Postnatal Exome Sequencing

Transcription

1 Postnatal Exome Sequencing Ata Bushehri, MD, PhD candidate Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran

2 Genetic Counseling Overview Pattern of Inheritance History and Physical Examination Diagnosis Risk assessment Genetic test design Data Analysis (Variant filtration, Annotation) Re-evaluation of the patients Literature review Data validation and Co-segregation analysis Phenotype-Genotype correlation Genetic counseling Disease management

3 A case study A 13 year old boy referred to Milad Hospital with CC of progressive ataxia Present illness: o Sensorineural hearing impairment o Ataxia o Motor and sensory polyneuropathy o Abduction - movement disorder in both eyes o Reduced Deep Tendon Reflexes o Consanguineous parents

4 History and Physical Examination Small for Gestational Age History of Developmental Delay especially in gross motor Dysartheria, staccato speech Learning difficulties Titubation of the head ARSHI (prelingual sensourineural and progressive) Oculomotor apraxia Nystagmus on lateral gaze Hyporeflexia, no Babinski sign Impaired Romberg test Impaired cerebellar examination (finger to nose, heel to shin, rapid supination-pronation) Saccadic dysmetria Ataxic gait Peripheral axonal neuropathy Muscular force in distal regions of lower extremities: 3/5 Pelvic girdle weakness Almost normal muscle tone and bulk IQ: 70-80

5 Paraclinic data EMG/NCV Brain MRI Brain stem OAE/ABR Liver Function Test Kidney Function Test Thyroid Function Test Lumbar Puncture Lactate/NH3/Ceruloplasmin PT/PTT CPK/LDH FANA/RF/ESR/CRP CBC/Hgb Motor and sensory polyneuropathy (axonal distal type) Cerebellar atrophy bilateral abnormal VEP SNHL normal normal normal normal CSF normal normal normal normal normal

6 Differential Diagnosis FXTAS Mitochondrial DNA depletion syndrome (SANDO, Alpers) Zellweger syndrome CAPOS Refsum disease SMA with Pontocerebellar Hypoplasia Cockayne syndrome Biotinidase deficiency CHN (Congenital Hypomyelinating Neuropathy) DSD (Dejerine Sottas Disease) MASA syndrome

7 Genetic counseling POI: AR Hx: SNHL/DD/lingual/learning difficulties/nystagmus P/E: LMND/Ataxia (sensory + cerebellar)/oculomotor problem No MCA/ID/ASD Diagnosis: Neurodegenerative disorder/ar-mitochondrial disorder Conclusion: single gene disorder Genetic heterogeneity Approach: WES

8 Variant prioritization Homozygote variants MAF > 0.01 in EXAC, 1000 Genome, Genome AD, EVS, ESP Located in exonic and splicing regions Non-sense, frameshift, canonical splice variants Genes related to phenotype Computational and conservatory predictive programs for missense variants

9 Candidate gene variants Candidate gene Disease HSD17B4: NM_ :exon17:c.C1508G:p.A503G Congenital disorders of Glycosylation type 2i Hereditary Perrault Joubert Spastic Syndrome Syndrome Paraplegia 54 Perrault Syndrome DDHD2: NM_015214:exon10:c.A1127G:p.D376G Axial hypotonia, hyporeflexia, esotropia HSP54 (Spastic Paraplegia) Molar tooth sign (MTS) in MRI Sensorineural Bilateral Developmental Spastic hearing delays, weakness loss intellectual lower disabilities, extremitiesataxia Hypotonia Ovarian Corticospinal Spinal deformities Dysfunction tract (scoliosis), deficits in women premature aging Developmental delays Family Hypogonadism, history History consistent hyperglycemia, with all AR hyperprolactimia types of mendelian inheritance CC2D2A: Abnormal NM_ :exon23:c.C2842T:p.R948W breathing pattern (tachypnea/ apnea) JBTS9 (Joubert Syndrome) Coagulopathy, impaired LFT No history of hearing loss COG5: NM_006348:exon12:c.A1355G:p.H452R CDG2i (Glycosylation Disorder)

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12 Perrault Syndrome Clinical Characteristics Diagnosis Management Genetic Counseling Treatment of manifestations Agents to avoid 50% 45% 40% Evaluation relatives at risk Hearing loss Sensorineural Hearing Impairments; Premature Ovarian prelingual/progressive 35% Biallelic Insufficiency loss-of-function pathogenic Ovarian 30% dysfunction; Gonadal dysgenesis to POI variants in HSD17B4 Learning difficulties 25% 25% and Developmental delay 25% Cerebellar D-bifunctional ataxia Hearing loss protein deficiency Motor Disorder 20% and sensory of fatty peripheral acid beta-oxidation neuropathy Nystagmus 15% specially on lateral gaze 10% 5% 50% Vibrotactile device Cochlear implantation Induce puberty Assisted reproduction Oocyte Cryopreservation Aminoglycoside drugs 0% affected carrier normal

13 Why to approach genetically? Gene mutational analysis giving much clearer answers on etiology than clinical classification Precise diagnosis: genotype may specify or reverse previous diagnosis or assumed mode of inheritance Accurate prognosis Family planning and accurate counseling Pre-symptomatic testing Allow prevention therapy somehow Increase surveillance Reproductive and career decisions

14 NGS as preferred method No major mutation or disease gene for such hereditary disorders Clear-cut genotype-phenotype correlations largely lacking, preventing efficient targeted Sanger sequencing Chip-based analysis detects only a fraction of causative alleles Gene-by-gene analysis by Sanger sequencing too laborious and expensive

15 WES advantages Hypothesis free trial Reducing dependence upon specific clinical diagnosis Different genetic backgrounds in Iran Reducing cost per locus of testing Extensively parallel genetic testing Collateral clinical findings Targeted NGS identifies mutations in 19-36% of simplex cases

16 Drawbacks Vast amount of incompletely characterized sequence variation confirming pathogenicity is problematic Cost of meaningful analysis of such variations in literature Inability to determine parental origin without family testing Financial and psychological cost of counseling

17 Clinical vs Genetic approach FINANCIALLY Approach Clinical Genetic Time Almost 13 years 6 weeks Precise Diagnosis No solid result Perrault Syndrome Prognosis Management Family planning Variable according to differentials Nothing No comment Accurately progressive Progressive HL Wheelchair bound POI Vibrotactile devices Cochlear implantation Induce puberty Prevent osteoporosis Oocyte Cryopreservation Exact Risk of Recurrence Specific risk for female offsprings Collateral findings No Yes Expenses Enormous (at least 4,500,000) 2,700,000

18 Thanks for your attention