Genomic Medicine in the NICU Joshua E. Petrikin, MD, Director of Neonatal Genomics

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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