Next generation sequencing technologies (NGS) for whole exome/genome sequencing (WES/WGS):

impact on daily clinical practice, in dementia and beyond

9ο Πανελλήνιο Διεπιστημονικό Συνέδριο Νόσου Alzheimer Θεσσαλονίκη 14-17/5/2015

Ζαγανάς Ιωάννης Νευρολόγος, Επίκουρος Καθηγητής Νευρολογίας

Βογιατζή Εμμανουέλλα, Βιολόγος-Γενετίστρια

Λατσούδη Λένα, Βιολόγος-Γενετίστρια

Introduction: Clinical whole exome sequencing as a tool to end the “diagnostic Odyssey”

Ζαγανάς Ιωάννης Νευρολόγος Επίκουρος Καθηγητής Νευρολογίας, Τμήμα Ιατρικής Πανεπιστημίου Κρήτης / Πανεπιστημιακό Γενικό Νοσοκομείο Ηρακλείου

9ο Πανελλήνιο Διεπιστημονικό Συνέδριο Νόσου Alzheimer Θεσσαλονίκη 14-17/5/2015

Lu et al, N Engl J Med, 2014

Η δική μας εμπειρία

Πρόγραμμα «Γενετικές αναλύσεις νέας γενιάς σε ασθενείς

με νευρολογικές και άλλες παθήσεις»

18-year old woman with limb-girdle muscular dystrophy

• Her sister similarly affected, but not her parents

• Central-type muscle weakness, severely depressed tendon reflexes, calf hypertrophy, scapular winging, waddling gait

• Subject to multiple tests, including muscle biopsy, with no diagnostic results obtained

Sarcolemma and proteins involved in muscular dystrophies (Mercuri and Muntoni, 2013)

ISPD: isoprenoid synthase domain containing

Sarcolemma and proteins involved in muscular dystrophies (Mercuri and Muntoni, 2013)

ISPD

Diagnosed by us (UOC)

Sarcolemma and proteins involved in muscular dystrophies (Mercuri and Muntoni, 2013)

ISPD

Diagnosed by us (UOC)

2-year old girl with recurrent lactic acidosis, epilepsy

• Hypotonia • Seizures • Mental retardation • Microcephaly

Diagnosed by us (UOC)

2 y.o. f., lactic acidosis, epilepsy

2 y.o. f., lactic acidosis, epilepsy

13 y.o. f., myalgias, ↑ CPK

6 y.o. f., myopathy

Diagnosed by us (UOC)

62-year old man with progressively worsening muscle weakness (A)

• About 15 years ago, weakness and muscular atrophy in the periphery of his extremities was noted (progressively worsening since then)

• Deep tendon reflexes abolished in all 4 extremities

• loss of sensory function in a stocking-glove distribution (pain, temperature, vibration)

• FH: Brother died at a young age from an, further un-specified, neurological disorder that led to quadriplegia

62-year old man with progressively worsening muscle weakness (B)

• Electrophysiology: sensorimotor demyelinating-type polyneuropathy (later on with a patchy distribution)

• LP: moderately increased protein • Testing for PMP22 duplication: negative • Patient subjected to several tests (at various

centers) with no diagnostic results • Treated with immunotherapy with no improvement

Rossor et al, Nat Rev Neurol,

2013

Rossor et al, Nat Rev Neurol, 2013

Diagnosed by us (UOC)

Jean-Martin Charcot (1825 – 1893)

Pierre Marie (1853-1940)

Howard Henry Tooth (1856–1925)

The application of whole exome sequencing in dementia and beyond: the clinician’s viewpoint

Ζαγανάς Ιωάννης Νευρολόγος Επίκουρος Καθηγητής Νευρολογίας, Τμήμα Ιατρικής Πανεπιστημίου Κρήτης / Πανεπιστημιακό Γενικό Νοσοκομείο Ηρακλείου

9ο Πανελλήνιο Διεπιστημονικό Συνέδριο Νόσου Alzheimer Θεσσαλονίκη 14-17/5/2015

Γενετικοί παράγοντες συνδεόμενοι με βεβαιότητα με τη νόσο Alzheimer

Χρωμό- σωμα

Αριθμός μεταλλάξεων (οικογένειες)

Ηλικία έναρξης

(έτη)

% περιπτώσεων πρώϊμης έναρξης

% συνολικών

περιπτώσεων

APP 21 33 (90) 45-65

Γονίδια σχετιζόμενα με FTLD ( AD and FTD Mutation Database, Nov 2014)

Μεταλλαγμένο Γονίδιο Φαινότυπος Locus Μεταλλάξεις(οικογένειες)

Expansion of a non-coding hexanucleotide repeat (C90RF72) FTLD/ALS 9p21 1 (336)

Progranulin (PGRN) FTLD 17q21-q22 69 (231)

Microtubule-associated protein tau (MAPT)

FTLD (FTDP- 17) 17q21-q22 44 (134)

TDP43 protein (TADPR) ALS/FTLD 1p36 34 (131)

Fused in sarcoma (FUS) ALS/FTLD 16p11.2 23 (49)

Valosin-containing protein gene (VCP) IBMPFD 9p21-p12 18 (48)

Charged multivesicular body protein 2B (CHMP 2B) FTLD 3p13-3p12 4 (5)

Genetic testing for familial dementia with additional neurological features (Loy et al, 2014)

18-year old woman with progressive myoclonic epilepsy and dementia

– At the age of 14 y.o. visual phenomena – Since 2-3 years myoclonus and possibly absence

seizures – Gradual decline in cognitive functions – FH: negative for neurologic disease – MRI: Normal – Initial response to levetiracetam, later evolution to

generalized seizures despite addition of valproate

PME Type Gene Locus Protein

Unverricht- Lundborg disease

EMP1 (CSTB) 21q22 Cystatin (protease inhibitor)

Lafora disease EMP2A EMP2B/NHLRC1

6q24 6p22

Laforin Malin

Neuronal ceroid lipofuscinosis (CLN1- 8, CLN10)

PPT1 (CLN-1) ……

1p32 Palmitoyl-protein Thioesterase- 1

MERRF syndrome A8344G Mitochondrial DNA Lys tRNA

Sialidosis Type Ι NEU1 6p21.33 Neuraminidase (glycoprotein metabolism)

DRPLA ATN1 12p13.31 Atrophin 1 (nuclear protein)

Progressive myoclonic epilepsy and dementia

Τύπος PME Γονίδιο Locus Πρωτείνη

Unverricht- Lundborg disease

EMP 1 (CSTB) 21q22 Cystatin (protease inhibitor)

Lafora disease EMP2A EMP2B/NHLRC1

6q24 6p22

Laforin Malin

Neuronal ceroid lipofuscinosis (CLN1- 8, CLN10)

PPT1 (CLN-1) ……

1p32 Palmitoyl-protein Thioesterase- 1

MERRF syndrome A8344G Mitochondrial DNA Lys tRNA

Sialidosis Type Ι NEU 1- 6p21.33 Neuraminidase (glycoprotein metabolism)

DRPLA ATN 1 12p13.31 Atrophin 1 (nuclear protein)

ΕΠ: Μ. Τζαρδή

Τύπος PME Γονίδιο Locus Πρωτείνη

Unverricht- Lundborg disease

EMP 1 (CSTB) 21q22 Cystatin (protease inhibitor)

Lafora disease EMP2A EMP2B/NHLRC1

6q24 6p22

Laforin Malin

Neuronal ceroid lipofuscinosis (CLN1- 8, CLN10)

PPT1 (CLN-1) ……

1p32 Palmitoyl-protein Thioesterase- 1

MERRF syndrome A8344G Mitochondrial DNA Lys tRNA

Sialidosis Type Ι NEU 1- 6p21.33 Neuraminidase (glycoprotein metabolism)

DRPLA ATN 1 12p13.31 Atrophin 1 (nuclear protein)

Τύπος PME Γονίδιο Locus Πρωτείνη

Unverricht- Lundborg disease

EMP 1 (CSTB) 21q22 Cystatin (protease inhibitor)

Lafora disease EMP2A EMP2B/NHLRC1

6q24 6p22

Laforin Malin

Neuronal ceroid lipofuscinosis (CLN1- 8, CLN10)

PPT1 (CLN-1) ……

1p32 Palmitoyl-protein Thioesterase- 1

MERRF syndrome A8344G Mitochondrial DNA Lys tRNA

Sialidosis Type Ι NEU 1- 6p21.33 Neuraminidase (glycoprotein metabolism)

DRPLA ATN 1 12p13.31 Atrophin 1 (nuclear protein)

65 year old man with muscular weakness, fibrillations and behavioral disorder

– Since 2010, according to his wife, language problems (“poor speech”), inability with rational associations, change in behavior, recklessness, poor grooming, flat affect, inability to perform his work, loss of interests

– On 2011 weakness of the left upper extremity, gradually worsening and extending centripetally and then to the other extremities and bulbar muscles, fibrillations, atrophies (on examination increased tendon reflexes)

– FH: Negative for neurological disorders

65 year old man with muscular weakness, fibrillations and behavioral disorder

Turner et al, 2013

Γονίδια σχετιζόμενα με FTLD ( AD and FTD Mutation Database, Nov 2014)

Μεταλλαγμένο Γονίδιο Φαινότυπος Locus Μεταλλάξεις(οικογένειες)

Expansion of a non-coding hexanucleotide repeat (C90RF72) FTLD/ALS 9p21 1 (336)

Progranulin (PGRN) FTLD 17q21-q22 69 (231)

Microtubule-associated protein tau (MAPT)

FTLD (FTDP- 17) 17q21-q22 44 (134)

TDP43 protein (TADPR) ALS/FTLD 1p36 34 (131)

Fused in sarcoma (FUS) ALS/FTLD 16p11.2 23 (49)

Valosin-containing protein gene (VCP) IBM