Birth of GENETIC TESTS

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1 1865 Malattie genetiche e test genetici Rosalind Franklin Sabrina Giglio Università di Firenze June 6th 2000: the Human Genome draft PGU: inizio 1990 fine prevista 2005 (15 anni) ma Change of Paradigm of Medicine TRADITIONAL MEDICINE GENETIC MEDICINE Epidemiological Phenodiagnostic Phenoterapeutical Prognostic Preventive Etiologic Individual Genodiagnostic Genotherapeutic Predictive Birth of GENETIC TESTS AMCI San Miniato 1

2 What is Genetic Testing? And what is its value? Definition of Genetic Testing: Carrier screening which involves identifying unaffected individuals who carry one copy for the disease to be expressed. The analysis of human DNA in any of its forms or related products (chromosomes, RNA, proteins) Pre implantation genetic diagnosis Pre natal diagnostic testing New born screening Pre symptomatic testing for estimating the risk of adult onset cancer and Alziemer s disease Two Main Types of Genetic Tests Conformational diagnosis of a symptomatic individual Forensic or identity testing Pre symptomatic testing for predicting adult onset disorders such as Huntington s chorea It allows the genetic disorder of vulnerabilities to inherited diseases It can be used to determine a child potentiality or person ancestry Constitutional Tests for mutations that affect ALL CELLS in the body, and have been there since conception Acquired Tests for changes that affect only certain cells or cell types in the body, and that occurred later in life AMCI San Miniato 2

3 Genetic Tests for Constitutional Mutations Molecular Test: Example Molecular Tests Cytogenetic Tests Biochemical Tests Analysis of DNA sequence in patient with a rare inherited disease Muscular Dystrophy Gene: DMD Clinical Picture 1 in 3500 male births progressive muscle weakness starting in early childhood wheelchair by age 12 death in 20s Molecular Test: Muscular Dystrophy Cytogenetic Test: Example Obtain blood sample from child Read the DNA sequence of the DMD gene Identify the mutation that caused the disease Karyotype to examine the chromosomal complement of an individual including number, form, and size of the chromosomes Frequently used for children who present with multiple anomalies, developmental delay, autism AMCI San Miniato 3

4 How is this information useful? Cytogenetic Test: Child with MCA and autism Can test Mom Is she an unaffected carrier of the mutation? Is she at risk to have more children with this disease? Can test siblings of affected child Can offer prenatal diagnosis in Mom s next pregnancy OR Can offer pre-implantation genetic diagnosis Can provide information about prognosis Obtain a blood sample Look at chromosomes Tecnologie che identificano il profilo genomico rappresentano un eccellente tool per la diagnosi clinica- genetica così come per la ricerca genomica Technology used to identify CNVsby comparing 2 genomic DNAs Il concetto di cariotipo molecolare ha cambiato significativamenteilfield dellacitogeneticaclinicae la stessa diagnosi clinica soprattutto in questi ultimi anni AMCI San Miniato 4

5 Dismorfismi/MCA/MR A.M. 7 m Piede sinistro equino-varo-supinato Lieve ritardo pm Palatoschisi Scarso accrescimento staturo-ponderale ad esordio prenatale Plagiocefalia Caratteristiche morfogenetiche particolari Lieve ipertonia generalizzata ARRAY CGH: delezionedi8.8 Mb in 18q de novo microcefalia occhi infossati fessure palpebrali corte microftalmia monolaterale punta del naso globosatip basso impianto orecchie palato alto, bocca stretta VSD RMNcerebrale: malformazione Dandy-Walker DIAGNOSI: sospetta trisomia 9 a mosaico Due cariotipi postnatali lassità legamentosa con displasia anca idronefrosi indipendenti da sangue periferico nella norma Trisomia 9 a mosaico scarso accrescimento staturo-ponderale, cardiopatia e cisti cerebrali peso 3280 kg (3 centile); CC34,5 cm (<-2DS) Percentuale delle cellule con cromosoma soprannumerario circa il 50% destrocardia microcefalia insufficienza della valvola tricuspide ampio difetto interatriale fronte ampia con ipetelorismo persistenza di ampio dotto arterioso rime palpebrali verso il basso e corte(da considerare l etnia di origine) piccoloangiomapianoalivellodellapalpebradisx radice del naso a sella con ipoplasia della columella, e naso appiattito filtro triangolare con incisura centrale e ben segnato bocca piccola e labbra sottili Clinodattilia del V dito della mano, bilateralmente. Evidente la lassità legamentosa e ipotonia RMNencefalo: cisti paraventricolari ipoplasia del corpo calloso AMCI San Miniato 5

6 Tel 3p-3q Tel 4p-4q CNVs Their functional impact has been demonstrated across the full range of biology, from cellular phenotypes, such as gene expression, to all classes of human disease with an underlying genetic basis: sporadic,mendelian,complex and infectious When analyzing array CGH data in a clinical setting, clinical cytogeneticists should categorize CNVs into those that are likely to be benign, those that are likely to be pathogenic and those of unknown clinical significance. Copy Number Variants (CNVs) Segments of DNA ranging in length that differ in number of copies btw any 2 individuals 10-20% of the human genome varies in the number of copies 1/17 children has new CNV; include deletions (most common), insertions, duplications, translocations; AMCI San Miniato 6

7 Biochemical Test Analyzes the quantity of a downstream product of a gene (e.g. not looking directly at the gene, or the chromosome). Example: Newborn Screening Mandated in all 50 states Twenty primary targets that all states do Over 4 million newborns tested each year Biochemical Test: PKU Phenylketonuria Inherited metabolic disorder If untreated, leads to mental retardation, seizures Affects 1 in 20,000 newborns Missing enzyme: Phenylalanine Hydroxylase Measure amount of Phenylalanine in baby s blood How is this information useful? Can diagnose the baby in time to treat and avoid all clinical consequences of the disease Treatment: Restrict phenylalanine in the diet Can test siblings of affected child to see if they are carriers for the disease (1 in 70 in the general population are carriers) Slide Title AMCI San Miniato 7

8 Slide Title TEST GENETICI PRESINTOMATICI PRO. Peace of mind Complicazioni trattabili (PKD, etc ) Pianificazione familiare Tipizzazione pre-trapianto (PKD, Adrenoleucodistrofia, etc ) CONTRO.. Mancanza di terapia Discriminazione (lavoro, assicurazione, etc.. Malattia di Huntington Atassia spinocerebellare AMCI San Miniato 8

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10 Slide Title FARMACOGENETICA La farmacogenetica è lo studio delle basi genetiche della variabilità della risposta ai farmaci. Comprende anche la farmacogenomica, disciplina che utilizza vari mezzi per indagare l intero genoma alla ricerca dei determinanti multigenici della risposta ai farmaci. La maggioranza dei geni contiene variazioni casuali della sequenza nucleotidica tra i diversi individui, sviluppatesi nel corso dell evoluzione AMCI San Miniato 10

11 Genome-Sequencing explosion AMCI San Miniato 11

12 Next Generation Sequencing Benefits for Patients What is Next Generation Sequencing? What is Next Generation Sequencing? Massively parallel sequencing What are the benefits for patients? How will the benefits be realised? Genomic DNA ACTGTAATGGCA Whole genome sequence consensus of aligned reads Fragmented library of small pieces all sequenced at same time A GT G A _T G A GT G A A GT G A GT G A Individual reads aligned to reference sequence What is Next Generation Sequencing? What is Next Generation Sequencing? Massive sequence output possible Terabytes of data (1,000,000,000,000) Highly scalable Lower output machine; fewer samples per run; faster results exomes targeted regions (eg disease specific set of genes) High throughput machine multiplex samples; target specific region to screen many samples for particular variant whole genome sequence Evolving technology Illumina HiSeq 2000 Life Technologies SOLiD 4 Ion Torrent PGM Illumina MiSeq Pacific Biosciences RS Roche 454 GS FLX Roche GS Junior and then there is the bioinformatics AMCI San Miniato 12

13 What are the benefits for patients? What are the benefits to patients? Would you like a copy of the results? Widely applicable technology variants in individual s DNA vs reference sequence may identify new disease genes high diagnostic yield increased efficacy of treatments reduced deleterious/no response to treatments preventative treatments differentiation of disease subtypes How will the benefits be realised? What are the benefits for patients? Marcel Nelen & Joris Veltman, Nijmegen. we think whole-genome-or exome-based approaches are currently most suited for diagnostic implementation in genetically heterogeneous diseases, initially to complement and later to replace Sanger sequencing, qpcr and genomic microarrays. Establishing the pathogenicity of individual genetic variants remains a daunting task, requiring novel bioinformatic tools and high-throughput functional approaches. Pharmacogenomics Apr;13(5): Genome and exomesequencingin the clinic: unbiased genomic approaches with a high diagnostic yield. Sharon and Ozzyboth had a genome test looked at genes predisposing to serious illness Ozzy s results perfect Sharon s results already knew she was genetically predisposed to colon cancer (and has been affected) She also carries a gene mutation predisposing to breast cancer She opted for a bilateral mastectomy at the moment cannot accurately predict if / when she would develop breast cancer AMCI San Miniato 13

14 How will the benefits be realised? How will the benefits be realised? Select new best friends Obstetrician Nephrologist Endocrinologist Cardiologist Bioinformaticist Medical genetics- University of Florence Lab Pathologist Neonatologist Oncologist Collaboration Networking Developing standardised protocols Using standardised locus specification and variant nomenclature Quality assuring sequencing processes Quality assuring data analysis processes Phenotype & genotype data sharing Providing equitable access to the right test for the patient Develop specialist knowledge define your service s unique strengths What are the benefits for patients? What are the benefits for patients? Higher diagnostic yield and more timely diagnosis Research describing the course of a disease or development of a disorder may allow it to be more effectively treated or prevented Hopefully, more choices about how to live with or manage their disorder AMCI San Miniato 14

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16 FROM MRI TO LIQUID BIOPSY Grazie per la vostra attenzione AMCI San Miniato 16