Transcript Next Generation Sequencing - Benefits for Patients

Next Generation Sequencing
– Benefits for Patients
Jo Whittaker/
Su Stenhouse
NGS – Benefits for Patients
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What is Next Generation Sequencing?
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What are the benefits for patients?
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How will the benefits be realised?
What is Next Generation Sequencing?
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Massively parallel sequencing
Genomic DNA
ACTGTAATGGCA
Whole genome sequence –
consensus of aligned reads
Fragmented library of small pieces
all sequenced at same time
A__GT___G__A
_T___G__A
GT___G__A__
A__GT___G
A__GT___G__A
Individual reads aligned
to reference sequence
What is Next Generation Sequencing?
Massive sequence output possible
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Terabytes of data (1,000,000,000,000)
Highly scalable
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Lower output machine; fewer samples per run; faster
results
exomes
‘targeted’ regions (eg disease specific ‘set’ of genes)
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High throughput machine
multiplex samples; target specific region to screen many
samples for particular variant
whole genome sequence
What is Next Generation Sequencing?
Evolving technology
Illumina HiSeq 2000
Life Technologies SOLiD 4
Ion Torrent PGM
Illumina MiSeq
Pacific Biosciences RS
Roche 454 GS FLX
Roche GS Junior
and then there is the bioinformatics
What are the benefits for
patients?
Would you like a
copy of the results?
What are the benefits to
patients?
Widely applicable technology
variants in individual’s DNA vs ‘reference’ sequence may
identify
new disease genes – high diagnostic yield
increased efficacy of treatments
reduced deleterious/no response to treatments
preventative treatments
differentiation of disease subtypes
How will the benefits be
realised?
Marcel Nelen & Joris Veltman, Nijmegen
…. we think whole-genome- or exome-based approaches are currently most
suited for diagnostic implementation in genetically heterogeneous diseases,
initially to complement and later to replace Sanger sequencing, qPCR and
genomic microarrays.
Establishing the pathogenicity of individual genetic variants remains a
daunting task, requiring novel bioinformatic tools and high-throughput
functional approaches……….
Pharmacogenomics. 2012 Apr;13(5):511-4.
Genome and exome sequencing in the clinic: unbiased genomic
approaches with a high diagnostic yield.
David Goldstein & colleagues
Duke University
Highlighted two challenges in particular
First, in our experience, laboratory-based functional analysis is an
important part of the evaluation, and it remains unclear how this would
be incorporated into routine clinical application of NGS……
Second, this work required substantial manual interrogation of both sequence data and
candidate genes. Although variant calling procedures are continually improved and there
are likely to be routines developed to simplify the process of candidate identification, it
seems likely that for the foreseeable future, some level of expert judgement will
continue to be required to identify causal mutations from sequence data, which will
contribute to the cost and time of this type of diagnostics.
JMG Online First, published on May 11, 2012 as 10.1136/jmedgenet-2012-100819
Clinical application of exome sequencing in undiagnosed genetic conditions
Anna C Need, Vandana Shashi, Yuki Hitomi, Kelly Schoch, Kevin V Shianna, Marie T McDonald, Miriam H Meisler, David B
Goldstein
What are the benefits for
patients?
Sharon and Ozzy both had a ‘genome test’ –
looked at genes predisposing to serious illness
Ozzy’s results – ‘perfect’
Sharon’s results – already knew she was genetically
predisposed to colon cancer (and has been affected)
She also carries a gene mutation predisposing to
breast cancer
She opted for a bilateral mastectomy –at the
moment cannot accurately predict if / when
she would develop breast cancer
How will the benefits be
realised?
We want to set the test up - there
are only 22 other labs doing it
We’ve got our own sequencer
It’s a secret……
Genetics is different
We don’t need to work with ‘x’ology
How will the benefits be
realised?
Select new ‘best friends’
Pathologist
Obstetrician
Nephrologist
Bioinformaticist
Neonatologist
Endocrinologist
Cardiologist
UKGTN
Lab
Oncologist
Develop specialist knowledge – define your service’s unique strengths
How will the benefits be
realised?
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Collaboration
Networking
Developing standardised protocols
Using standardised locus specification and variant
nomenclature
Quality assuring sequencing processes
Quality assuring data analysis processes
Phenotype & genotype data sharing
Providing equitable access to the right test for the
patient
What are the benefits for
patients?
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Higher diagnostic yield and more timely
diagnosis
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Research describing the course of a disease
or development of a disorder may allow it to
be more effectively treated or prevented
What are the benefits for
patients?
Hopefully, more choices about how to live
with or manage their disorder