Molecular genetic diagnostics of monogenic diseases Jana Zídková zidkova.jana@fnbrno.cz University Hospital Brno Centre of molecular biology and genetics Department of inherited genetic disorders Molecular genetic diagnostics of rare diseases: • Neuromuscular diseases • Epilepsies • Skin diseases • Connective tissue diseases • Metabolic diseases Molecular genetic diagnostics of monogenic diseases 1. Confirmation of clinical diagnosis Ø psychological support Ø prediction of the course of the disease Ø specific treatment - certain disease, certain mutation (example at the end of the lecture) 2. Segregation of variants/disease in family members Ø early treatment (in preclinical phase) Ø genetic counseling – testing of partner, preimplantation diagnostics, prenatal diagnostics Why are we actually finding out? Molecular genetic diagnostics of monogenic diseases Germline mutation/mutations in one gene, not large deletions/insertions containing several genes: Ø identification of small scale variants: nucleotide substitutions nonsense mutation (creating premature stop codon) missense mutation (change of amino acid) affecting the splice site (aberrant splicing) small deletions/insertions change in amino acid chain (without/with creating premature stop codon) Ø whole exon deletions / duplications (copy number variations, CNV) His-Stop CAC TGA GTACAC CGA GTA His-Arg-Val Nonsense mutation: CAC CGA GTA His-Arg-Val CAC GGA GTA His-Gly-Val Missense mutation: EXON1 EXON2 EXON3 EXON1 EXON2 EXON3 EXON1 EXON2 EXON3 EXON1 EXON3 Aberrant splicing: in-frame frame-shift CAC CGA GTA His-Arg-Val CAC GTA His-Val Deletion of amino acid: in-frame frame-shift Molecular genetic diagnostics of monogenic diseases Germline mutation/mutations in one gene, not large deletions/insertions containing several genes: Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions Ø whole exon deletions/duplications (copy number variations, CNV) in-frame - change in amino acid chain without creating premature stop codon frame-shift - change in amino acid chain with creating premature stop codon EXON1 EXON2 EXON3 5’end 3’endintronintron EXON1 EXON2 EXON3 DNA nucleotides mRNA nucleotides protein aminoacids EXON1 EXON3 5’end 3’end EXON1 EXON3 In frame Frame-shift EXON1 EXON3 Deletion of one exon: 1. Classic Sanger sequencing 2. Next generation sequencing 3. MLPA – CNV detection 4. RP-PCR - detection of repeat expansions 5. Southern blot and hybridization - detection of repeat expansions / deletions Material: DNA isolated from the whole blood Molecular genetic diagnostics of monogenic diseases 1. Classic Sanger sequencing Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions Ø Method description: 1. PCR (polymerase chain reaction, amplification of known target sequence) 2. sequencing 3. result 1. Classic Sanger sequencing Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions Ø Method description: 1. PCR (polymerase chain reaction, amplification of known target sequence) > 2. sequencing > 3. result https://www.thermofisher.com/ 1. § PCR amplifies a specific region of a DNA § specific primers - complementary to the target region § reagents: DNA polymerase, primers, deoxynucleoside triphosphates (dNTPs), buffer solution, bivalent cations (typically magnesium) § volume of 10–100 μL in small reaction tubes § thermal cycler - heats and cools the reaction tubes to achieve the temperatures required 1. PCR 1. start denaturation 94°C/6min 2. denaturation 94°C/1min 3. annealing 60°C/1min 4. elongation 72°C/1min 5. final elongation 72°C/6min cycling steps2-4; 20-40x PCR procedure 1. Classic Sanger sequencing Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions https://www.thermofisher.com/ 1. 2. Ø Method description: 1. PCR (polymerase chain reaction, amplification of known target sequence) > 2. sequencing > 3. result § determining of nucleotide order § chain termination method § one primer § sequencing reaction in cycler > capillary electrophoresis 2. sequencing 1. Classic Sanger sequencing Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions https://www.thermofisher.com/ 1. 2. 3. result Ø Method description: 1. PCR (polymerase chain reaction, amplification of known target sequence) > 2. sequencing > 3. result § nucleotide order § change of one/several nucleotides § heterozygote / homozygote 1. Classic Sanger sequencing A. Sequencing of the certain part of the gene including the position of pathogenic variant • segregation of variant in family members B. Sequencing of the whole gene by several PCR reactions: • in past: gene by gene approach (time-consuming and costly) • gene with clear clinical-genetic relationship, not a very long gene (example: phenylketonuria) Patient with autosomal recessive limb girdle muscular dystrophy, 2 pathogenic variants in CAPN3 gene CAPN3: c.245C>T and c.550delA Presence of variants in: § mother § father § brother § sister c.550delA c.245C>T not detected c.245C>T c.550delA not detected not detected c.245C>T not detected not detected not detected c.245C>T c.550delA not detected unaffected but carrier of one pathogenic variant: - parents: 25% probability of child with disease (preimplantation diagnostics, prenatal diagnostics) - sister: testing of partner 1. Classic Sanger sequencing A. Sequencing of the certain part of the gene including the position of pathogenic variant • segregation of variant in family members not detected not detected unaffected – risk of disease the same as in the population 1. Classic Sanger sequencing A. Sequencing of the certain part of the gene including the position of pathogenic variant • segregation of variant in family members B. Sequencing of the whole gene by several PCR reactions: • in past: gene by gene approach (time-consuming and costly) • gene with clear clinical-genetic relationship, not a very long gene (example: phenylketonuria) Phenylketonuria (PKU) autosomal recessive metabolic disease (deficiency of phenylalanine hydroxylase); gene PAH (12q23.2) • diagnosed by newborn screening, on the basis of increased phenylalanine and the ratio phenylalanine/tyrosine • increased Phe and Phe/Tyr is the indicator for DNA analysis of the PAH gene encoding the phenylalanine hydroxylase 1. Classic Sanger sequencing B. Sequencing of the whole gene: gene with clear clinical-genetic relationship, not a very long gene example: phenylketonuria • in 98% of cases, two pathogenic variants in the PAH gene are identified = clinical diagnosis of PKU is confirmed 1. Classic Sanger sequencing 2. Next generation sequencing 3. MLPA – CNV detection 4. RP-PCR - detection of repeat expansions 5. Southern blot and hybridization - detection of repeat expansions / deletions Material: DNA isolated from the whole blood Molecular genetic diagnostics of monogenic diseases 2. Next generation sequencing (NGS) https://lifescience.roche.com Ø 1. DNA samples are converted into sequencing libraries • DNA is randomly sheared into smaller fragments by mechanical or enzymatic methods • adapters for sequencing and multiplexing are added to DNA ends • regions of interest within the library are captured using oligonucleotide probes (hybridization) • probe-targeted fragment complex is separated from other fragments that are not bound to probes • amplification of targeted regions Ø 2. sequencing • NGS of targeted regions • sequences millions of fragments in a massively parallel fashion • improving speed and accuracy while reducing the cost of sequencing oligonucleotide probes: • targeted panel sequencing - selected sets of genes or gene regions • whole exome sequencing (WES) • whole genome sequencing (WGS) 2. Next generation sequencing (NGS) Ø 3. data analysis • the instrument software identifies nucleotides (a process called base calling) and the predicted accuracy of those base calls • by commercial software or bioinformatics pipelines • includes alignment of NGS reads • identification and annotation of sequence variants 2. Next generation sequencing (NGS) Identification of a large number of sequence variants Result: Identification of whole exon deletions / duplications: by comparing the number of reads for individual exons § patient § control Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions Ø whole exon deletions / duplications (copy number variations, CNV) 2. Next generation sequencing (NGS) Example: Patient’s case: Patient has complained of difficulties in running a climbing stairs since his early teens. Patient has elevated creatine kinase levels. Proximal weakness in the upper and lower limbs has been progressive and he displays wasting of trunk muscles and slight hyperlordosis. Neurologist requests analysis of genes associated with muscular dystrophy. 2. Next generation sequencing (NGS) Muscular dystrophies and myopathies • to date, 162 genes associated with clinical manifestation of muscular dystrophy/myopathy • clinical, biochemical, pathological,…. findings are mostly not specific enough for selection of a gene for molecular genetic analysis • Which gene to analyse? In past before NGS: • genes analysed sequentially by classical DNA sequencing • starting with a gene with the most likely mutation occurrence > negative result > another gene • TIME AND FINANCIALLY CONSUMING • only a certain number of genes analysed NGS era: • all genes associated with the disease analysed at the same time (in parallel) = targeted panel • FAST AND RELATIVELY CHEAP Example: 2. Next generation sequencing (NGS) Muscular dystrophies and myopathies • to date, 162 genes associated with clinical manifestation of muscular dystrophy/myopathy • clinical, biochemical, pathological,…. findings are mostly not specific enough for selection of a gene for molecular genetic analysis • Which gene to analyse? In past before NGS: • genes analysed sequentially by classical DNA sequencing • starting with a gene with the most likely mutation occurrence > negative result > another gene • TIME AND FINANCIALLY CONSUMING • only a certain number of genes analysed NGS era: • all genes associated with the disease analysed at the same time (in parallel) = targeted panel • FAST AND RELATIVELY CHEAP Example: We use panel including all 162 genes 2. Next generation sequencing (NGS) Identification of a large number of sequence variants Result: Interpretation of causality Identification of whole exon deletions / duplications: by comparing the number of reads for individual exons § patient § control Ø identification of small scale variants: nucleotide substitutions, small deletions / insertions Ø whole exon deletions / duplications (copy number variations, CNV) Example: 2. Next generation sequencing (NGS) 1.Benign sequence variants 2.Likely benign sequence variants 3.Sequence variants of uncertain significance 4.Likely pathogenic sequence variants 5.Pathogenic sequence variants Interpretation of sequence variants 2. Next generation sequencing (NGS) Result: A) Identification of pathogenic variant/variants e.g. two pathogenic variants in CAPN3 > confirmed diagnosis of limb girdle muscular dystrophy CAPN3 (NM_000070.3): c.245C>T p.(Pro82Leu) / c.550delA p.(Thr184Argfs*36) B) Identification of variants of uncertain significance: e.g. variant in DYSF Ø genetic-clinical correlation Ø segregation of variant in family Ø type of inheritance C) Only benign variants identified - diagnosis was not confirmed Ø pathogenic variant in unanalyzed gene, in noncoding region Ø WES, WGS Interpretation of sequence variants Patient’s case: Patient has complained of difficulties in running a climbing stairs since his early teens. Patient has elevated creatine kinase levels. Proximal weakness in the upper and lower limbs has been progressive and he displays wasting of trunk muscles and slight hyperlordosis. 2. Next generation sequencing (NGS) Limitations of NGS: • panel + WES: analysis of coding regions sequencing about 95-98% of selected regions • occurrence of pseudogene, regions with high similarity: difficult non-specific mapping • is not a suitable method for diseases associated with the expansion / deletion of repetitive sequences Interpretation of sequence variants 1. Classic Sanger sequencing 2. Next generation sequencing 3. MLPA – CNV detection 4. RP-PCR - detection of repeat expansions 5. Southern blot and hybridization - detection of repeat expansions / deletions Material: DNA isolated from the whole blood Molecular genetic diagnostics of monogenic diseases 3. MLPA (Multiplex Ligation-dependent Probe Amplification) • gold standard for CNV detection (whole exons deletions/duplications) • targeted analysis of a specific gene/genes • available for certain genes 3. MLPA (Multiplex Ligation-dependent Probe Amplification) Method description: MLPA probe 1. Sample denaturation and probe hybridisation 2. Probe ligation 3. Probe amplification 4. Fragment separation 5. Data analysis 3. MLPA (Multiplex Ligation-dependent Probe Amplification) Duchenne muscular dystrophy, gene DMD (chromosome X): Ø whole exon deletions (68%) and duplications (10%) Ø MLPA is the first choice method Ø man = affected woman = carrier control 10 exons deletion, hemizygous, man First example: Boy has delayed motor function acquisition and proximal muscle weakness. Due to severely elevated creatine kinase levels (15,000 U/L), neurologist suspects a clinical diagnosis of Duchenne muscular dystrophy. due to the large DMD size, the MLPA has two parts, the second part is not shown Result: • deletion of exons 22-41 hemizygous • out-of-frame deletion leading to creation premature stop codon • confirmed diagnosis of Duchenne muscular dystrophy 3. MLPA (Multiplex Ligation-dependent Probe Amplification) Duchenne muscular dystrophy, gene DMD (chromosome X): Ø whole exon deletions (68%) and duplications (10%) Ø MLPA is the first choice method Ø man = affected woman = carrier 10 exons deletion, heterozygous, woman First example: due to the large DMD size, the MLPA has two parts, the second part is not shown Result: • deletion of exons 22-41 heterozygous • out-of-frame deletion leading to creation premature stop codon • mother is carrier of Duchenne muscular dystrophy 10 exons deletion, hemizygous, man Boy’s mother Second example: 3. MLPA (Multiplex Ligation-dependent Probe Amplification) Spinal muscular atrophy (SMA), gene SMN1 Yuji Kubo, J Hum Genet 2015 Chromozom 5q13.2 https://assets.thermofisher.com/ EXON 7 EXON 7 • autosomal recessive disease • incidence: 1 in 6,000 - 10,000 live births • second most frequent fatal disease with autosomal recessive inheritance (after cystic fibrosis) • characterized by degeneration of alpha motor neurons • newborn screening Ø 95% caused by homozygous deletion of the SMN1 gene Ø SMN1 has its almost identical copy – SMN2 gene (SMN1 and SMN2 are homologous to except for few nucleotides) Ø copy number variation of SMN1 and SMN2 in human genome Ø clinical severity is modified by copy number the SMN2 gene Control: 2x SMN1, 2x SMN2 SMA: 0x SMN1, 3x SMN2 SMA: 0x SMN1, 5x SMN2 3. MLPA (Multiplex Ligation-dependent Probe Amplification) Second example: Spinal muscular atrophy (SMA), SMN1 Ø patients with homozygous SMN1 deletion Ø heterozygous carriers of SMN1 deletion Ø SMN2 copy number 1. Classic Sanger sequencing 2. Next generation sequencing 3. MLPA – CNV detection 4. RP-PCR - detection of repeat expansions 5. Southern blot and hybridization - detection of repeat expansions / deletions Material: DNA isolated from the whole blood Molecular genetic diagnostics of monogenic diseases 4. RepeatPrimed-PCR (RP-PCR) Ø Method description: • PCR with three primers • characteristic profile of amplicons of increasing length, which differ by the length of a repeat unit (3 bp) Ø detection of repeat expansions (usually three nucleotides) Ø presence / absence of expansion Ø does not determine length of expansion (number of repeats) V. Mootha, Inv. ophthal. & vis. science 2014 Negative – 2 alleles Positive – 1 allele and amplicons separated by 3bp RP-PCR and fragment analysis: 20x CTG tccgcggccg gcgaacgggg ctcgaagggt ccttgtagcc gggaatgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgggg ggatcacaga ccatttcttt ctttcggcca ggctgaggcc ctgacgtgga tgggcaaact gcaggcctgg 140x CTG tccgcggccg gcgaacgggg ctcgaagggt ccttgtagcc gggaatgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgctg ctgctgctgc tgctgctgct gctgctgggg ggatcacaga ccatttcttt ctttcggcca ggctgaggcc ctgacgtgga tgggcaaact gcaggcctgg 4. RepeatPrimed-PCR (RP-PCR) Example: Myotonic dystrophy type 1 Øexpansion of CTG repeat in 3’UTR of DMPK (9q13.32) Øautosomal dominant inheritance Øcorrelation between number of repeats and severity of the phenotype: §5-37 repeats - unaffected §38–50 repeats - premutation, asymptomatic §51–149 repeats - mild adult-onset form §150–1000 repeats - classic MD1 §>1000 repeats - congenital form MD1 Ø anticipation - the number of repeats tends to increase in size over generations. Expansion of the CTG repeats commonly occurs during meiosis. As a result, children of affected individuals tend to have severe symptoms and earlier onset than their parents. Patient is displaying subtle signs of myotonia as well as ptosis and weak eye lid closure. Neurologist requested testing for myotonic dystrophy 1. Myotonic dystrophy type 1 – mechanism: § toxic effect of expansion § accumulation of RNA with expansions in the nucleus, sequestration of RNA-binding protein > formation of nuclear inclusions § altering mRNA splicing of other genes Image shows the location of the Mbnl1 splicing factor (green) and the second image shows the location of RNA repeats (red) inside the cell nucleus (blue). The white arrows point to two large foci in the cell nucleus where Mbnl1 is sequestered with RNA. Photos by Hongqing Du Mignon, IONIS-DMPK Clinical Program in Myotonic Dystrophy Turner, Journal of Neurology, Neurosurgery & Psychiatry 2010 4. RepeatPrimed-PCR (RP-PCR) 4. RepeatPrimed-PCR (RP-PCR) Myotonic dystrophy type 1 – result: Ø presence of expansion Ø not the length Positive – 1 allele and amplicons separated by 3bp RP-PCR and fragment analysis: Example: Patient is displaying subtle signs of myotonia as well as ptosis and weak eye lid closure. Neurologist requested testing for myotonic dystrophy 1. confirmed diagnosis of myotonic dystrophy type 1 Solution: Southern blot and hybridization 1. Classic Sanger sequencing 2. Next generation sequencing 3. MLPA – CNV detection 4. RP-PCR - detection of repeat expansions 5. Southern blot and hybridization - detection of repeat expansions / deletions Material: DNA isolated from the whole blood Molecular genetic diagnostics of monogenic diseases 4. Southern blot and hybridization Ø Method description: • DNA is cleaved by a restriction endonuclease • electrophoresis • transfer to membrane • hybridization with radioactive labeled probe • autoradiography Ø detection of repeat expansions / deletions Ø determination of the size 4. Southern blot and hybridization Myotonic dystrophy type 1 – result: Ø presence of expansion Ø not the length 12216 11198 10180 9162 bp M 1 2 3 4 5 MD1: 1 – negative control 2-5 – expansion Example: Ø according to the size of the fragment, we determine the number of repeats 4. Southern blot and hybridization Example: Facioscapulohumeral dystrophy 1 (FSHD1) • the third most prevalent muscular dystrophy, AD inheritance • weakness and wasting of the face, shoulder and upper arm muscles, with later involvement of the trunk and lower extremities • FSHD develops through complex genetic and epigenetic events that converge on a common mechanism of toxicity with mis-expression of the transcription factor DUX4 hypomethylation open chromatin 4qA polyadenylation signal 4qB AAAA stable mRNA mRNA degradation transcription transcription Dillon N et al., Trends Genet. 2002 DUX4 transcription • 4q35 • repeats D4Z4 (contain DUX4 gene) • 11-100 repeats → heterochromatin • 1-10 repeats → chromatin conformational changes, hypomethylation 4. Southern blot and hybridization Example: Facioscapulohumeral dystrophy 1 (FSHD1) • 4q35, repeats D4Z4 (contain DUX4) • 11-100 repeats → unaffected • 1-10 repeats → affected E EB X we determine the number of D4Z4 repeats according to the size of the product Molecular genetic diagnostics: • the results must be interpreted with knowledge of the molecular nature of the disease and knowledge of the structure and function of encoded protein • the results must be interpreted in relation to the patient 's phenotype and results of other patient examinations (biochemistry, pathology, NMR, EMG, etc.) • it is necessary to return to the results of already examined patients with an unconfirmed genetic diagnosis and test them with new techniques and perform new interpretations of the identified sequence variants • it is necessary to participate in international quality control of DNA diagnostics for individual diseases Example of specific treatment - certain disease, certain mutation Spinal muscular atrophy (SMA) Spinal muscular atrophy (SMA) Yuji Kubo, J Hum Genet 2015 Chromozom 5q13.2 https://assets.thermofisher.com/ EXON 7 EXON 7 • gene SMN1, autosomal recessive disease • incidence: 1 in 6,000 - 10,000 live births • second most frequent fatal disease with autosomal recessive inheritance • characterized by degeneration of alpha motor neurons • newborn screening – started last year Ø 95% caused by homozygous deletion of the SMN1 gene Ø SMN1 has its almost identical copy – SMN2 gene (SMN1 and SMN2 are homologous to except for few nucleotides) Ø copy number variation of SMN1 and SMN2 in human genome Clinical severity is modified by copy number the SMN2 gene Not enough SMN protein, so the motor neurons shrink and die. As a result, the brain can’t control voluntary movements, especially motion in the head, neck, arms and legs. Spinal muscular atrophy Schorling DC, J Neuromuscul Dis. 2020; 7(1): 1–13. 4 clinical types of SMA Type I – 60% of SMA, severe muscle weakness and hypotonia at birth or within the first 6 months; death from respiratory failure occurs usually within the first 2 years Type II – first symptoms begin 6-18 months, live into adulthood; patients are able to sit but unable to walk independently Type III - first symptoms after 2 years of life; patients are able to walk but often wheelchair-bound; no significantly shorten life expectancy Type IV – rare form, symptoms appear in adulthood; patients have mild motor impairment Spinal muscular atrophy Motoneuron degeneration in SMA • functional degeneration of central synapses and neuromuscular junctions and subsequent axonal damage > motoneuron loss • complete loss of motoneuron is a irreversible change • The beneficial effects of SMA therapies are dependent on disease duration at the time of intervention. Disease duration before treatment is critical and a delayed intervention leads to a less efficient rescue. The effect of SMA therapies is strongest in pre-symptomatic patients. Hensel N. Frontiers in Neurology 2020 Vol 11 Spinal muscular atrophy SMA therapies 1. modifying splicing of SMN2 (production of more amount of full length mRNA) 2. replacing the SMN1 gene Schorling DC, J Neuromuscul Dis. 2020; 7(1): 1–13. Spinal muscular atrophy SMA terapies 1. modifying splicing of SMN2 (production of more amount of full length mRNA) A. Nusinersen (Spinraza®) • an antisense-oligonucleotide (ASO) that enhances the inclusion of exon 7 in mRNA transcripts of SMN2 • administered intrathecally B. Risdaplam (Evrysdi®) • administered orally 2. replacing the SMN1 gene C. Onasemnogene Abeparvovec-xioi (Zolgensma®) • children younger than two • one-time intravenous infusion • adeno-associated virus 9 (AAV9) delivering cDNA which codes the full length SMN protein • = replacement of a missing or faulty SMN1 gene with a functioning gene SMA therapies SMA neonatal screening pilot project in Czech republic Spinal muscular atrophy Øearly detection of neonates in the preclinical asymptomatic stage Øtreatment before irreversible complete loss of motoneuron QUESTIONS?