Post on 09-Mar-2020
Xuezhong Liu, M.D., PhD., F.A.C.S.
July 11, 2019
Global Impact and Screening Strategy for Deafness Genes in Individuals with CI
Disclosures
No conflicts of interest to disclose in relation to this presentation.
Grant support: NIH/NIDCD
Second largest medical Center in USA
Jackson Memorial
UMHC/Sylvester Cancer Cent
Veterans AdministrationAnne Bates Leach HospitalUniversity of Miami Hospital
Serving a diverse patient population from the South Eastern United States to Latin America and the Caribbean
University of Miami Ear Institute
Center for Hereditary Deafness
Cochlear Implant Program
Skull Base Treatment Center
Clinical Audiology
Hearing Aid Center
The Center for Advanced Treatment of Meniere's Disease and Balance Disorders
Facial Nerve Disorders
Microsurgery Training Center (RMSB)
Barton G CI Family Resource Center
Thomas Balkany, MD Simon Angeli, MD
Christine Dinh, MD Adrien Eshraghi, MD
Fred Telischi, MD Xue Z. Liu, MD, PhD
University of Miami Ear Institute
Hillary Snapp, AuD, PhD Michael Hoffer, MD
• Extremely heterogeneous with at leas >800 genes involved
• Only >100)Identified genes with diverse function
• 2-3 genes accounting for major component of human deafness
• 20-60% patients identified to have mutations in known genes
Gene Identification
Genetic mapping
Candidate genesPositional/functional candidate genes
Gene
Mouse models
Sequential screening
Gene
Inbred/large families
Cochlear cDNA libraries
Small families
NGS - Exome Sequencing
The discovery that genes at only 2-3 loci account for a major component of human deafness suggested to us that the sequential screening of DNA samples from probands in multiplex sibships for mutations at selected candidate loci would be an effective strategy for identifying new genes for hereditary deafness. And mutations
Nance WE, Liu XZ, Pandya A, Lancet 2000
Sequential Screening Strategy
SequentialScreening ofNon syndromic
DeterminePhenotypicFrequencies &Distribution ofMutantAlleles.
Screening forMYO7A
Screen forCx26 &MitochondrialMutations
Screen forotherconnexinmutations
Cx26Het
Mit-Cx26- Cx26+ Mit+ Mit+ Cx26+ Mit-
Cx26- Cx26 het
Non-syndromic
Screen for otherHuman/mousecloned genes
_
+
+
+_
+
_
_
+
_
Reserve for future genomic tech available
Screening forUSH2A
Screen forotherconnexinmutations
Estimate %genetic deafness
Multiplex Simplex
Identify newDeafness genes
Liu et al, 2003
Full sequence analysis by direct sequencing of individual genes -Dideoxy or Sanger chain termination method
Multigene SNP mutation chips-selected number of mutations in a small number of genes
Next Generation Sequencing (NGS)+Targeted Sequence Capture (TSC)-fully sequence all known deafness genes
NGS + exome sequencing -fully sequqence all coding regions of genome
Third generation Sequencing introduced in a research setting - used with TSC; exome or whole genome sequencing approaches
NGS in widespread use across research setting
whole genome sequencing by third generation sequencing technology may be available in clinical setting
60-70 known genes associated with hearing loss Developments in the speed/cost of
sequencing enable knowledge in the field of genetic hearing loss to proceed at a rapid pace
Potentially all 500 genes involved with hearing loss identified
Sequencing of all 20,000-25,000 genes in the genome may be possible a reasonable cost. Identify all conditions with a genetic basis - issue for all services within the NHS
2010/2011 2013
2015-2016 2020
2012
}
0 yrs
5yrs
3yrs
10yrs
Sequencing technology
Knowledge of genetic hearing loss
Timeline of developments in genetic screening for hearing loss
Screening methods available for genes causing hearing loss in USA
- Sanger sequencing; DNA Array; NGS
Treatment of Hearing Loss
• Ultimate goal is to customize HL treatment based on the particular mutation
• Prevention and early treatment of HL– Prior to giving known ototoxic drugs, screen for pre-disposing
mutations (e.g. m.A1555G)– Early rehab w/ HA or CI and speech therapy– More predictable response to CI or ABI
• Gene therapy• Stem cells• Preimplantation genetic diagnosis
DNA sample collection, population-based cohort data, gene mapping, &
whole exome sequencing
In vitro and in vivo therapeutic Gene/cell/drug-based studies
Clinical Management & Diagnosis
diagnosis, counseling, personalized sequence profile
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oII:1
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MiamiOtoGenomic Diagnostic and Therapeutic Platform
Multidisciplinary collaboration effort
Center for Hereditary Deafness (CHD)
Department of Otolaryngology
Department of Human
Genetics
Department of Biology
HIHG-iPSc Miami OtogeneticCenter
Div of Audiology ECHO
Ear InstituteHearing Loss Clinics (Clinical Services, clinical research)
HIHG
Cochlear implant research Labs
CI Program
Multidisciplinary collaborations & integrate biomedical research and medicine
The Miami Hearing Loss Clinic
The Miami Hereditary Hearing Loss Clinic
Molecular Genetic Lab
The Miami Hearing Loss Clinic
CHD
Miami Molecular Otogenetic Program Miami Clinic Otogenetic Program
Gene Function Lab
HIHG
Case Presentation
• 10 y/o boy with congenital profound HL• CI when 3 y/o, but outcome was poor• USH1B with MYO7A mutations 2010• Autism 2010• Using implant more for environment contact
and preparing worsening eye-sight deteriorates
For 7 Cutler Bay Siblings Born Deaf from genetic etiology, Sweet Sounds
Most families would take the buzz of four kids chirping away over homework for granted, but for the Guillou children, sound was never heard until recently. NBC 6's Keith Jones reports. (Published Monday, Nov 25, 2013)
GJB2/GJB6
Blood SampleTumor tissue Skin Biopsy
Genetic Testing Establish Cell Lines
Therapy
Evaluate Mutations
Test Efficacy of Gene and Drug TherapiesCreate Transplantable Cells
Therapeutic Strategies for genetic deafness
iPSCVirus based therapies
Genome based based therapies
Stem cell based
iPSC
Etiology of Hearing LossIncreasing Importance in Cochlear Implantation
• There are differences in auditory performance that are not attributable to age at implantation or auditory training
• In DFNB1, cochlear nerve and spiral ganglion cells are preserved and this suggests the potential for excellent performance
• Most common identified etiology of congenital deafness in children receiving CI (18-40%)
• Positive GJB2 screening results establish an etiologic diagnosis and provide prognostic, genetic, and therapeutic information
• Better speech performance/preservation of central cognition functionfrom different countries
Vivero et al, Int J of Ped Otol 2010
Vivero… Liu, Int J of Ped Otol 2010
CI in Cx26 Related Deafnessn=31 of 44 Pediatric CI recipients (10/98 – 4/05)
• Mean duration of follow-up: 32 months (12-102)• 1 Med-el, 2 Clarion, 28 Nucleus-24• Verbal comprehension score:
DFNB1: 80%Non-DFNB1: 64% (p<0.001)
• Expressive language scoreDFNB1 75%Non-DFNB1 65% (p=0.04)
• DFNB1 patients show higher scores in Language Development tests, andfaster and more uniform gains on speech perception tests than non-DFNB1patients
Connell…Liu et al Otolaryngol Head Neck Surg 137:596-602 (2007)
Language Skills
• DFNB1 children who use cochlear implants show greater gains in expressive language than non-DFNB1 children, independent of age at implantation and duration of implant use
CI in Usher Syndrome
• Most common deaf-blind disorder
• 7% in congenital deaf patients with CI
• Virtually all members of the deaf community view
the visual impairment as a devastating handicap
• ERG for early diagnosis, genetic tests available now
• Studies showing the best perceptive results found in
children implanted before 9 y/o *Liu XZ, Angeli SI, et al. Cochlear implantation in individuals with usher type 1 syndrome. Int J PediatrOtorhinolaryngol. 2008;72(6):841-847.
Genetic variants in the peripheral auditory system significantly affect cochlear implant performance
Shearer, 2017Etiologic diagnosis INCLUDING neural vs sensory genetic defect is the biggest predictor of post-implant performance (18%). Further work: would different CI programming/rehab work better for neural defects?
Nine Common Deafness Mutations Screening – CapitalBioMiamiArray for Caucasian Populations (Yan et al, PLOS ONE, 2017)
Gene Mutation(s) Frequency in patients (%)
Occurrence in the gene (%)
GJB2 35delC 25.4 Up to 88W44C 0.38 0-3.6L90P 0.29 0-1.47
SLC26A4 L236P 16T416P 15
MT-RNR1 1555A>G 0-3.6 37.6-100
7444G>A 1.6-1.84GJB6 309 kb deletion
Monogenic0.5
309 kb deletion Digenic with GJB2
16-21
A custom capture panel of 180 known deafness geneswith a target size of approximately 1MB (Agilent SureSelect DNA Design). These results prove the accuracy andreliability of the custom capture experiment.
27%
52%
7% 6% 8%
DominantRecessiveBothX-LinkedResearch Purpose
39%44%
7%
2%
8%
Syndromic
Non-syndromicBoth
miRNA
Identifying Causative Gene VARIANTS for Hearing Loss Using a Target Enrichment/Next Generation Strategy – MiamiOtoGenes (MOG)
Tekin et al, 2015; Yan et al, 2016
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21 1 1 1 1 1
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10
MY
O15
AM
YO
7AS
LC
26A
4W
FS
1U
SH
2AT
MC
1T
RIO
BP
OT
OF
MY
O6
ILD
R1
LR
TO
MT
TM
PR
SS
3C
DH
23U
SH
1GO
TO
AD
FN
B31
TE
CT
AD
FN
B59
ES
PN
EY
A4
GIP
C3
KC
NE
1L
AR
S2
MY
H9
PC
DH
15P
OU
3F4
PO
U4F
3S
IX1
TM
IEE
PS
8C
IB2
CO
L4A
5M
AR
VE
LD
2P
TP
RQ
USA IRAN INDIA TURKEY TUNISIA NIGERIA SOUTH AFRICA
Ethnic-Based Sequential Screening Strategy to diagnose genetic deafness and to identifying new genes.
YES
NO
Probands/Pedigrees
Screen GJB2, SLC2CA4, MTRN1
Homozygous or Compound Heterozygous
Pathogenic Variants
YES
Stop
Targeted Sequence All Deafness Genes(MiamiOtoGenes Panel)
NO
Gene Identified
Whole Exome Sequencing
Novel new genes
Screen Repository
In vitro and In vivo Studies
Molecular Epidemiology
YES
Confirm pathogenic Variants CLIA Lab
Miami Clinical Otogenic Program
Sanger SequencingPopulation/Ethnic based GenechipsCapitalBioMiamiArray
MiamiOtoGenes (MOG) used for identification of the remaining cases.
Who should be offered genetic screening in CI patients?
1) Expert opinion by the members of the International Pediatric Otolaryngology Group (IPOG), 2016. After audio, comprehensive genetic testing has highest diagnostic yield of any test for SNHL (62% agree)
2) Non-syndromic children with unilateral HL should NOT be offered genetic testing with initial workup (62% agree)
3) Identification of HL caused from the peripheral auditory system
• CI team will need to become increasingly familiar with available tests and their interpretation in order to use them effectively and counsel patients regarding prognosis and treatment
Conclusions
• Genetic deafness affects 50% of all individuals with hearing loss• > 70% genetic deafness is nonsyndromic• Connexin 26 is the most common etiology• Usually CI given good to excellent outcomes are favorable An appropriate
management algorithm facilitates effective patient careLearn to recognize syndromes and their special considerations
• CI team will need to become increasingly familiar with available tests and their interpretation in order to use them effectively and counsel patients regarding prognosis and treatment
Thank You