Genomic biomarkers in human diseaseBorut Peterlin [email protected] Genomic biomarkers...
Transcript of Genomic biomarkers in human diseaseBorut Peterlin [email protected] Genomic biomarkers...
Borut Peterlin [email protected]
Genomic biomarkers in human disease
Modern Molecular- biochemical Markers in Clinical and Experimental Medicine - 2019
7– 9 November 2019, Prague
Genomics for healthcare
Genome medicine
Diagnosis of rare diseases
Personalized medicine
67 % Disease
panels
Clinical geneticist Center for Mendelian Genomics
Clinical Institute of Medical Genetics
Family doctors
Medical specialties
Medical specialties
Several familial MS cases
Primary MS – malignant melanoma family
Sporadic MS cases
Presentation outline
Human Genome initiatives
1.11.2019
Public health challenge
Primary service
S/T service
Specialized (international)
Cummulative point prevalence of Rare diseases
3.5-5.9% EJHG 2019, PMID:31527858
Diagnostic approach
Panels Exomes Genomes
Trio design HPO target definition
+
Medical interpretation of NGS data
NGS in the diagnosis of rare diseases
History Physical & examination
Key features -> Clinical diagnosis
Definite diagnosis
Final diagnosis
Creativity in NGS diagnostics
Clinical/differential diagnosis
Clinical symptoms & signs
Gene target
G1
G2
Gn
Ge
Classification of genetic variants
Genetics in Medicine 2015
AJHG 2016
There is remarkable convergence in bioinformatic techniques,
but medical interpretation and reporting are areas that require
further development by many groups.
Brownstein et al. Genome Biology 2014, 15:R53
Alzheimer disease Frontotemporal
dementia Parkinson’
s
Parkinsonism
Hallucination
Dementia
Language impairment
Personality changes
Parkinsonism Dementia
Bradykinesia
Personality changes
APP
PSEN
1
PSEN
2
SORL
1
C9Orf7
2
GRN MAPT
CHMP2
B
SNCA
LRRK2 PRKN
PINK1
Apathy Disinhibition
Dementia
PSEN
1
TREM
2
LRRK
2
Seizures
Language impairment
Agitation
Confusion
TREM
2
TOMM4
0
Resting tremor
Rigidity
Parkinsonism
Postural instability
PARK7
Alzheimer disease Frontotemporal
dementia Parkinson’
s
Parkinsonism
Hallucination
Dementia
Language impairment
Personality changes
Parkinsonism Dementia
Bradykinesia
Personality changes
APP
PSEN
1
PSEN
2
SORL
1
C9Orf7
2
GRN MAPT
CHMP2
B
SNCA
LRRK2 PRKN
PINK1
Apathy Disinhibition
Dementia
PSEN
1
TREM
2
LRRK
2
Seizures
Language impairment
Agitation
Confusion
TREM
2
TOMM4
0
Resting tremor
Rigidity
Parkinsonism
Postural instability
PARK7
Alzheimer disease Frontotemporal
dementia Parkinson’
s
Parkinsonism
Hallucination
Dementia
Language impairment
Personality changes
Parkinsonism Dementia
Bradykinesia
Personality changes
APP
PSEN
1
PSEN
2
SORL
1
C9Orf7
2
GRN MAPT
CHMP2
B
SNCA
LRRK2 PRKN
PINK1
Apathy Disinhibition
Dementia
PSEN
1
TREM
2
LRRK
2
Seizures
Language impairment
Agitation
Confusion
TREM
2
TOMM4
0
Resting tremor
Rigidity
Parkinsonism
Postural instability
PARK7
Genetic heterogeneity of pediatric neurologic disorders
Developmental delay
(1629 genes)
Epilepsy (870 genes) Metabolic
disorders (615 genes)
Brain malformation
disorders (377 genes)
Neuronal migration disorders
(377 genes)
Hereditary myopathies (237 genes)
Hereditary ataxia
(201 gene)
Neuromuscular disorders
(220 genes)
Intellectual disability
(161 genes)
Hereditary neuropathies (161 genes)
Epileptic encephalopathies
(116 genes)
Leukodystrophies (116 genes)
Myasthenias (56 genes) Microcephaly/po
ntocerebellar hypoplasia (57
genes)
NBIA (15
genes)
Hereditary spastic
paraplegia (54 genes)
Hereditary dystonia
(67 genes) Basal ganglia calcification (27 genes)
Hereditary neurodegeneration
(18 genes) Rett and Rett-Like
syndromes (23 genes)
High genetic heterogeneity of referrals to exome sequencing Over 1000 variants in 618 distinct genes reported in pediatric neurologic conditions
Diagnosis of rare diseases is challenging
• > 7000 diseases
• > 5200 genes
• Clinical & Genetic heterogeneity
• Rarity -> Lack of diagnostic expertise
EUCERD 2014 report
Case 3&4: No obvious hypothesis
Symptoms and signs • Female 14 years • Severe developmental delay • Epilepsy • Corpus callosum hypoplasia • Microcephaly with Brachycephaly • Hearing impairment • Strabismus • Thin, fragile nails • Decreased lacrimation
Differential diagnosis
Chromosome 1p36 deletion syndrome Sotos Dodge syndrome Pallister Killian syndrome Aspargine synthetase deficiency
• Female 52 years • Carpal tunnel syndrome • Mild intellectual disability • Dysplasia of metacarpal bones • Small stature • Hearing impairment • irregular menstrual cycle • Hypothyroidism
Symptoms and signs
Differential diagnosis
Pseudohypoparthyroidism 45 X syndrome Acrodysostosis
Frameshift variant in POGZ gene POGZ:NM_015100.3:c.2771delC
POGZ:NM_015100.3:c402_409dupTGCCAATC
White Sutton syndrome
White Sutton syndrome
Epilepsy Corpus callosum hypoplasia Dysplastic nails Decreased lacrimation
Carpal tunnel syndrome Dysplasia of metacarpal bones Irregular menstrual cycle Hypothyroidism
Autism Visual problems GIT problems
Case 3
Case 4
Full clinical picture
Diagnostic yield / approach
67 % Disease panels
Exome sequencing & interpretation
Disease
Phenotypes
Symptom 1
Sign 1
Symptom 3
Symptom 2
Sign 2
Gene candidates
Gene candidates
Gene candidates
Gene candidates
Gene candidates
Gene candidates
Gene candidates
Diagnostic yield / approach
67 % Disease panels
21 % New diagnosis
67 % Disease panels
21 % New diagnosis
New associations
Reinterpretation
Whole Genome Sequencing
Patient with suspected Angelman like syndrome
2014
Negative report
No mutation found in
the exome sequencing data.
Reinterpretation of exome sequencing data
2015
New data in the literature
We conclude that the identified
EEF1A2 variant presents a likely
cause of the referral clinical
presentation.
2016
Establishment of a diagnosis
Clinical geneticist Center for Mendelian Genomics
Clinical Institute of Medical Genetics
Family doctors
Medical specialties
Medical specialties
Clinical pathway for NGS testing at KIMG
Clinical pathway for patient referral
02
03
04
01
28%
18%
14%
DIrectly Neurologist to laboratory
Combination Combination of approaches
Team
Clinical geneticist
35%
Prioritisation of NGS in diagnostic algorithm
46% First tier diagnostic diagnostic tool
After traditional diagnostic workup 54%
Referring physician Molecular geneticist MD +
Bioinformatician Clinical geneticist
Different specialities
Pathway for NGS diagnostics at KIMG
Diagnostic yield: KIMG experience
Positive
41,2% Negative
45,0%
VUS
13,8%
WGS
+ 0,2%
New diagnostic alghorithms
Primary prevention of genetic diseases
US/biochemical NIPT
Down syndrome Congenital anomalies Inherited diseases
Karyotyping
QF-PCR
aCGH
Next generation sequencing
Targeted testing
AC/CVS PGD
Preconceptional genetic testing
Preimplantation genetic diagnosis (PGD)
Polar body biopsy Cleavage stage biopsy Blastocyst biopsy
Blastocentesis
Structural rearrangement by NGS
• Mother 46,XX,t(4;5)(p15.3;p15.1)
• Father 46,XY
Disease
Location
Eiberg 1985
Reverse genetics – positional cloning
Gene Rommens 1989
Description of new syndrome & gene
Identification of new genes
Disease
Gene
Clinical exome Whole exome
sequencing
Whole mitochondrial
genome sequencing
Sequencing > 5000
known genes associated
with human diseases
Sequencing of all
predicted human genes –
20 000
Sequencing of the whole
mitochondrial genome
Whole genome
sequencing
Sequencing of the whole
human genome
A boy with prematurely aged appearance, growth retardation, hypoplastic terminal phalanges with features of premature aging
included reduced subcutaneous fat, wrinkled skin, scant hair
Suspected Petty syndrome, Petty type (gene not known yet)
Fotografija: Irena Lesjak, delo.si
Pat
ien
t M
oth
er
Fat
her
SLC25A24 p.Arg217His PPP1R13B p.Thr391fs
Exome sequencing in the patient
Matchmaking in a progeria syndrome with yet
unknown causative gene (all identified cases share the same de novo variant)
French case Our case
Italian case Spanish case
Germany (multiple cases)
All patients shared
de novo variants affecting
Arg217 residue in
SLC25A24 protein
G A
wt/wt wt/wt
PArg217His/wt
wt/wt wt/wt
P
wt/wt
P
wt/wt
Arg217Cys/wt
wt/wt wt/wt
PArg217His/wt
Arg217His/wt
French familySlovenian family
Spanish family* Italian family
G A C G G G A C G G
G A Y G G
G A C G G G A C G GG A
C/T
G A Y G GC/T
* results from single base extension assay
denotes sample availability for testingP denotes familial proband
G A
G A Y G GC/T
G A C G GG A C G G
Writzl et al, AJHG, 2017.
p.Arg217Cys or p.Arg27His Causes Significant Structural Changes within the SLC25A24 Transmembrane Domain
A boy with prematurely aged appearance, growth retardation, hypoplastic terminal phalanges with features of premature aging
included reduced subcutaneous fat, wrinkled skin, scant hair
Suspected Petty syndrome, Petty type (gene not known yet)
Fotografija: Irena Lesjak, delo.si
Patient with seizures, polymicrogyria and developmental delay of unknown etiology
A de novo missense variant in SCN3A gene
Although SCN1A and SCN2A have been reported, the role of de novo SCN3A variants in epilepsy was unknown at the time (early 2016)
Variant of uncertain significance in a gene of unknown significance
46
Our case
Several cases with de novo SCN3A
variants and an overlapping phenotype
New York case
UK cases (several)
Washington case
Germany case
Pennsylvania case
Monogenic vs. complex (polygenic + environment) disorders
G
Clinical Matcmaking
51
French
case
Our
case
nature genetics • volume 33 • january 2003 Neuroscience Letters 650 (2017) 25–32
Conclusion: Poor evidence for association
NR4A2 role suggested but unconfirmed
High genetic heterogeneity of referrals to exome sequencing Since introducing NGS we reported over 3000 variants in 1124 distinct genes
Economic innovation & sustainability
0
100
200
300
400
500
600
700
2011 2012 2013 2014 2015 2016 2017
Solved cases VUS Negative result
Diagnostics abroad Diagnostic exome sequencing
• Clinical pathways – NGS in health system
• Diagnostic approach – exome sequencing & interpretation
• Diagnostic algorithms
• Funding
• Telegenetics
• Identification of Mendalian disorders in health system
• Routine diagnostics meets research
• “Future” personalized medicine
Genomic inovations in the Slovene Health System
Genome screening
Setting the scene for personalized genomic medicine
• Primary purpose of carrier screening
• Carrier screening panels
• Evidence
• Timing of screening
• Information and support
• Informed consent
• Voluntary participation
• Quality of services
• Maximizing quality of care
• Professionals and public education and dialogue
• Governance
Family history screening in primary care
13%
Family history tool into the primary health system
Clinical geneticist Center for Mendelian Genomics
Clinical Institute of Medical Genetics
Medical specialties
Would you like to know if you/partner are carriers for genetic predisposition which might affect your child?
1- not at all, 5-very much
Slovenian Genomic Variability db
Coding variants • 164,301 SNVs & Indels
• 79,800 SNVs & Indels / patient
• 78,146 rare variants
• 22,724 rare variants not in GnomAD
• 43.7 rare variants / patient
1. CEMGPdb
2. Variant Interpretation Platform
3. New genes for human diseases
“Future” Personalized Medicine
54 %
3 %
Preconceptional genetic screening Screening for preventable AO disorders
• 293 genes associated with drug response • 24 known actionable pharmacogenetic variants • 61 variants with PharmaGKB 2A or 2B support • 308 novel potentially actionable variants
Monogenic contribution to complex disorders
Parkinson’s disease
Multiple sclerosis
Alzheimer’s disease
Ataxias Choreas
ALS
G
G ?
G
G
G
Genetic predisposition for MS
Common variants
“Missing heritability”
Rare variants
Shared environment
Individual environment
Ristori G et al., Ann Neurol 2006, 59: 27–34
IMSGC, Cell 2018, 175, 1679–1687
Several familial MS cases
Primary MS – malignant melanoma family
Sporadic MS cases
Searching for monogenic forms and disturbed pathways in Multiple sclerosis
The role of inflammasome in MS
Are mutations in the GJB1 gene risk factor for multiple sclerosis?
No other mutation in the GJB1
gene In our cohort of familial
and sporadic MS patients
No increased burden in panel of
genes for demyelinating
neuropathies
Human endogenous viruses
HERVs
Coding region
HERV insertions as risk factors for MS
HERV-K insertions in the introns of
RASGRF2 and PTPRN2 genes
are a heritable risk factor for MS
Thank you!