Presentation Molecular Diagnostics

PowerPoint Presentation: 

Molecular Diagnostics : Hype or Hope ? Patrick Willems GENDIA, Antwerp, Belgium

We now know how God wrote the book of life Bill Clinton: 

We now know how God wrote the book of life Bill Clinton

But do we know how to read the book ?: 

But do we know how to read the book ?

Genetic Diagnostics : 

Genetic Diagnostics Cytogenetic tests FISH Molecular tests

Molecular Diagnostics : 

Molecular Diagnostics Diagnosis of infectious diseases Genetic identification Diagnosis of genetic diseases

Diagnosis of infectious diseases : 

Diagnosis of infectious diseases HPV Chlamydia Hepatitis HIV Toxoplasmosis

Genetic Identification: 

Genetic Identification - Paternity Testing - Forensics

Paternity Testing: 

Paternity Testing

Forensic testing: 

Forensic testing

Diagnosis of genetic diseases : 

Diagnosis of genetic diseases - Somatic rearrangements in cancer - Genetic risk factors Pharmacogenetics - Mutations in monogenic diseases

PowerPoint Presentation: 

Rearrangements in Cancer Cells Chromosomal breaks produce fusion genes These cause leukemias and lymphomas D iagnosis determines treatment and prognosis

Rearrangements in Cancer Cells: 

Rearrangements in Cancer Cells Lymphocytic Leukemia t(9;22) : BCR - ABL t(12;21) : TEL - AML1 t(1;19) : E 2 A - PBX1 t(4;11) : MLL - AF4 Myeloid Leukemia Inv(16) : CBF - MYH11 t(8;22) : AML - ETO t(9;22) : BCR - ABL

Diagnosis of genetic diseases : 

Diagnosis of genetic diseases - Somatic rearrangements in cancer - Genetic risk factors Pharmacogenetics - Mutations in monogenic diseases

Genetic Risk Factors: 

Genetic Risk Factors Monogenic diseases are caused by a deleterious mutation in a single gene: Disease-causing mutations Multifactorial diseases are caused by a combination of variations in multiple genes: Genetic Risk Factors

Genetic Risk Factors: 

Genetic Risk Factors Deep venous thrombosis Cardiovascular disease Alzheimer disease Osteoporosis

Genetic Risk Factors: 

Genetic Risk Factors Most single risk factors have NO clinical significance in individual patients

Genetic Risk Factors: 

Genetic Risk Factors Deep venous thrombosis Factor V Factor II MTHFR

Diagnosis of genetic diseases : 

Diagnosis of genetic diseases - Somatic rearrangements in cancer - Genetic risk factors Pharmacogenetics - Mutations in monogenic diseases

Pharmacogenetic tests: 

Pharmacogenetic tests Drug specificity Drug efficacity - toxicity

Drug specificity: 

Drug specificity Herceptin : HER2 Tyrosine kinase inhibitors BCR / ABL KIT PDGFR A/B EGFR

Drug efficacity / toxicity : 

Drug efficacity / toxicity Cytochromes CYP2D6 CYP2C9 CYP2C19

Diagnosis of genetic diseases : 

Diagnosis of genetic diseases - Somatic rearrangements in cancer - Genetic risk factors Pharmacogenetics - Mutations in monogenic diseases

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Monogenic Diseases: 

Monogenic Diseases > 4.000 monogenic diseases > 2.000 disease genes isolated

Gene testing: 

Gene testing Most countries : limited number (< 50 genes) Few countries : large number (300-500 genes) Nowhere : network complete availability (> 1000 genes)

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Disease Mutations: 

Disease Mutations Easy tests : Single - common mutations Difficult tests : Private mutations

Disease Mutations: 

Disease Mutations Single mutations Fragile X Sickle Cell Anemia Common mutations Deafness Hemochromatosis Panel of mutations Cystic Fibrosis Private mutations Breast Cancer Colorectal cancer

Easy tests: 

Easy tests Disease Gene Mutation Fragile X FMR1 Repeat FRAXE FMR2 Repeat Friedreich ataxia FRDA Repeat Haw River DRPLA Repeat Huntington type 1 HD Repeat Kennedy AR Repeat Myotonic dystrophy type 1 DMPK Repeat Spinocerebellar ataxia SCA1,2, 3, 6, 7, 8,10, 12,17 Repeat Alpha 1 antitrypsin PI 2 common mutations Charcot-Marie-Tooth Type 1A PMP22 1 common mutation Cystic fibrosis CFTR Common mutations Deafness GJB2 1 common mutation Hemochromatosis type1 HFE 2 common mutations Hereditary neuropathy (HNPP) PMP22 1 common mutation Sickle cell anemia HBB 1 common mutation Spinal muscular atrophy SMN1 1 common mutation Beta thalassemia HBB 1 exon

Difficult tests: 

Difficult tests Disease Gene Mutation Breast cancer BRCA1 Private BRCA2 Private Colon cancer MLH1 Private MSH2 Private MSH6 Private

BRCA testing: 

BRCA testing BRCA1 : 23 exonen, 1863 AA, 6.200 bp BRCA2 : 28 exonen, 3418 AA, 10.300 bp Totaal : > 17.000 bp sequence

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Mutation Detection: 

Mutation Detection 1. Point mutations, frame shifts : A. Sequencing B. WAVE 2. Deletions : MLPA

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Cost : 

Cost Single mutations : cheap (200 E) Prevalent mutations : cheap (300 E) Panel of mutations : moderate (300 E) Private mutations : expensive (1000 E)

Cost : 

Cost Socioeconomic situation Social security Reimbursement by insurance

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Common Genetic Diseases: 

Common Genetic Diseases ?

Common genetic diseases : 

Common genetic diseases Disease Frequency Mutation Genes Mutations Conclusion Hemochromatosis 1 / 600 1 / 400 HFE 2 common mutations Easy / cheap Breast Cancer 1 / 20 1 / 500 BRCA1 BRCA2 Mutations in 23 exons Mutations in 28 exons Complicated / expensive Hypercholesterolemia 1 / 500 1 / 750 LDLR Mutations in 16 exons Complicated / expensive Colorectal Cancer 1 / 25 1 / 1.000 MLH1 MSH2 MSH6 APC MUTYH Mutations in 19 exons Mutations in 16 exons Mutations in 10 exons Mutations in 15 exons Mutations in 16 exons Complicated / expensive Cystic fibrosis 1 / 2.500 1 / 2.500 CFTR Common mutations Easy / cheap Prelingual deafness 1 / 1.500 1 / 4.000 GJB2 1 common mutation Easy / cheap Fragile X syndrome 1 / 5.000 1 / 5.000 FMR1 Only 1 mutation Easy / cheap SMA 1 / 10.000 1 / 10.000 SMN1 Only 1 mutation Easy / cheap Beta Thalassemia variable variable HBB Only 1 exon Easy / cheap

Most frequent DNA tests: 

Most frequent DNA tests Thalassemia Cystic fibrosis Breast cancer Colorectal cancer FRAXE SCA F5 Leiden

Usual portfolio of DNA tests: 

Usual portfolio of DNA tests Easy tests Common tests Research tests

Genetic testing in Europe: 

Genetic testing in Europe inhabitants per country : 10 million births per year : 100.000 disease frequency : 1 on 10.000 new patients per year : 10 genetic labs : 10 New patients per lab per year: 1

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Current Organisation: 

Current Organisation Small local labs : small portfolio’s ( < 50 tests ) Same spectrum of tests : common + easy tests Majority academic labs : research -diagnostic setting Many academic labs give up diagnostic testing No (inter)national network

Diagnostic bottle necks: 

Diagnostic bottle necks Number of diseases Nature of disease mutation Technology Cost Number of samples Organisation

Gene testing : 

Gene testing Unreliable Expensive Slow

Unreliable : 

Unreliable 10 % mistakes in easy tests such as CF Nature Genetics 2000; 25: 259 - 260

Expensive : 

Expensive RESEARCH DIAGNOSTICS 1 genome 1 gene < 1000 USD 200 – 5.000 USD Ratio : 25.000

Slow : 

Slow RESEARCH DIAGNOSTICS 100 genomes 1 gene in 10 days in 100 days Ratio 25 million

Message in a bottle: 

Message in a bottle Many different tests Many uncommon tests Many esoteric tests Many expensive tests International network needed

Mission: 

Mission A global network of diagnostic labs Large portfolio Reliable Fast Affordable

PowerPoint Presentation: 

GENDIA GEN etic DIA gnostic Network www.GENDIA.net

The GENDIA network: 

The GENDIA network

GENDIA Network: 

GENDIA Network 1000 Referral labs 1 Central lab 100 Test labs

Advantages GENDIA: 

Advantages GENDIA 1 lab to send samples to 1 lab to get results from > 2.000 genetic tests Large portfolio Best first selection of test Best Reflex testing

Looking into the future: 

Looking into the future

Next generation sequencing: 

Sequencing power : billion bp / day Will rapidly multiply Cost : 100.000 Euros Will rapidly decrease to 1000 Euro Whole genome sequencing of Watson and Venter Sequencing all patients Next generation sequencing

PowerPoint Presentation: 

DNA Sequencing 1980-1990 1990-2005 > 2005 Radio - gel Fluorescent - capillary Next generation Thousand bp / day Million bp / day Billion bp / day