGGT 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
#differentwords
word frequency

Accumulating Fragments: 20,000
#differentwords
word frequency

Accumulating Fragments: 50,000
#differentwords
word frequency

Accumulating Fragments: 100,000
#differentwords
word frequency

Accumulating Fragments: 200,000
#differentwords
word frequency

Accumulating Fragments: 500,000
#differentwords
word frequency

Accumulating Fragments: 1,000,000
#differentwords
word frequency

Differentiating True and False Words
#differentwords
word frequency

Estimated Genome Size
Isolate Number
EstimatedGenomeSize(Mbp)

Isolate Number
TrueWordFraction
True Word Fraction

Why This is Valuable
Quantifiable Robust
Efficient
Species
Independent
Actionable
Interpretable

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Jeremy
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