J.B. Le Pichon, MD, PhD Section of Neurology - PowerPoint Presentation

Slide1

J.B. Le Pichon, MD, PhDSection of Neurology

On the role of genomic medicine in the practice of neurology, an updateSlide2

The last 15 years set the stage for genomic medicine

First Human Genome sequencing:

6 to 8 years

$1 billionCompleted April 14, 2003

If had started over on April 14, 20033 to 4 months$30M to $50MApril 30, 20131 to 2 days$4,000

-

Genome.gov

: National Genome Research Institute The 10-year anniversary of the Human Genome ProjectSlide3

http://

www.genome.gov

/

sequencingcosts/

Data from the NHGRI Genome Sequencing ProgramSlide4

Genomics in Practice

Today a genome sequence ~

$4,000

Today an MRI ~ $4,000In 10 years price has dropped 25,000 fold$250,000 home 

$10$25,000 car  $1

In 10 years the time to sequence dropped ~ 2,500 fold

40hr week



11.4 years

How was it done: Massively parallel DNA sequencingSlide5

Where are we now?

We have now sequenced the genome of:

112 vertebrates

455 non-vertebrate eukaryotes>900 prokaryotes (bacteria)Now have genomic data for all branches of the evolutionary tree!

-Genome.gov: National Genome Research Institute The 10-year anniversary of the Human Genome ProjectSlide6

-

Green,E

. et al, Nature, 2011, 470:204-13

10 years of genomicsSlide7

So how did we do it?Next Generation Sequencing

Based on massive parallel sequencing method.

Basically a modification of Sanger sequencing.

Allows for very rapid sequencing of many fragments of DNA, but fragments are short.Requires complex computer algorithms to line up the reads.

Subject to error if a single region is not read multiple times (depth of sequencing).Slide8

DNA fragment library generation.

Eleanor Raffan, and Robert K. Semple Br Med Bull 2011;bmb.ldr029

© The Author 2011. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comSlide9

The Illumina sequencing process.

Eleanor Raffan, and Robert K. Semple Br Med Bull 2011;bmb.ldr029

© The Author 2011. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.comSlide10

Cheep but all equal?

Miller, Neil A., et al. "A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases."

Genome medicine

7.1 (2015): 1-16.Slide11

Interpretation of results remains the challenge

1 Known pathogenic; 2 Novel, expected

to be pathogenic;

3 Novel, uncertain pathogenicity (Genet

Med. 2008 Apr;10(4):294-300)Slide12

So what did we find?

Only 1.5% of the 3 billion bases code for ~20,000 genes and 180,000 exons

Roughly 99.9% of our genome is identical base by base

Leaves ~3 to 4 million SNPs to account for genetic susceptibility to inherited diseases~85% of Mendelian

disease are caused by mutations in the exomeOnly 1/3 of the most highly conserved sequences across species code for proteinsSlide13

Some definitions

Microarrays (

aCGH

): microchip platform allowing the detection of microdeletions and duplications.

Next generation sequencing: All methods using massively parallel DNA sequencing.Whole Exome Sequencing (WES): Entire set of exons sequencing (~200,000 exons coding for ~20,000 genes and 1.5% of the genome).Whole Genome Sequencing (WGS)

: Entire genome (~3 billion base pairs)

Single Nucleotide

Polymorphysms

(SNPs)

: Point mutations in the normal DNA sequence

-

Genome.gov

: National Genome Research Institute The 10-year anniversary of the Human Genome ProjectSlide14

Genomics today

Microarrays routinely used for the detection of

microdeletions

and duplicationsPharmacogenomics now performed routinely before giving certain medicationsPrenatal genomics

Genomics in the NICUGenomics for NDDDirect to Consumer marketingIncidental findings?Slide15

Neonatal testing

~1/20 infants in the NICU has a genetic disease

3,500 monogenetic disease now known, about 500 have treatments

Infants with terminal illnesses can linger in the NICU weeks to months, cost: $8,000/dayFirst four infants to have genome sequencing and analysis done in <50 hours. Cost: $13,000 per genome

Infant DNA test Speeds Diagnosis od Rare Diseases, New York Times, October 3, 2012, Saunders et al, Science Translational Medicine, 2012, 4(154);1-13Slide16

Genome in the Neonatal ICU

35 infants with acute illnesses enrolled in

STATseq

(rapid genome sequencing)20 returned a diagnosis, 13 de-novoMedian time to genome analysis 5 daysMedian time to genome result 23 days

4 had diseases with strongly favorable effects of management6 were started on palliative careWillig, Laurel K., et al. "Whole-genome sequencing for identification of

Mendelian

disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings."

The Lancet Respiratory Medicine

3.5 (2015): 377-387.Slide17

Preimplantation diagnosis

Genetic testing prior to fertilization: The case of IVF

Cost: ~$20,000

Use: Recent survey: 2% of 27,000 uses of preimplantation

diagnosis to choose the sex.In the USA: No regulation limiting this technologyOne center in Chicago tested>2,500 embryos looking for >425 different gene mutationsGene Tests, Healthy Children and Ethical Doubt

New York Times, February 4, 2014Slide18

Genetic testing and IVF

Example of

Gerstmann-Straussler-Scheinker

(GSS): Transmissible Spongiform Encephalopathy26 yo

finds she has GSS, likely develop dementia and die 30-50yoIVF now has healthy twins“people who carry a gene like GSS have a moral duty to use preimplantation diagnosis-if they can afford it-to spare the next generation” Janet Malek, bioethicist,

Brody School of

Medicine (as reported by NYT article)

Are we willing to argue that such people should not be allowed to exist?

Gene Tests, Healthy Children and Ethical Doubt New York Times, February 4, 2014Slide19

What would our world be like without these people

Woody Guthrie:

H

untington’s diseaseFrederic Chopin: ? Cystic FibrosisMiles Davis: Sickle Cell AnemiaJohn F. Kennedy: Addison’s diseaseMaurice Ravel:

Frontotemporal dementiaLou Gehrig: ALSRonald Reagan: Alzheimer’s diseaseCharles K. Kao (Nobel prize in physics, father of fiber optics and broad band): Alzheimer’sStephen Hawking: ALSSlide20

Testing for Intellectual Disability

Prior to microarrays: ~4% of patients had a diagnosis

With Microarray: additional ~20%

Whole exome & genome sequencing: 107 children with ND d/o

56 WES, 4 WGSMean age sx onset: 1yo, mean age dx: 7yoDefinite dx: 38%, 10% novel candidate genes

Soden

et al,

Diagnostic rate, cost and change-in-care

following genome

and

exome

sequencing in pediatric neurodevelopmental

disabilities

refractory to traditional

diagnosisSlide21

WES and WGS for NDD at CMH

Positive:

ACMG

category 1, Novel: ACGME category 2 or 3Slide22

Diagnoses and inheritance patterns in 100 NDD families tested by genome or exome sequencing

Soden

, Sarah E., et al. "Effectiveness of

exome

and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders." Science translational medicine 6.265 (2014): 265ra168-265ra168.Slide23

Financial Impact of Genomic Diagnoses

Mean total charge prior to genomic testing: $19,100 per family ($3,248-$55,321)

With a 40% positive return rate genomic testing becomes cost effective at $2,996 per individual in a trio.

Note: ICU and other medical care costs NOT included.

Soden, Sarah E., et al. "Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders." Science translational medicine 6.265 (2014): 265ra168-265ra168.Slide24

Clinical impact of genomic diagnoses

Soden

, Sarah E., et al. "Effectiveness of

exome

and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders." Science translational medicine 6.265 (2014): 265ra168-265ra168.Slide25

When Next-Gen Sequencing makes a difference

BVVL, Riboflavin transporter deficiency

Three children

Each diagnosed initially with a neuroimmune disorder for

wks to yrsFatal disorderTreatment Vitamin B2No toxicityStops the progression of the diseaseSlide26

When Next-Gen Sequencing makes a difference

Infant evaluated at 6

mo

Hypotonia, GDD, resp. distressAcute resp. decomp

. With hospitalizationRapid WGS: Combined D-and L-2-Hydroxyglutaric AciduriaPolycitra supplementation startedNow oldest living child with this disorder

Soden

, Sarah E., et al. "Effectiveness of

exome

and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders."

Science translational medicine

6.265 (2014): 265ra168-265ra168.Slide27

Direct to Consumer (DTC)Good, bad or ugly?

23andMe

: Personal Genome Service (PSG): Single-nucleotide polymorphism chip capable of identifying mutations in genes associated with 254 specific diseases and conditions.

Consumer’s right to know

Medical (governmental) paternalismRight to information about ourselves (medical records)Raw genetic data accessible to the consumer.Biobank of genetic information: used and sold for medical research and patentable discoveries.

New England J. Med., 03/13/14, 370;11:985-988Slide28

23andMe Consent

Alerted before purchase that:

“Results may evoke strong emotions and has the potential to alter your life and worldview (e.g. your father is not genetically your father, surprising facts related to your ancestry…”Slide29

23andMe and the FDA

“Immediately discontinue marketing Personalized Genome Service (PGS)”

“Some of the uses for which PGS is intended are particularly concerning, such as assessments for BRCA-related genetic risk and drug responses because of the potential health consequences that could result from false positives or false negative assessments for high risk indications such as these.”

Fair criticism?

FDA, Doc#: GEN1300666, Nov 22, 2013Slide30

Incidental Findings

10 month old infant girl, normal milestones

First seizure at 6 months, since 12 more seizures, all generalized and less than 3 minutes

EEG and MRI wnlMicroarray: 111kb deletion Xq24, a region associated with X-linked disability in boys. Significance in girls is unknown.

What should we tell the parents (if anything)?What should we tell the child and when (if anything)?Slide31

ACMG recommendations for reporting Incidental findings

56 Genes including: BRCA1&2, VHL, TSC1&2, NF2, COL3A1, RYR1, CACNA1S

“Constitutional

mutations found in the genes on the minimum list should be reported by the laboratory to the ordering clinician, regardless of the indication for which the clinical sequencing was

ordered”“It is the responsibility of the ordering clinician/team to provide comprehensive pre- and posttest counseling to the patient”.

Green RC et al, Genet Med. 2013, 15:565-

574 Clarification

, Genet Med. 2013, 15:664-666Slide32

Consequences, intended and unintended

Individuals should actively choose if they wish to learn about certain genomic findings.

Example: James Watson DNA was sequenced on condition that his APOE status never be disclosed.

Yet, under ACMG recommendation, if a patient agrees to undergo NEXT-Gen sequencing they forfeit their right not to know about genomic variants for genes on the list.

Can these results be legitimately called incidental?Lyon, GJ. There is nothing ‘incidental’ about unrelated findings. Personalized Med., 2012;9(2):163-6Slide33

P3

G statement in pediatric

r

esearchPublic Population Project in Genomics and SocietyWGS results that are scientifically valid, clinically

useful, and reveal conditions that are preventable and actionable during childhood should be offeredMutations that predispose the child to develop an adult-onset disorder, even if accidentally discovered in the

research process

, generally should not be

returned.

Knoppers

BM, et al, Return of whole-genome sequencing results in

paediatric

research: a statement of the P

3

G international

paediatrics

platform.

Eur

J Hum Genet 2013, Slide34

Topics I wanted to discussbut ran out of time

…

A new concept: The

neurogenomic clinicDeveloping a new approach to complex polygenetic disease

GWAS not the answer (5 to 10%)Is there an additive phenomenon: “Mutational load”?Should we be studying pathways rather than single genes: “Candidate network analysis”Slide35

In conclusion some practical tips:

Actual costs charged by our lab

Routine karyotype: $1,969

High resolution karyotype: $2,250Microarray: $3,615Genome: $15,000 (includes trio)

TAG-Scan (572 genes): Full symptom driven scan $3,180 (CMH only)2 to 5 genes: $1,7001 gene: $1,250Slide36

Genomes at CMH commercially available since August 2015

Genomes, since August 2015

25 genomes, 19 resulted (60% diagnostic)

2 for patients on 100% CMH financial assistance6 for patients that were ordered inpatient9 were approved by insurance including Kansas Medicaid

12 week turn aroundRequires consent (ACGME 56 gene incidental findings)Slide37

Things to come at CMH

Symptom driven

exome

platformEpilepsy and other disease driven panelsRoll out planned within the next 2 monthsExome array: Microarray targeted only at genes (currently send out).Slide38

http://

www.childrensmercy.org

/library/

uploadedFiles/childrensmercyorg/

Clinics_and_Services/Clinics_and_Departments/Pathology_and_Laboratory_Medicine/Molecular%20Genetics%20Requisition%206.2013.pdf

Molecular genetic requisition form at CMHSlide39

Thank you

Genome center

: Lee

Zellmer (Senior Laboratory Genetics Counselor), Carol Saunders (Clinical

Director, Center for Pediatric Genomic Medicine), Sarah Soden (Director, Center for Pediatric Genomic Medicine)Kernicterus research group: Steve Shapiro, Doug

Bittel

, Sean Riordan