Bruno Dallapiccola

Making the best use Making the best use

of genetic testingof genetic testing

“Genetic tests detect the presence or absence of, or a change in, a

particular gene or chromosome, or a gene product or other specific

metabolite that is primarily indicative of specific genetic change”

Human Genetic Commission, 2009,

http://www.hgc.gov.uk/Client/Content.asp?ContentId=816.

Specific to a given disease:

the test relates to a unique disorder (e.g. LRP5 homozygous

mutations in osteoporosis-pseudoglioma syndrome).

Non-specific:

the test applies to patients who share a common clinical feature (e.g.

a-CGH analysis in mentally retarded subjects)

Genetic testing

Allelic gene mutations can result in distinct disorders i.e. diseases caused by LMNA/C gene mutations

Hutchinson-Gilford progeria (HGPS)

Mandibulo-acral dysplasia (MAD)

Familial partial lipodystrophy (FPLD2)

Restrictive dermopathy, lethal (RD)

Muscular dystrophy limb-girdle, type 1B (LGMD1B),

Lipoatrophic diabetes

Cardiomyopathy, dilated 1A (CMD1A)

Emery-Dreifuss musculardystrophy, type 2 (EDMD2)

Charcot-Marie-Tooth disease,axonal, type 2B1 (CMT2B1)

Identical/similar disorders can be caused by non-allelic mutations: genetic heterogeneity

i.e. retinitis pigmentosa

1. To make a diagnosise.g. to recognize disorders in which the clinical assessment per se is not conclusive

• B.L. 10 ys

• mild mental retardation

• long face, rounded chin, ptosis, upward slanted palpebral

fissures, thick alae nasi, anteverted nares, prominent philtrum

• pectus excavatum

• incomplete elbows extension

• long tapering fingers

• camptodactylous fingers/toes

dup16p13.3

2. To validate a clinical diagnosise.g. Microcephalic Osteodysplastic Primordial Dwarfism, type II, MOPDII (OMIM 210720)

• L.A. 27 ys

• prenatal/postnatal growth retardation

• adult height 123 cm

• microcephaly (OFD 49 cm)

• dysmorphic facial features

• acanthosis nigricans

• tapering fingers, flat brittle nails

• borderline mental development

• diabetes mellitus

• arterial stenosis

• mesomelic limbs’ shortenig

3. To choose the most appropriate therapye.g. congenital adrenal hyperplasia

Detection of CYP21A gene homozygous mutations, prompts

dexamethasone therapy of affected patients to prevent

female virilization and male precocious puberty.

4. To establish genotype-phenotype correlations andto delineate the natural history of diseases

i.e. to predict the outcome of Noonan syndrome based on analysis of genes in the RAS-MAPK pathway

Noonan syndrome LEOPARD syndrome Noonan-like syndrome Noonan syndrome Noonan syndromePTPN11 ex 3 PTPN11 ex 12 PTPN11 ex 13 NRAS KRASclassic form lentigines polyarticular villonodular severe form

cardiomyopathy sinovitis NS1 (OMIM 163950) LS1 (OMIM 151100) (OMIM 163955) NS6 (OMIM 164790) NS3 (OMIM 609942)

Noonan syndrome Noonan syndrome Noonan syndrome Noonan syndrome Neurofibromatosis-Noonan syndrome

SHOC2 SOS1 RAF1 BRAF NF1“loose anagen hair” mild form,normal stature cardiomyopathy CFCS-like mild NF1

(OMIM 607721) NS4 (OMIM 610733) NS5 (OMIM 611553) (OMIM 115150) (OMIM 601321)

LS2 (OMIM 611554)

5. To outline the heterogeneity of genetic diseasesi.e. Joubert syndrome (JS)-related disorders sharing the molar tooth sign (MTS) on brain MRI

JS + congenital heaptic fibrosis

±±±± ocular colobomas (COACH)TMEM67

6a. To identify newborns at risk of developing a RD by ‘genetic screening’e.g. metabolic disorders benefiting of prompt therapy

6b. To identify at risk individuals by ‘population genetic screening’e.g. to recognize individuals heterozygous for ß-thalassemia in at risk populations

6c. To identify unaffected at risk individuals by ‘cascade screening’ within a familye.g. to recognize SMN gene heterozygotes in families segregating spinal muscular atrophy

7. To identify individuals at risk of developing adult onset diseasese.g.. CTG triplet expansion within DMPK gene in myotonic dystrophy

I:1 I:2

II:1 II:2 II:3 II:4 II:5II:6

III:1 III:2 III:3

II:7

III:4 III:5

II:8

III:6

II:9

III:7 III:8

8. To avoid non useful investigationse.g. genetic testing in families with Adenomatous Polyposis of the Colon (APC gene)

To identify individuals who are heterozygous for the pathogenic mutation and those have the wild genotype, in order to decide who needs to undergo a periodic check using colonoscopy

9. To elucidate the mechanism underlying a rare disease e.g. triallelic inheritance in Bardet-Biedl syndrome

10. To improve genetic counselinge.g. risk assessment in Nablus-syndrome

• 21 month-old girl• parents originating from a small village in Sicily, likely related• micro-brachycephaly, upswept frontal hairline, blepharophymosis, flat supraorbital ridges, high-arched, misaligned eyebrows, long prominent philtrum, flattened maxilla, receding chin, abnormal ears• expressionless face • borderline mental retardation

“Molecular diagnosis is only one part of battery of tests in which clinical suspicion

and your own clinical expertise are the basis of most diagnoses”Surth J Am Can Med Ass J 1994: 150, 49-52

Appropriateness of genetic testing in Italy Dallapiccola et al., Genet Test Mol Biomarkers. 2010; 14:17-22

36.4351140Achondroplasia

FGFR3 mutations

17.53112639Prader-Willi syndrome

del15qpat/mat disomy/SNRPN mutations

8.8352589Angelman syndrome

del15qmat/pat disomy/UBE3A mutations

4.172245.374Fragile X syndrome

FMR1 mutations

3.341233.683DiGeorge/Velo-Cardio-Facial syndrome

del22q11.2

2.82742.628Williams syndrome

del7q11.23

% confirmed

clinical

diagnoses

Samples with

mutationsNumber of testsGenetic tests

Genetic testing is a powerful tool for diagnosis and management

of rare diseases. In order to improve the best practice of genetic

testing a number of points should be considered:

• The request for a genetic test must be clinically driven;

• Before requesting a genetic test, first consider its usefulness

and the potential impact onto the patient or his/her family;

• The quality of testing is critical for diagnosis and management;

• Pre- and post-test counseling must be available.

Conclusion