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Next Generation Sequencing – Benefits for Patients. Jo Whittaker/ Su Stenhouse. NGS – Benefits for Patients. What is Next Generation Sequencing? What are the benefits for patients? How will the benefits be realised?. What is Next Generation Sequencing?. Massively parallel sequencing.

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ngs benefits for patients
NGS – Benefits for Patients
  • What is Next Generation Sequencing?
  • What are the benefits for patients?
  • How will the benefits be realised?
what is next generation sequencing
What is Next Generation Sequencing?
  • Massively parallel sequencing

Fragmented library of small pieces

all sequenced at same time

Genomic DNA

A__GT___G__A

_T___G__A

GT___G__A__

A__GT___G

A__GT___G__A

ACTGTAATGGCA

Individual reads aligned

to reference sequence

Whole genome sequence –

consensus of aligned reads

what is next generation sequencing1
What is Next Generation Sequencing?

Massive sequence output possible

  • Terabytes of data (1,000,000,000,000)

Highly scalable

  • Lower output machine; fewer samples per run; faster results

exomes

‘targeted’ regions (eg disease specific ‘set’ of genes)

  • High throughput machine

multiplex samples; target specific region to screen many samples for particular variant

whole genome sequence

what is next generation sequencing2
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
What are the benefits for patients?

Would you like a

copy of the results?

Help!

Help!

what are the benefits to patients
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 oftreatments

reduced deleterious/no response to treatments

preventative treatments

differentiation of disease subtypes

how will the benefits be realised
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 exomesequencing in the clinic: unbiased genomic approaches with a high diagnostic yield.

david goldstein colleagues duke university
David Goldstein & colleaguesDuke 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 patients1
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 realised1
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 realised2
How will the benefits be realised?

Pathologist

Select new ‘best friends’

Obstetrician

Nephrologist

Bioinformaticist

Neonatologist

Endocrinologist

Cardiologist

Oncologist

UKGTN

Lab

Develop specialist knowledge – define your service’s unique strengths

how will the benefits be realised3
How will the benefits be realised?
  • 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 patients2
What are the benefits for patients?
  • Higher diagnostic yield and more timely diagnosis
  • 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 patients3
What are the benefits for patients?

Hopefully, more choices about how to live with or manage their disorder