Abstract

AbstractThis document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012.

Highlights

  • In
 making
 suggestions
 please
 keep
 in
 mind
 the
 overriding
 constraints
 implicit
 in
 such
an
endeavor:
first,
the
final
VP
must
be
able
to
declare
a
winner
or
winners
in
 the
 Archon Genomics X PRIZE (AGXP)
 without
 controversy;
 second,
 any
 suggested
 changes
 should
 likely
 reduce
 the
 actual
 cost
 of
 carrying
 out
 the
 physical
 and
 bioinformatic
 procedures
 of
 the
 AGXP
competition

  • Will enable the ascertainment of sequencing accuracy of contestant’s genomes in these regions. These loci will be enriched from each DNA sample and sequenced to generate ~100x average coverage per sample9

  • Completeness The AGXP recognizes that there is no absolute standard against which to judge the completeness of a competitor submission

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Summary

History of This Document

This
document
is
the
collaborative
work
of
many
individuals
led
by
Granger
Sutton,
 Edison
Liu,
Victor
Jongeneel,
and
Larry
Kedes. C. Uniqueness of the Archon Genomics X PRIZE (AGXP) for Sequencing: The
Sequencing
requirements
of
the
AGXP
are
unusual
in
respect
to
the
complexity
 of
 the
 judging
 criteria. Many
 X
 PRIZE
 competitions
 have
 a
 singular
 and
 definable
 threshold
to
be
“crossed”:
e.g. flying
to
the
moon
and
returning,
or
staying
aloft
for
X
 period
 of
 time. 
the
sequencing
for
the
AGXP
has
an
“asymptotic”
goal
of
achieving
a
defi‐ nition
of
perfection. Though
 the
 primary
 goal
 of
 the
 AGXP
 is
 to
 reward
 the
 most
 advanced
 sequencing
 technologies,
we
are

aware
that
the
judging
process
and
criteria,
and
the
mate‐ rials
used
for
judging
(i.e.,
the
DNA
samples
and
cell
lines,
mapping
and
comparison
 algorithms)
will
be
important
standards
for
clinical
sequencing. 
our
goal
 will

be
to
develop
protocols
that
can
be
used
as
industry
benchmarks

Test Criteria
Random fosmid sequencing validation5
Targeted sequencing via genome enrichment
Processing of the Validation Dataset
Data Deposition and Format
Scoring12
Accuracy

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