Prof. T.Sarkisian Prof. H.Hayrapetyan

Single-gene microdeletions / microduplications

Single-gene Reciprocal microdeletions / or oligogenic common microduplications syndromes diseases

Intellectual disability Developmental delay Autism Schizophrenia Coronary diseases

By Lupski et al., Cell, 2011, with modifications

1 Clinical Genetics is an important part of clinical practice. Medical genetics is confined to thousands of rare diseases and is becoming a central point of our understanding of most major pediatric and adult diseases: heart, diabetes, cancer, psychiatric, neurological, metabolic disorders, etc…

Clinical geneticist: is a physician who diagnosis and prescribes the treatment for patients with genetic conditions. Genetic counselling: communication of information regarding risks, prognosis, estimation of Inheritance of disease in families, determination specific genetic tests that need to be performed & interpretation for patient. GENOME (ome: from Greek- all): the complete set of human genes. Genomic medicine: large-scale analysis of genome, control of gene expression, understanding mapping of disease genes, location on chromosomes, interactions with environment, for medical care. At the beginning of XXI century: Human Genome Project: provided complete sequence of human DNA. How Genes contribute to health & disease? Genetic diseases are caused by mutations: →that are inherited from the parents and are present in an individual at birth. →that are acquired mutations in a gene or group of genes that occur during a person's life. Such mutations are not inherited from a parent, but occur either randomly or due to some environmental exposure: many cancers… Genetics is often more complex… than initially thought. New mutation? Cause 1: An error during meiosis: Nondisjunction: • causes a defect in a sperm/ovarium cell. If one of this gametes is involved in fertilization, it usually results in miscarriage. But in a few cases, a baby will develop genetic disorder. Examples: • Aneuploidy: deviation from a normal number of chromosomes by gain or loss: Monosomy: only 1 of a pair present • Trisomy: 3 instead of 2 present

Cause 2: Result of mutated genes. A defective gene present in one or both of parents is inherited directly by the child.

Cause 3: Most noncommunicable diseases involve many genes, in addition to environmental influences. An individual may not be born with a disease but may be at high risk of acquiring it. This is called as genetic predisposition or susceptibility. The genetic susceptibility to a particular disease due to the presence of one or more gene mutations: Cancer, Diabetes, Cardiovascular diseases, Asthma… Aetiologic classification of genetic disorders: → Monogenic disorders: mutation in one gene, → Multifactorial disorders: combination of mutations in multiple genes and environmental factors, → Chromosomal disorders: changes in the number or structure of entire chromosomes (the structures that carry genes). → Somatic cell Disorders (Dysplasias- Cancer) → Mitochondrial Disorders •Down syndrome Chromosome • occuring 1/every 150 live births Mutation •Cystic fibrosis (genetic Gene • Haemophilia change) • Huntington disease Multiple •Cancer genes + • Diabetes environmental • Heart disease factors How genomics apply to medicine?

Pediatricians Rheumatologists

Hematologists Neurologists

Ophtalmologists Psychologists

Oncologists Psychiatrists

Neonatologists Orthopedics Therapists Gynecologists RARE DISEASES: affecting less than 1 in 2,000 individuals Over 8,000 different rare diseases 6 to 8% of the population over lifespan 1 in 17 people are affected by a ‘rare disease’ 60 million people living with a rare disease in Europe and USA 300 million people living with a rare disease in the world All ages, mostly children Some main groups: metabolic, neuro-muscular, autoimmune, developmental anomalies, bleeding disorders, cardiovascular, respiratory, skin diseases, rare cancers… Оnly 5% of RD have treatment 1 in 10 GP visits is for a patient whose condition has a genetic cause. Characteristics of Rare Diseases: .Chronic, progressive, degenerative, disabling and frequently life-threatening 50% pediatric beds occupied •34% deaths in childhood •50% causes deafness and blindness

Examples of autosome-dominant disorders: Fetal alcohol syndrome & Phocomelia induced by Thalidomide

PHENOCOPY: an individual whose phenotype is environmentally induced to mimic the genetically determined phenotype. These changes are not mutations/alterations of DNA sequences. These changes are not heritable. Mendelian (and non-traditional) inheritance

We all know them already from the school -or do we?

In medical genetics Monogenic inheritance Autosomal dominant By "Mendelian inheritance" we Autosomal recessive mean monogenic disorders. This X-linked dominant means diseases that are caused X-linked recessive (almost exclusively) by mutations Y-linked in one gene (pair). In everyday language: The genes are in the chromosomes Autosomal dominant inheritance = A normal human being has 46 dominant inheritance chromosomes Autosomal recessive inheritance = There are 44 (22 pairs) of autosomal recessive inheritance chromosomes or autosomes X-linked recessive inheritance = Sex-chromosomes are X and Y X-linked inheritance (and dominant is specifically mentioned) Mendelian/monogenic diseases Traditional view •Prevalence <0.05%, EU •“Simple”: monogenic •One gene <> one disease •Mendel’s laws of segregation

Modern view •Rare, but collectively > 6% population •Pleiotropy 2937 genes → 4163 Mendelian phenotypes •Genetic heterogeneity: one disease ↔ many genes •Mendel’s laws exceptions: incomplete penetrance, DNMs

Future plans •Genes for 50% Mendelian phenotypes still unknown •Improve clinical interpretation of human genomic variation •Understand the widespread overlap with common diseases •Translate basic biological concepts into medically usable knowledge AUTOSOMAL DOMINANT INHERITANCE

→ The responsible gene is located on autosome (chr #1-#22) → The disease hits males and females → Diseased individuals follow in each generation → Any child of affected person has 50% risk to inheriting the trait → Vertical transmission of the disease phenotype, a lack of skipped generations → In phenotypically normal individual the children will be healthy AUTOSOME DOMINANT INHERITANCE Three distinct causes of differences in expression: •Penetrance is the probability of gene expression: Penetrance is <100%: the gene has reduced penetrance. 80%: only 80% expression of phenotype; a gene carrier may be without symptoms, but the child – will develop symptoms. • Age-related penetrance: Late-onset of dominantly inherited diseases with variability in clinical manifestations and age at which symptoms first appear: HD, Alzheimer`s, Macular degeneration, etc.

•Pleiotropy. When a gene produces different phenotypic effects, its expression is said to be pleiotropic.

•Expressivity is the degree (severity) of expression of the phenotype. When the phenotype differs in people with identical genotypes, the phenotype has variable expressivity (allelic heterogeneity).

→New mutations in gametes of normal parent NON-COMPLETE PENETRANCE: Example: Sickle cell anemia: advantage in case of malaria: during 1500 y. = 60 generations: selective resistance/advantage of heterozygotes. Norm allele of β-globin: HbA Sickle-cell: Homozygotes: HbS/HbS Heterozygotes: HbA/HbS: HbA: dom; HbS: non-complete dom. Co-dominant inheritance: expression of the alternative alleles: blood groups ABO: Blood groups: Antigens present Antibodies present (I) O Universal donors No No (II) AA,AO A Antigen Anti-B (III) BO,BB B Antigen Anti-B (IY) AB Universal recipient A & B Antigen Anti-A & Anti-B → Variable expressivity: disease is differently expressed within family: Neurofibromatosis: symptoms on skin/nervous system. Type 1: “NF von Recklinghausen”: mutations of Neurofibromine gene: NF1(17q 11.2). Incidence 1:3500 -4000: 90% of all NF cases Neurofibromas (nerve tissue growth tumors /tumors of Schwann cells) on or under the skin. 2 or more neurofibromas; number increase with age. “Cafe au lait” spots Axillary freckling Lisch nodules (affecting the iris) → → → → → Tumors on the optic nerve (optic gliomas) Scoliosis Epilepsy Macrocephaly on 30-50% of children with NF

Type 2: “Central NF”: Mutations of gene Neurofibromin 2: NF2 (22q12). Incidence 1:45000: -Bilateral acoustic neuromas (schvannoma) of cranial nerve 8; -Brain tumors; meningiomas -Hearing loss, balance problems, deafness -Paralysis of face: tumors of cranial nerve 7. -NF1 & NF2 genes: tumor suppressor genes Factors that may complicate Mendelian inheritance patterns: Highly variability in the phenotypic manifestations of mutant genes:

Plexiform neurofibroma In this case: The father, child, grand-father: were short, had very personal facies and sandal-gap as shown in the picture. The diagnosis was unknown but the inheritance was, according to the family history, autosomal dominant. Pleurotropy: Marfan syndrome: frequency 1:10.000 mutation: FIBRILLIN-1 (FBN1: 15q21.1): fibrillin: connective tissue protein; 30% de novo mutations. Clinical diagnosis is based on Ghent nosology (Loeys et al, JMG, 2010): affects 3 major systems: •CARDIOVASCULAR: prolapse of the mitral valve (1-3% in general population); dilatation of blood vessels, aortic aneurisms (90%), pneumothorax; •SCELETAL: gothic palate, joint hypermobility; pectus excavatum (“hollow chest”); pectus carinatum (“pigeon chest”); tall stature, dolichostenomelia (long, slender limbs), arachnodactyly (spider-like fingers), scoliosis. •OCULAR: myopia, subluxation of the lens (50-80%) Current treatment strategy: •Medication (beta-blocker): slows down the progression of •aortic root dilation •Surgery (aortic replacement): preventive at aortic root diameter of 5 cm

Skeletal dysplasias: FGFR Gene Family mutations: Prevalence: 1 in 2000 births Large group of clinically and genetically different disorders of bone and cartilage development. Premature fusion of one or more cranial sutures leads to head deformity and facial asymmetry. Lack of space for the growing brain: raised intracranial pressure, cranial nerve damage (hearing & visual abnormalities), learning disabilities/mental retardation, neurological problems.

Pfeiffer syndrome: FGFR1, -2 Sæthre-Chotzen syndrome: TWIST1 APERT SYNDROME Gene FGFR2: Acrocephalosyndactily CROUSON SYNDROME: Gene FGFR 2: mid-face hypoplasia, ocular proptosis. Distraction Osteogenesis is an innovative treatment option in craniofacial surgery Achondroplasia: bone dysplasia/dominant dwarfism: bone deformity, disproportional shortness, normal trunk, Frequency: 1:40000. 90%: new mutations. FGFR3 gene/chr. 4p16.3: Point GOF mutation G380R; failure in cartilage formation.

Ac ac x Ac ac ↓ 1 AcAc lethal 2 Acac sick 1 acac healthy HYPERCHOLESTERINEMIA TYPE IIa: Frequency: 1:500 (Aa) and 1:1,000000 (AA) Lipid metabolic disorder: enhanced blood cholesterol level (>200 mg/dl) due to low-density lipoproteins LDL- receptor-gene-defect (chr.19q13.2). LDL-levels in heterozygotes are 270-550 mg/dl and in homozygotes 650- 1000 mg/dl. Fat in skin, xanthomas, risk for heart attacks & peripheral vascular diseases.

LACTOSE INTOLERANCE: Lactose: disaccharide: consists of 2 sugars: glucose & galactose. Lactase breaks lactose down into these sugars to be absorbed into bloodstream. Lactose is found in milk, and every child is born with ability to digest it. But 75% of world population is lactose intolerant: lactose molecules cannot be digested in small intestine. The cause are SNP differences in nucleotide sequence of lactase gene between lactose tolerant and intolerant people. AUTOSOMAL -RECESSIVE INHERITANCE: is typical for gene mutation localized on a non-sex chromosome/autosome. Both copies of the gene need to be defective for the disorder to be expressed. If one copy of the gene is affected but the other is normal: the person is “carrier”. Inheritance is horizontal:the disease appears in sibs, not in their parents, offspring or other relatives. The parents of the affected child may be consanguineous On the average, 1/4 of the sibs of the proband are affected: Recurrence risk: 25% Manifestation – in homozygotes and compound heterozygotes. Affected patients don`t appear in 2 following generations. ♂ & ♀ hit in same frequencies. Each person has 1.1 mln ancestors when going back 40 generations. Inbreeding/consanguinity: blood relationship: relation and have inherited mutations from common ancestor. Consanguinity increases the chance that a couple will carry the same. disease-causing mutation & increases the frequency of recessive◄ diseases/mortality. Ex. Xeroderma pigmentosum (20% of cases result from marriages between cousins). In cousin marriage child-mortality is 3.5% higher, but not deleterious for population. Quantitative expression of consanguinity is the Inbreeding coefficient. Gabsburg lip: inbreeding was over several generations: Inbreeding coefficient increased from 0.025 (1516) to 0.254. Germany: Coefficient of inbreeding: 0.1-0.3% South Turkey: Coefficient of inbreeding: 28%. Incest: couple between 1st -degree relatives (siblings or parent-child): .

Autosomal Recessive Genetic Disorders

Cystic fibrosis Phenylketonuria Galactosemia 1:3900 1:8000 – 1:18000 1:55000

On chromosome 7: On chromosome 12 On chromosome 9 Affects respiratory / Affects breaking Affects ability digestive sys. down protein in the to break down body. galactose.

Mutation in gene that Prevents liver enzyme Lack enzyme affects salt movement, PAH:phenylalanine GALT (converts thus produces thick hydroxylase mutation: galactose into Sticky mucous on accumulation of PhA glucose). outside of cell. →phenylpyruvate → This mucous clogs severe MR, seizures. airways. >Cystic fibrosis: disturbed function of exocrine glands. • Incidence about 1:2500 in Europe • 1:15000 in Africa •

>1300 mutations in CFTR gene: (chr 7q31.2) In healthy: CFTR protein – transporter of chloride-ions to the cell membranes be brought out of the cells.

In CF-children: viscous mucous in lungs → pneumonia, chronic cough, infections, meconium ileus (10% newborns). Less severe forms: male infertility. FMF is inherited and ethnically restricted disorder affecting populations of Mediterranean ancestry.

First information about recurrent inflammatory syndrome in Armenians was reported in ancient manuscripts in XII Century. FMF: the most common known inherited periodic autoinflammatory disorder of the group of inherited inflammatory disorders of innate immunity so-called autoinflammatory diseases predominantly affects people of Mediterranean origin.

1999: “Cell”: the term “AUTOINFLAMMATORY DISORDERS”: different from autoimmune syndromes: genetically driven dysregulated innate immune response, elevated secretion of pro- inflammatory cytokines and consequent damage to host tissues. AUTOINFLAMMATORY SYNDROMES/HEREDITARY PERIODIC FEVERS: >500 gene mutations revealed in last 10 y. OMIM DISEASE GENE CHROMOSOME TYPE OF LOCATION INHERITANCE 142680 TRAPS: TNF- Receptor Associated Periodic fever Syndrome: 1999: Type 1 TNF-α AD L.M.Williamson etc., 1982 receptor gene (TNFRSF1A): Chromosome 12p13.31 260920 HIDS: Hyperimmunoglobulinemia D Syndrome 1999: Mevalonate kinase AR Hyper IgD syndrome; gene (MVK): Chromosome 12q24.11 604416 PAPA: Pyogenic arthritis, pyoderma gangrenosum, PSTPIP1 gene: AD acne syndrome Chromosome 15q24.3 612852 DIRA: Deficiency of IL-1 Receptor Antagonist: IL1RN gene: AR severe skin and bone inflammation, and other organs Chromosome 2q14.1 604416 CAPS: Cryopyrin associated periodic fever syndromes: 1999-2001 – NLRP3 gene AD Familial Cold Autoinflammatory syndrome (FCU) encoding cryopyrin protein: 1962: Muckle-Wells syndrome (MWS) Chromosome 1q44. Neonatal-onset multisystem inflammatory disease (NOMID) & Chronic infantile neurologic cutaneous and articular syndrome (CINCA)

615934 STING: STING-associated vasculopathy with onset in infancy STING-transmembrane AD (SAVI) protein gene : Chromosome 5q31.2

108300 Stickler syndrome: facial appearance, eye Type II Collagene gene AD abnormalities, hearing loss, and joint problems. Chromosome 12q13.11 154780 PFAPA: Marshall syndrome: periodic fever, COL11A1 gene, AD aphthous stomatitis, pharyngitis, and adenopathy Chromosome 1p21.1 What are typical findings for FMF? Recurrent attacks of moderate to high fever (1-3 days) Painful serositis: Abdominal pain (peritonitis in 90%) Thoracic pain (secondary to pleuritis in 45%) Mono-/oligo- articular arthritis:hip,knee, ancle (in 75%) Less common: Erysipeloid erythema Myalgia Severe complication: renal amyloidosis Age of onset: Can occur at any age, < 20 yr in 80% . During attacks: Leukocytosis, ESR↑, CRP ↑ Risk of amyloidosis: SAA ↑. M:F  1.5-2 Type of inheritance: autosomal recessive. 1997: Tel Hashomer diagnostic criteria: 2 major criteria: Recurrent febrile attacks/amyloidosis/arthritis/favorable response to Colchicine Or 1 major + 2 minors: Erysipelas-like erythema/mialgy/family history

2012: Guidelines of the genetic diagnosis of hereditary recurrent fevers. 2019: Guidelines of the genetic diagnosis of hereditary recurrent fevers. 1997: Int. FMF Consortium & French FMF Consortium: MEFV gene responsible for Familial mediterranean fever (FMF) was described. inflammation.

http://fmf.igh.cnrs.fr/ISSAID/infevers/: 305 mutations MEFV mutations: Prevalent among people of Mediterranean РАСПРОСТРАНЕННОСТЬdescent, but may affectМУТАЦИЙ any ethnicГЕНА group. MEFV Increase of FMF frequency ??? Genetic drift and isolation! Age of MEFV mutations: 7000…- 30000 y.o. …

Data on more than 40000 individuals revealed high prevalence of MEFV mutations carrier rate in Armenians: 1:3. FMF: Clinical significance of MEFV mutations: >98% Complex alleles E148Q - L110P: first described in Turkey and M694I also presents in Turkey.  Japan: M694I, E148Q - L110P, R761H, E84K.  Complex alleles: E148Q - L110P, M694I in Japan & Turkey  China: High level mutation E148Q – No FMF “SILK ROAD”??? “Silk Road Disease”: Endemic in Japan and North-eastern Mediterranean region (Turkey & Iran):The Silk Road was a network of trade routes connecting China and the Far East with the Middle East and Europe. Established when the Han Dynasty in China officially opened trade with the West in 130 B.C. (“Before Christ”), the Silk Road routes remained in use until 1453 A.D. (Anno Domini: After Death), when the Ottoman Empire boycotted trade with China and closed them. Although it’s been nearly 600 years since the Silk Road has been used for international trade, the routes had a lasting impact on commerce, culture… Affected patients do not appear in two following generations... • Exceptions to this rule: •Quasi-dominant inheritance: recurrence risk 50%: when an affected homozygote mates with a heterozygote. If the allele-frequency in population is high then pseudo-dominance may appear: in children of a homozygote and a heterozygote parent there is a likelihood to be diseased of 50 % .

A woman homozygous for an autosomal recessive disorder whose husband is heterozygous for the same disorder. Their children have a 1 in 2 (50%) chance of being affected i.e.homozygous – the pedigree shows pseudodominant inheritance Genomic instability disorders: heterogenous group of 160 rare genetic syndromes of defects in DNA repair: a high disposition to cancer, immune deficiency, chromosomal breaks. Autosomal-recessive type of inheritance.

Xeroderma pigmentosum: dry and pigmented skin in UV-exposed regions of the skin: development of multiple skin tumors. FANCONI anemia: FANCA mutations in 65% Genetically heterogeneous group of 16 diseases. Pancitopenia Grouth deficiency Hypoplastic/absent thumbs Malformations Mental retardation ATAXIA-TELANGIECTASIA (Louis Barr):нейро-эктомезодермальная дисплазия: мутации ATM: 11q22-23 Incidence: 1:40000 Manifestation in early childhood: Immune defects Cerebellar ataxia Teleangiectasia of the conjunctiva High sensitivity to irradiation Prone to lymphomas and leukemias BLOOM syndrome: Congenital Telangiectactic Erythema: BLM gene mutations: 15q26.1 (founder mutation in Ashkenazi jews) Incidence among Ashkenazi jewish origin: 1:100. Prenatal &postnatal growth deficiency disorder. Distinct phenotype: narrow face, Sunlight-induced facial erythema, Immune deficiency Increased risk of malignancies, Adult height approximately 150 cm. Progeria – beyond the Werner and HGP syndromes

•Rothmund-Th. •Trichothiodys. •Bloom syndr. •Dyskeratosis c. •Seckel syndr. Kraemer, Neuroscience Arboleda, AJMG 2011;A155:1712 Cohen, AJMG 1991;41:488 2007;145:1388 •Cutis laxa Wiedemann - HGP Hallermann- Cockayne •Gerodermia o. Rautenstr. syn. syndrome Streiff syndrome syndrome • ……

Atypical / non- categorized cases of unknown Kraemer, Neuroscience Rajab, AJMG 2008;A146:965 2007;145:1388 Cabanillas, AJMG 2011;A155:2617 etiology Wrinkly Xeroderma Nestor- Werner skin syndrome pigmentosum Guillermo P. syndrome X & Y LINKED INHERITANCE:

X & Y submetacentric chromosomes The X is large gonosome - Over 1600 genes (5-6% of genome) over 100 disease-associated mutations.

The Y is small - Over 400 genes. - No relevant genetic diseases apart from problems in sperm differentiation. The Lyon’s Hypothesis: 1 X-chromosome in each cell is inactivated during the early embryonic development of females by formation of X-chromatin. • Normally, inactivation of the X chromosome is random event (50% mat - 50% pat); X-linked Recessive Inheritance: Affected individuals – males: inherit the mutant allele from mother. Any son of a carrier female has a 50% risk of inheriting the trait. • Female heterozygous for X-chromosome mutation has 50% risk of being a carrier and of an affected son. • No male-to-male transmission •All daughters of an affected males are carriers of X-linked mutation. MUSCULAR DYSTROPHY: most severe DUCHENNE MD: 1:3500 males. Mutations in Dystrophin gene (Xp21.2): is the largest gene (79 exons): hundreds mutations are known: DMD: 2/3: frameshift deletions; 1/3: point mutations. 30% of patients: with new mutation. Dystrophin: muscular protein in membrane of sarcolemma, absent in DMD and truncated in BMD. Clinical: onset: 3 to 5 yrs: progressive degenerative muscles changes, weakness, pseudohypertrophy of the calves: infiltration of muscles by fat, reduced motor function by 2 to 3 years. Degeneration of sceletal muscules: by the age of 6 to 10: atrophy of heart muscles, respiratory and heart failure. •As muscle cells die, CK is moved to the blood stream: level CK: 20 t. >N •Death: results from respiratory and cardiac failure.

•BMD: 1:18000 males. In-frame mutations: reduced protein, manifestation by 10-15 y.o., progressing more slowly. Hypertrophic leg muscle Standing from supine position HEMOPHYLIA A: mutation of gene (Xq28) of clotting factor YIII: the most common of severe bleeding disorders. Frequency: 1:5000 – 1:10000 males. Factor YIII: a key component of the clotting cascade. Defective FYIII: affected fibrin formation/spontaneous bleeding. HEMOPHYLIA B: bleeding disorder deficiency of clotting factor IX. X-linked Dominant Inheritance: Characteristics

Two times more frequently females are affected than males. XhY XHXh Skipped generations are uncommon.

XhXh XHY XhXh XHXh XhY Father-to-son transmission is not seen.

Affected man may have diseased daughters & healthy sons. XHXh XhY XHXh XhY XhXh XHY XhY Hemizygozity in male & homozygosity in women can be lethal.

Often the clinical expression is more severe in hemizygous males than in heterozygous females. HypophosphatemicRett/Vitamin syndrome: D – resistant a childhood rickets onset (phosphate disorder, diabetes) affecting Mutations in phosphatefemales.-regulating Period of endopeptidase normal development gene (chr is betweenXp22.1) 6- The kidneys are impaired18 months, in their after: ability loss toof purposefulreabsorb too use much of hands, phosphate: abnormalwith ossification/bone hand winring and development. other stereotypic Frequency: movements; 1:25000. 50% develop seizures, breathing irregularities with apnea, in later age-scoliosis, limitation of mobility. Mutation in gene on the X chromosome, lethal in males. Y CHROMOSOME:

Only males have Y chromosomes • All Y-linked traits are expressed • Passed from father to sons (Holandrian) • Approximately three dozen Y-linked traits are known. • Male infertility: SRY gene is responmonal changes, responsible for male development. Azoospermia factor:AZF (most often deletion): Yq11.2 Hypertrichosis pinnae Retinitis pigmentosa Genotype XYY: aggression, learning disability, skin problems, obesity Hypertrichosis pinnae

Retinitis pigmentosa MODES OF INHERITANCE NOT FOLLOWING MENDEL`S RULES 1.MITOCHONDRIAL 2.MULTI-FACTORIAL OR POLYGENIC 3.GENOMIC IMPRINTING 4.TRINUCLEOTID-REPEAT-AMPLIFICATION

Mitochondrial Inheritance: 10-500 mitochondria per cell. Mitochondria: part of cells oxidation, urea and citrate cycles. Have their own circular DNA, independent replication, translation, triplet code, 22 transfer-RNAs. mtDNA: 97% coding, 37 genes. No recombination. High mutation rate. Oocytes: 50000-100000, sperm – no mitochondria. Males and females equally affected Diseased male not have diseased offsprings. • Diseased mother → ALL of her offspring Manifestations: brain muscles, heart, liver, kidney, endocrine pancreas… >10 encephalomyopathies: progressive muscular weakness, lactate acidosis, seizures, intellectual degradation, nervus opticus atrophy, neuropathy, cardio-myopathy…

Nervus opticus atrophia type Leber: degeneration of fibers of optical nerve. • Severity of the mitochondrial diseases depends on the types of mutations and number of mutated mitochondria in the cells.

LHON Leber hereditary optic neuropathy: Onset of blindness in age of 10-12.

MELAS Мyopathy, encephalomyopathy, stroke like episodes, lactic acidosis.

MERRF Мyoclonic epilepsy, myopathy, ataxia, deafness, dementia;

KSS Kearns-Sayre syndrome: progressive myopathy, cardiomyopathy, heart block, ptosis, ataxia, diabetes, rtc. CPEO Progressive ophtalmoplegia Genomic imprinting: is an epigenetic process of different expression of an allele or chromosomal segment depending on maternal and paternal origin. The term genomic imprinting describes the expression of specific genes in a parent-of-origin specific manner - i.e. they are expressed only from the maternal or from the paternal gene copy, but not biparentally. Congenital imprinting disorders (IDs) are characterised by molecular changes in chromosomal regions and genes, i.e. genes that are expressed in a parent-of-origin specific manner. About 100-200 genes underlie “genomic imprinting”. These genes need one active allele from one parent; the allele from other parent is switched by metylation. These two very different neurogenetic developmental syndromes are caused by the same deletion: 15q11-13. Prader-Willi: paternal Angelman: maternal origin deletion: muscular origin deletion: severe weakness, massive obesity, MR, lack of speech neurological developmental development, seizures, delay . hyperactivity. Unstable Repeat Expansion/Trinucleotide-Repeat-Amplification: an earlier age of onset /more severe expression in generations.

About 30 diseases affecting central nervous system. Examples: Fragile - X syndrome (FRAXA) Syndromes (FRAXE, FRAXF, FRAX16A) Huntington Disease Kennedy Disease Spinocerebellar Ataxia types 1 - 10 Oculopharyngeal Dystrophy Repetive sequencies are frequent in genome: predispose for “dynamic mutaions” (dom & rec) cause severe neurological diseases. Anticipation: elongation the repeats predispose to earlier clinical signs and more severe disease. Fragile X Syndrome: 2-8% of all MR: FMR1 gene: Xq27.3 region contains a small microsatellite area of CGG-repeats. Caused by mutations (expansions of CGG repeat) in FMR1 gene. Normal allele: up to 5-50 copies; Pre-mutation: 50-200 copies; Full mutation: 230-2000 copies. Frequency in males: 1: 4000. Age of onset: childhood Moderate mental retardation. Dysmorphic facies

Increasing numbers of affected offspring are observed in later generations of an affected family (genetic anticipation) HUNTINGTON DISEASE: inherited neurodegenerative disorder. HD: progressive, neural cells death (localized in the brain), motor disturbance, cognitive loss, psychiatric manifestations (ie: dementia, and depression). Frequency: about 1 in 1000. IT15 gene (4p16.3) was discovered in 1993. IT15 gene produces a “Huntingtin” protein, which is necessary for normal growth and development. HD is a Dominant Lethal Allele- one copy of the normal gene is not sufficient for normal development. IT-15 gene has a highly polymorphic region that consists of (CAG)n - repeats which are located in Exon 1. In healthy "CAG" occurs <30 times. This region is expanded in people with HD more than 36 times. People with a CAG repeats in "grey zone“: between 30 and 36 repeats. Is not sure that somebody "high in the grey zone" may get the disease at a late age (above 60 or later) or not. Offspring of an afflicted individual has 1 in 2 (50:50) chance of inheriting the condition and transmitting it to offspring. HD is a family disease. Are the children at risk? Each child of an affected parent has 50% chance of inheriting the gene that causes HD, and is "at risk". People who carry the gene will develop Huntington’s. HD does not “skip a generation".

? Genetic test is used for diagnosis by counting the number of CAG’s repeats. Treatment for HD takes many forms it is preferable to locate a neurologist with expertise in HD. New mechanisms revealed by odd pedigree patterns • MYOTONIC DYSTROPHY: DMPK – protein kinase gene (chr19): expanded CTG trinucleotide repeats. The number of these repeats strongly correlates with severity: Unaffected persons: 5-37 copies; Mildly affected : 50-100 copies; Severe phenotype: 100 and more copies. Myotonic Dystrophy Huntington's disease

Presentation worsening with successive generations Reproductive Genetics

◄ 10-15% of pregnancies end in a miscarriage. 3-5 % of one of parent carry a balanced chromosomal abnormality (reciprocal or Robertsonian translocation). ◄ Primary amenorrhea: Turner syndrome (45,X). ◄ Androgene intensity syndrome (AIS) - testicular feminisation syndrome 46, XY, Xq11-mutations of androgene receptor gene in females. ◄ Gonadal agenesis/dysgenesis: 20% of XY females have mutated SRY gene (deletion). ◄Klinefelter syndrome: 47, XXY: prevalence: 1/500-1/800 male births. ◄ Congenital bilateral aplasia syndrome: mutations of CFTR gene. ◄ Yq-microdeletions : in 15% of males with azoospermia. ◄ 46,XX males: due to the translocation of SRY gene into the X- chromosome. CAH (congenital adrenal hyperplasia): is an autosomal recessive disorder of the adrenal cortex . Incidence 1:10,000–15,000 caused in about 95% of cases by genetic defects in the steroid 21-hydroxylase gene CYP21A2. ◄ CAH summarizes metabolic disorders that lead to inadequate synthesis of adrenal steroid hormones (cortisol, aldosterone). ◄ Clinical manifestations of CAH as disorder of adrenal steroid metabolism symptoms are highly variable and may include virilization of female newborns and life-threatening salt-wasting conditions. ◄ Various degrees of genital virilization in females (46,XX) are present at birth, whereas males (46,XY) may appear inconspicuous with hypospadia, etc. ◄ Appropriate treatment demands early diagnosis

◄ Neonatal genetic testing is an important confirmatory tool for early and reliable CAH diagnosis. Моsaicism/mosaics: tissue of individuals made up of genetically different cells, of the same zygotic origin. Mutation occur at conception or at different stages of thje zygote division. The proportion of normal/abnormal cells depends on the stage of the mutation occurs. Multifactorial/complex diseases: a variety of genetic and environmental factors may contribute to the disease phenotype. • most frequent genetic disorders • multiple genes are involved • strong influence of environment • genetic – only “starting point” • The recurrence risk is greater in members of at-risk families. These disorders with familial tendency in which the trait does not appear to have a mendelian single-gene pattern but occurs more often that it accounted by chance.

In many isolated birth defects (heart diseases, spina bifida, cleft lip/palate) if a single first-degree relative is affected, the recurrence risk is 3-5%; if 2 first-degree relatives are affected, the risk is doubles (10%); if 3 first-degree relatives are affected, the risk is doubled again (20%). In adult-onset complex disorders the recurrence risk is lower.

Tools to study complex diseases: Twin studies; Linkage studies: indirect DNA analysis: use of normal DNK polymorphisms that are near to disease gene of interest to track within a family the inheritance the disease- causing mutation in that gene. Association studies: statistical relationship between 2 and more events. •PREDICTIVE TESTING USINF MOLECULAR TECHNOLOGIES Respiratory organs Endocrine diseases (bronchial asthma, (diabetes,հypo- & Bone & connective chronic bronchitis) hyperthyroidism) tissues (osteoporosis, arthrosis)

Multifactorial common disorders

Gynecological Cancer diseases (endometriosis, Cardiovascular miscarriages…) diseases Homework: To further assess your understanding of Mendelian inheritance versus inheritance of imprinted genes 1. Define imprinting in your own words. 2. Look at the following pedigree and answer the questions below.

• Is this disease dominant? Why or why not? • Is this disease recessive? Why or why not? • Can the disease be inherited from the paternal side? • Can the disease be inherited from the maternal side? • Does this show Mendelian inheritance? GLOSSARY Proband – person with genetically determined trait who came to the attention of a clinician. Sibs – brothers and sisters; Sibship – family of sibs 1st degree relatives: 50% common genes: parents/children; brothers/sisters 2nd degree relatives: 25% common genes: uncles/aunts; nephews/nieces; grandparents 3rd degree relatives:12.5% common genes: 1st cousins. A Genetic Locus is a specific position or location on a chromosome. Frequently, locus is used to refer to a specific gene. Alleles are alternative forms of a gene, or of a DNA sequence, at a given locus. Polymorphism means the existence of multiple (two or more) common allelic forms at a specific locus. If both alleles at a locus are identical, the individual is Homozygous at that locus (a Homozygote for that condition). If the alleles at a locus are different: 1 N and 1 mutant, the individual is Heterozygous (a Heterozygote carrier for that condition). If the both mutant alleles at a locus are different, the individual is compound Heterozygous The Genotype is the genetic composition of an individual, referring to the alleles at a specific genetic locus. The Phenotype is the observable expression of the gene; phenotype is influenced by environmental factors and interactions with other genes.