Post on 07-Dec-2014
description
Sequencing)output)
IT)processing)throughput)
Human)exper6se)
Genomic(sequencing(
Puta0ve(muta0ons(
Proteins(or(epigene0cs(
Func0on(
Clinical(effect(
Sequencing(output(
IT(processing(throughput(
Human(exper0se(
Genome&assembly&
Computa0onal&comparison&
and&annota0on&
Visualiza0on&
Experimental&planning&and&data&collec0on&
Desktop&integra0on,&and&So>ware&as&a&Service&(SaaC)&
Sequencing&output&
IT&processing&throughput&
Human&exper0se&
Genomic&sequencing&
Puta0ve&muta0ons&
Proteins&or&epigene0cs&
Func0on&
Clinical&effect&
Integrate(medical(condi/on(with(informa/on(on(gene/c(varia/on,(and(protein(func/on.( Provide(through(a(user:friendly(
query(and(visualiza/on(interface.(
Data$
Raw$sequence$
Informa+on$
Assembled$and$annotated$
data$
Knowledge$
Informa5on$applied$to$par5cular$purpose$
© 2013 Winton Gibbons
To iden2fy leverage | pressure points—presen2ng both opportuni2es and problems—the NGS clinical transla2on process should be viewed as analogous to a manufacturing plant. For opportuni2es or leverage points, follow the work in process (WIP). Where there is too much, new capacity is required downstream to convert it into useful informa2on. This is oMen through new soMware, but can be through new instrumenta2on, or even clinical data. At any 2me, there will be over and under capacity for various stages, e.g., too much raw sequence data | too few assembled genomes | fewer clinical databases | yet fewer transla2onally trained doctors | insufficient integra2on among gene2cs, drugs and regulatory. Different vendors and users will likely be honed for various steps in the process, not fully integrated. Some may choose to integrate, but that is likely best done through acquisi2on of the best-‐of-‐breed. The balance will not always stay the same. It is likely there will yet be an oversupply (not just overproduc2on) of sequencing capacity. Sequencer and reagent growth might stall. Clinical databases will catch up for some condi2ons, and not for others. For some medical special2es, use of gene2cs will come before it does for others. Regulatory and reimbursement will lag always.
Gene$c Tests related to Cancer
2006 2011 new 2013 new Total
21
81
66
178
Breast 20
Colorectal 9
Hematologic 4
Lung 4
Prostate 4
Genitourinary 3
Ovarian 2
Mul2ple 8
Other 12
Recent
Knowledge Informa$on Data
Screening
Latent Diagnosis
Staging Treatment planning Prognosis
Monitoring
Data source: Surveys, AHRQ
-‐60% -‐40% -‐20% 0% 20% 40% 60%
Prognosis for metastasis
Prognosis for progression
Treatment monitoring
Prognosis for recurrence
Staging
Treatment planning
Screening
Latent / early Dx
Diagnosis
Assay Uses for which Doctors S$ll Want the Most Improvement