Genomic Medicine in the NICU

© The Children's Mercy Hospital, 2014. 11/14
Center for Genomic MedicineCenter for Genomic Medicine
Joshua E. Petrikin, MDJoshua E. Petrikin, MD
Director of Neonatal GenomicsDirector of Neonatal Genomics
Genomic Medicine in the NICUGenomic Medicine in the NICU

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DisclosuresDisclosures
• I have no conflicts of interest to
disclose
• I will not be discussing off label
medication uses

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OverviewOverview
• Discuss past and current genetic
testing
• Define Genomic Medicine
• Speculate on future directions for
genomics
• Elucidate some ethical considerations
in Neonatal genomic testing

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Genetic TestingGenetic Testing
• The analysis of human DNA, RNA,
chromosomes, proteins, and certain
metabolites in order to detect heritable
disease-related genotypes, mutations,
phenotypes or karyotypes for clinical
purposes.
• Prenatal, newborn, and carrier screening
included.

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http://www.indiana.edu/~oso/lessons/Genetics/MyFamily2.html

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Genetic Testing:Genetic Testing:
Chromosome KaryotypeChromosome Karyotype

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ExampleExample
Patient #1 is a 10 year old girl with short stature and a broad neckPatient #1 is a 10 year old girl with short stature and a broad neck

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Microarrays aka “CHIPS”
• Short oligos are
attached to a solid
support
(microarray).
• Hybridize with
fluorescently
labeled PCR
products
containing SNP of
interest.
• Can analyze many
mutations at once
• Currently > 740k
SNP per chip

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Array-CGH
(comparative genomic hybridization)

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Deletion on array
Muscular Dystrophy
• Since 65-85% of cases
are due to deletions,
start with deletion
testing.
• The lab we use for
dystrophin deletion
testing uses an “exon
array” with high density
probes spanning entire
dystrophin gene.
• Case 4 patient has a
deletion including
exons 44-48 (not shown
here).
• If no deletion
detectable, sequence
entire DMD gene (79
exons!).

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Genomic MedicineGenomic Medicine
• A structured approach
to disease diagnosis &
management that
prominently features
genome sequence
information.
• Decoding Genomes to
diagnose diseases better
and help choose the best
treatments

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Monogenic DiseasesMonogenic Diseases
J Clin Invest. 2008;118:1590-1605. doi:10.1172/JCI34772.

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7,700 monogenic diseases7,700 monogenic diseases
• 4,174 causal genes known
• Affect 4% of children
• Cause 20% of infant deaths
• Cause 17% of pediatric hospitalizations
• Genome Variants determine phenotype
• Genome variants = individual changes in the DNA
sequence from “normal”
• Proving ground for genomic medicine
• 20 year experience with sequence-based diagnosis
• 1-gene-at-a-time
• Slow (months – years)
• Expensive ($2500 - $10,000)
• Requires right gene to be nominated

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Neonatal Intensive CareNeonatal Intensive Care
• 4.1 million babies born in US / year
• 1 in 20 admitted to NICU
• 220,000 (5.4%) NICU admissions/year
• 30% due to congenital abnormalities
• 19,000 neonatal deaths/year
• 6.8/1000
• 22% due to congenital abnormalities
• $3,000 - $8,000 per day

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Neonatal Diseases are UniqueNeonatal Diseases are Unique
• Emergencies
• Rapid results can guide management
• Largely stereotyped presentation
• Broad differential diagnosis workups
• Considerable genetic heterogeneity
• Molecular diagnoses almost never made

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Neonatal Genomic Medicine
NICU
$3,000 - $8,000 per day
Rapid Genome Sequence
• Test for things too rare and/or
heterogeneous to be considered
• Identification of genotype before
phenotype fully manifests
• Diagnose or rule out known
mutations
• Reduce unnecessary tests &
empiric therapies
• Improve prognostic assessment,
genetic counseling
• Unique opportunity to intervene
before irreversible disease
processes manifests with
irreversible symptoms

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Genomic Sequencing – Sanger

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Human GenomeHuman Genome
3.2 billion base pairs, 6.4 billion nt
Equal to typing 60 words/min x 8hrs/day x 50 years
20,000 genes (just 2% of genome)
which encode 100,000 proteins
7700 Monogenic diseases

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Primary Analysis – Base CallingPrimary Analysis – Base Calling
• In Illumina sequencing, each sequencing cycle produces 4 images, one for
each base, where clusters that show that base are lit up
• Base calling done by
• detecting the coordinates of each cluster
• measuring the intensity of the signal at each cluster for each base
• determining which base has the strongest signal
• strength of call results in a quality score for each base
Whiteford N
et al.
Bioinformatics
2009;25:
2194-2199
http://www.
clinchem.or
g/content/5
5/4/641/F4.l
arge.jpg

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Shotgun SequencingShotgun Sequencing
• Shotgun sequencing techniques rely on breaking long strands of DNA
into fragments and then sequencing them individually
• NextGen Sequencing is massively parallel, ultra high throughput
• HiSeq 2500 run produces 1 trillion base pairs in 8 billion 125 bp reads
• Interpreting an individual’s DNA sequence means taking all the pieces
and putting them together into some meaningful context

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Sequence Alignment – Read MappingSequence Alignment – Read Mapping
AGCTATTTATGACCATGATTTTTCTTTTTTTATTTTTTCCATATAAGATAAGATGGAGACGGTCTTTTCTTGTGAGTCTGTTTTTCTGTATTCA
AGCTATTTATGACCATGATTTTTCTTTTTTTATTTTTTCCATATAAGATA
TTTATGACCATGATTTTTCTTTTTTTATTTTTTCCATATAAGATAAGATG
GACCATGATTTTTCTTTTTTTATTTTTTCCATNTAAGATAAGATGGAGAC
TGATTTTTCTTTTTTTATTTTTTCCATATAAGATAAGATNGAGACGGTCT
TTTCTTTTTTTATTTTTTCCATATAAGATCAGATGAAGACGGTCTTTTCTTG
CCATATAAGATAAGATGGAGACGGTCTTTTCTTGTGAGTCTGTTTTTCTG
TATAAGATAAGATGGAGACGGTCTTTTCTTGTGAGTCTGTTTTTCTGTAT
TAAGATAAGATGGAGACGGTCTTTTCTTGTGAGTCTGTTTTTCTGTATTC
• Most human sequence analysis is done by mapping reads to the
human reference genome
• Alignment results are stored in a compact standard file format called
Sequence Alignment Map (SAM) or its binary version BAM
• Each alignment records:
• read position in reference (e.g. chr10:1000-1125)
• mismatch between read and reference
• strand read aligned to
• mapping quality score

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Alignment Visualization in theAlignment Visualization in the
Integrative Genomics Viewer (IGV)Integrative Genomics Viewer (IGV)
• Red reads pointing right aligned to the forward strand
• Blue reads pointing left aligned to the complement strand

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SubstitutionsSubstitutions

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DeletionsDeletions

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Infant CMH487
Diagnosis!
Bioinformatic Filter 5

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Newborn TestingNewborn Testing
• ““If medical or psychosocial benefits of
genetic test will not accrue until adulthood,
as in case of carrier status or adult-onset
diseases, genetic testing should be
deferred…”
• Guides gene analysis/interpretation
• Do not analyze newborns for carrier status or
adult conditions or off-target diseases

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SecondarySecondary Findings
• Also called incidental or unanticipated
findings
• Highly likely, if not inevitable, whenever
WGS/WES is performed
• Examples include:
• finding of a previously unsuspected high risk of
future disease
• discovery of a disorder in an asymptomatic
individual
• detection of carrier status

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Incidental Findings inIncidental Findings in
Neonates?Neonates?
• Mandate to avoid violating a child’s right to
an open future?
• Considerations
• Parents of critically-ill children “just tell me where
to sign”
• Feasibility of reporting secondary findings -
accuracy, expectations, defining the scope
• Impacts:
• Test design (SSAGA)
• Consent
• Communication of results

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Francis Collins, Director of the NIH,Francis Collins, Director of the NIH,
Wall Street Journal, July 8, 2014
 "Over the course of the next few decades,
the availability of cheap, efficient DNA
sequencing technology will lead to a
medical landscape in which each baby's
genome is sequenced, and that
information is used to shape a lifetime of
personalized strategies for disease
prevention, detection and treatment."

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Not quite inexpensive
enough for generalized
newborn screening—
but right up there for
diagnosis of ill infants
in the NICU

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Adapted from Sir George Poste,
circa1999

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Take Home PointsTake Home Points
• Genomic Medicine hold promise, but is
not the final answer
• Proteinomics, metabolomics, epigenetics
• WGS compares most of a patient’s
genome against a reference genome
• Deletions, insertions, triplet repeats
centrimeric anomalies undetected
• The focus on care will shift from disease
centered to patientcentered

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Take Home PointsTake Home Points
• Whole genome sequencing is not ready for
prime time use for newborn screening
• Don’t invest in WGS equipment and
bioinformatics tools yet
• Ethical questions arise as to the use of WGS
for NBS
• Adult onset disorders
• Variants of unknown significance
• Paternity

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Children’s Mercy Hospital
Center for Pediatric Genomic Medicine
Supported By
Clements
Foundation
Marion Merrell Dow
Foundation
National Institutes of
Health
WT Kemper
Foundation
Patton Trust
Director Dr. Stephen Kingsmore

Genomic Medicine in the NICU

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