Molecular Diagnostics

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Molecular Diagnostics Hype or Hope ? Patrick
Willems GENDIA, Antwerp, Belgium
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(No Transcript)
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We now know how God wrote the book of life
Bill Clinton
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But do we know how to read the book ?
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Genetic Diagnostics

• Cytogenetic tests
• FISH
• Molecular tests

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Molecular Diagnostics

• Diagnosis of infectious diseases
• Genetic identification
• Diagnosis of genetic diseases

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Diagnosis of infectious diseases

• HPV
• Chlamydia
• Hepatitis
• HIV
• Toxoplasmosis

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Genetic Identification

• - Paternity Testing
• - Forensics

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Paternity Testing
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Forensic testing

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Diagnosis of genetic diseases

• - Somatic rearrangements in cancer
• - Genetic risk factors
• Pharmacogenetics
• - Mutations in monogenic diseases

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

• Lymphocytic Leukemia
• t(922) BCR - ABL
• t(1221) TEL - AML1
• t(119) E2A - PBX1
• t(411) MLL - AF4
• Myeloid Leukemia
• Inv(16) CBF - MYH11
• t(822) AML - ETO
• t(922) BCR - ABL

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Diagnosis of genetic diseases

• - Somatic rearrangements in cancer
• - Genetic risk factors
• Pharmacogenetics
• - Mutations in monogenic diseases

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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

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Genetic Risk Factors

• Deep venous thrombosis
• Cardiovascular disease
• Alzheimer disease
• Osteoporosis

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Genetic Risk Factors

• Most single risk factors
• have NO clinical significance
• in individual patients

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Genetic Risk Factors

• Deep venous thrombosis
• Factor V
• Factor II
• MTHFR

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Diagnosis of genetic diseases

• - Somatic rearrangements in cancer
• - Genetic risk factors
• Pharmacogenetics
• - Mutations in monogenic diseases

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Pharmacogenetic tests

• Drug specificity
• Drug efficacity - toxicity

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Drug specificity

• Herceptin HER2
• Tyrosine kinase inhibitors
• BCR / ABL
• KIT
• PDGFR A/B
• EGFR

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Drug efficacity / toxicity

• Cytochromes
• CYP2D6
• CYP2C9
• CYP2C19

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Diagnosis of genetic diseases

• - Somatic rearrangements in cancer
• - Genetic risk factors
• Pharmacogenetics
• - Mutations in monogenic diseases

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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Monogenic Diseases

• gt 4.000 monogenic diseases
• gt 2.000 disease genes isolated

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Gene testing

• Most countries limited number
• (lt 50 genes)
• Few countries large number
• (300-500 genes)
• Nowhere network complete
  availability
• (gt 1000 genes)

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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Disease Mutations

• Easy tests Single - common mutations
• Difficult tests Private mutations

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Disease Mutations

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

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Easy tests
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Difficult tests
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BRCA testing

• BRCA1 23 exonen, 1863 AA, 6.200 bp

BRCA2 28 exonen, 3418 AA, 10.300
bp Totaal gt 17.000 bp sequence
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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Mutation Detection

• 1. Point mutations, frame shifts
• A. Sequencing
• B. WAVE
• 2. Deletions MLPA

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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Cost

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

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Cost

• Socioeconomic situation
• Social security
• Reimbursement by insurance

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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Common Genetic Diseases
?
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Common genetic diseases
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Most frequent DNA tests

• Thalassemia
• Cystic fibrosis
• Breast cancer
• Colorectal cancer
• FRAXE
• SCA
• F5 Leiden

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Usual portfolio of DNA tests

• Easy tests
• Common tests
• Research tests

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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

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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Current Organisation

• Small local labs small portfolios ( lt 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

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Diagnostic bottle necks

• Number of diseases
• Nature of disease mutation
• Technology
• Cost
• Number of samples
• Organisation

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Gene testing

• Unreliable
• Expensive
• Slow

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Unreliable

10 mistakes in easy tests such as CF
Nature Genetics 2000 25
259 - 260
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Expensive

• RESEARCH DIAGNOSTICS
• 1 genome 1 gene
• lt 1000 USD 200 5.000 USD
• Ratio 25.000

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Slow

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

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Message in a bottle

• Many different tests
• Many uncommon tests
• Many esoteric tests
• Many expensive tests
• International network needed

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Mission

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

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GENDIA GENetic
DIAgnostic Network
www.GENDIA.net
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The GENDIA network
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GENDIA Network
1000 Referral labs 1 Central lab
100 Test labs
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Advantages GENDIA

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

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Looking into the future

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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
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DNA Sequencing

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