3. Genome in a Bottle Consortium
Whole Genome Variant Calling
Sample
gDNA isolation
Library Prep
Sequencing
Alignment/Mapping
Variant Calling
Confidence Estimates
Downstream Analysis
• gDNA reference materials to
evaluate performance
– materials certified for their
variants against a reference
sequence, with confidence
estimates
• established consortium to
develop reference
materials, data, methods,
performance metrics
• Characterized Pilot Genome
NA12878
• Ashkenazim Trio, Asian Trio
from PGP in process
genericmeasurementprocess
5. Sequencing
from DNA -> Raw Sequence Data
Evidence to be
established
Standards/Evidenc
e developing
Stakeholders
Example
Knowledge Gaps
Accurate
(unbiased)
sequencing
Fit-for-purpose
characteristics
Well-characterized
genomic DNA
reference materials
Documentary
standard describing
sequencing
characteristics
appropriate for
different clinical
indications
Standards Labs
Clinical labs
Sequencing
Technology
Developers
Academic Labs
developing
methods
Genome Centers
Sequencing
“difficult” regions
Platform artifacts
High quality
benchmark
genomes
Performance
expectations
(sensitivity/specific
ity)
6. Sequence Bioinformatics
Raw Sequence Data -> VCF
Evidence to be
established
Standards/Evidence
developing
Stakeholders
Example Knowledge
Gaps
Unbiased
processing of
sequence data
(mapping/asse
mbly)
Accurate variant
calling
Accurate and
unambiguous
representation,
interoperability
Protocols to critically
evaluate processes,
informed by platform
idiosyncrasies
Data representation
standards
Reference
data/implementation:
benchmark VCF files
Reference software to
evaluate VCF files
Standards Labs
Clinical labs
Sequencing
Technology
Developers
Academic Labs
developing
methods
Genome Centers
Assembly/mapping in
“difficult” regions
Artifacts
Benchmark genomes
Performance
expectations
SDO and
Accreditation body
fluency with
bioinformatics