On the role of genomic
medicine in the practice of
neurology, an update
J.B. Le Pichon, MD, PhD
Section of Neurology
© The Children's Mercy Hospital, 2014. 03/14
The last 15 years set the
stage for genomic medicine
• First Human Genome
sequencing:
• If had started over on
April 14, 2003
– 6 to 8 years
• 3 to 4 months
– $1 billion
• $30M to $50M
– Completed April 14, • April 30, 2013
2003
• 1 to 2 days
• $4,000
2
-Genome.gov: National Genome Research Institute The 10-year anniversary
of the Human Genome Project
© The Children's Mercy Hospital, 2014. 03/14
Data from the NHGRI Genome
Sequencing Program
http://www.genome.gov/sequencingcosts/
3
© The Children's Mercy Hospital, 2014. 03/14
Genomics in Practice
• Today a genome
sequence ~ $4,000
• Today an MRI ~
$4,000
• In 10 years price has
dropped 25,000 fold
– $250,000 home $10
– $25,000 car  $1
4
• In 10 years the time
to sequence dropped
~ 2,500 fold
– 40hr week  11.4
years
• How was it done:
Massively parallel
DNA sequencing
© The Children's Mercy Hospital, 2014. 03/14
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 Project
5
© The Children's Mercy Hospital, 2014. 03/14
10 years of genomics
-Green,E. et al, Nature, 2011, 470:204-13
6
© The Children's Mercy Hospital, 2014. 03/14
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).
7
© The Children's Mercy Hospital, 2014. 03/14
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.com
© The Children's Mercy Hospital, 2014. 03/14
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.com
© The Children's Mercy Hospital, 2014. 03/14
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.
10
© The Children's Mercy Hospital, 2014. 03/14
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)
11
© The Children's Mercy Hospital, 2014. 03/14
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 exome
• Only 1/3 of the most highly conserved sequences
across species code for proteins
12
© The Children's Mercy Hospital, 2014. 03/14
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
13
-Genome.gov: National Genome Research Institute The 10-year anniversary of
the Human Genome Project
© The Children's Mercy Hospital, 2014. 03/14
Genomics today
• Microarrays routinely used for the detection of
microdeletions and duplications
• Pharmacogenomics now performed routinely before
giving certain medications
• Prenatal genomics
• Genomics in the NICU
• Genomics for NDD
• Direct to Consumer marketing
• Incidental findings?
14
© The Children's Mercy Hospital, 2014. 03/14
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/day
• First 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);1-13
15
© The Children's Mercy Hospital, 2014. 03/14
Genome in the Neonatal ICU
• 35 infants with acute illnesses enrolled in
STATseq (rapid genome sequencing)
• 20 returned a diagnosis, 13 de-novo
• Median time to genome analysis 5 days
• Median time to genome result 23 days
• 4 had diseases with strongly favorable effects of
management
• 6 were started on palliative care
16
Willig, 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.
© The Children's Mercy Hospital, 2014. 03/14
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 technology
– One center in Chicago tested>2,500 embryos
looking for >425 different gene mutations
17
Gene Tests, Healthy Children and Ethical Doubt
New York Times, February 4, 2014
© The Children's Mercy Hospital, 2014. 03/14
Genetic testing and IVF
– Example of Gerstmann-Straussler-Scheinker (GSS):
Transmissible Spongiform Encephalopathy
• 26 yo finds she has GSS, likely develop dementia and die 3050yo
• IVF 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?
18
Gene Tests, Healthy Children and Ethical Doubt New York Times, February 4, 2014
© The Children's Mercy Hospital, 2014. 03/14
What would our world be like
without these people
• Woody Guthrie:
Huntington’s disease
• Frederic Chopin: ? Cystic
Fibrosis
• Miles Davis: Sickle Cell
Anemia
• John F. Kennedy:
Addison’s disease
• Lou Gehrig: ALS
• Ronald Reagan:
Alzheimer’s disease
• Charles K. Kao (Nobel
prize in physics, father of
fiber optics and broad
band): Alzheimer’s
• Stephen Hawking: ALS
• Maurice Ravel:
Frontotemporal dementia
19
© The Children's Mercy Hospital, 2014. 03/14
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 WGS
– Mean age sx onset: 1yo, mean age dx: 7yo
– Definite dx: 38%, 10% novel candidate genes
20
Soden et al, Diagnostic rate, cost and change-in-care following genome and exome
sequencing in pediatric neurodevelopmental disabilities refractory to traditional
diagnosis
© The Children's Mercy Hospital, 2014. 03/14
WES and WGS for NDD at CMH
Positive: ACMG category 1, Novel: ACGME category 2 or 3
21
© The Children's Mercy Hospital, 2014. 03/14
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.
22
© The Children's Mercy Hospital, 2014. 03/14
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.
23
© The Children's Mercy Hospital, 2014. 03/14
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.
24
© The Children's Mercy Hospital, 2014. 03/14
When Next-Gen Sequencing makes
a difference
• BVVL, Riboflavin
transporter deficiency
• Three children
• Each diagnosed initially
with a neuroimmune
disorder for wks to yrs
• Fatal disorder
• Treatment Vitamin B2
• No toxicity
• Stops the progression of
the disease
25
© The Children's Mercy Hospital, 2014. 03/14
When Next-Gen Sequencing
makes a difference
• Infant evaluated at 6 mo
• Hypotonia, GDD, resp. distress
• Acute resp. decomp. With
hospitalization
• Rapid WGS: Combined D-and
L-2-Hydroxyglutaric Aciduria
• Polycitra supplementation
started
• Now 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.
26
© The Children's Mercy Hospital, 2014. 03/14
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) paternalism
– Right 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;11:985-988
27
© The Children's Mercy Hospital, 2014. 03/14
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…”
28
© The Children's Mercy Hospital, 2014. 03/14
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 BRCArelated 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, 2013
29
© The Children's Mercy Hospital, 2014. 03/14
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 wnl
• Microarray: 111kb deletion Xq24, a region associated with Xlinked 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)?
30
© The Children's Mercy Hospital, 2014. 03/14
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”.
31
Green RC et al, Genet Med. 2013, 15:565-574 Clarification, Genet Med. 2013,
15:664-666
© The Children's Mercy Hospital, 2014. 03/14
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?
32
Lyon, GJ. There is nothing ‘incidental’ about unrelated findings. Personalized Med.,
2012;9(2):163-6
© The Children's Mercy Hospital, 2014. 03/14
3
PG
statement in pediatric
research
• Public Population Project in Genomics and Society
• WGS results that are scientifically valid, clinically
useful, and reveal conditions that are preventable
and actionable during childhood should be offered
• Mutations that predispose the child to develop an
adult-onset disorder, even if accidentally discovered
in the research process, generally should not be
returned.
33
Knoppers BM, et al, Return of whole-genome sequencing results in paediatric research: a
statement of the P3G international paediatrics platform. Eur J Hum Genet 2013,
© The Children's Mercy Hospital, 2014. 03/14
Topics I wanted to discuss
but ran out of time…
• A new concept: The neurogenomic clinic
• Developing 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”
34
© The Children's Mercy Hospital, 2014. 03/14
In conclusion some practical tips:
Actual costs charged by our lab
• Routine karyotype: $1,969
• High resolution karyotype: $2,250
• Microarray: $3,615
• Genome: $15,000 (includes trio)
• TAG-Scan (572 genes):
– Full symptom driven scan $3,180 (CMH only)
– 2 to 5 genes: $1,700
– 1 gene: $1,250
35
© The Children's Mercy Hospital, 2014. 03/14
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 assistance
– 6 for patients that were ordered inpatient
– 9 were approved by insurance including Kansas
Medicaid
– 12 week turn around
– Requires consent (ACGME 56 gene incidental
findings)
36
© The Children's Mercy Hospital, 2014. 03/14
Things to come at CMH
• Symptom driven exome platform
• Epilepsy and other disease driven panels
• Roll out planned within the next 2 months
• Exome array: Microarray targeted only at
genes (currently send out).
37
© The Children's Mercy Hospital, 2014. 03/14
38
http://www.childrensmercy.org/library/uploadedFiles/childrensmercyorg/Clinics_and_Services/Clinics_and_Departments/Path
ology_and_Laboratory_Medicine/Molecular%20Genetics%20Requisition%206.2013.pdf
© The Children's Mercy Hospital, 2014. 03/14
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
39
© The Children's Mercy Hospital, 2014. 03/14