1. Making the best use
of genetic testing
Bruno Dallapiccola

2. “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

3. Lipoatrophic diabetes
Hutchinson-Gilford progeria (HGPS)
Cardiomyopathy, dilated 1A (CMD1A)
Mandibulo-acral dysplasia (MAD)
Emery-Dreifuss muscular
dystrophy, type 2 (EDMD2)
Familial partial lipodystrophy (FPLD2)
Charcot-Marie-Tooth disease,
axonal, type 2B1 (CMT2B1)
Restrictive dermopathy, lethal (RD)
Muscular dystrophy limb-girdle, type 1B (LGMD1B),
Allelic gene mutations can result in distinct disorders
i.e. diseases caused by LMNA/C gene mutations

4. Identical/similar disorders can be caused by non-allelic mutations:
genetic heterogeneity
i.e. retinitis pigmentosa

5. • 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
1. To make a diagnosis
e.g. to recognize disorders in which the clinical assessment per se is not conclusive

6. • 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
2. To validate a clinical diagnosis
e.g. Microcephalic Osteodysplastic Primordial Dwarfism, type II, MOPDII (OMIM 210720)

7. Detection of CYP21A gene homozygous mutations, prompts
dexamethasone therapy of affected patients to prevent
female virilization and male precocious puberty.
3. To choose the most appropriate therapy
e.g. congenital adrenal hyperplasia

8. Noonan syndrome LEOPARD syndrome Noonan-like syndrome Noonan syndrome Noonan syndrome
PTPN11 ex 3 PTPN11 ex 12 PTPN11 ex 13 NRAS KRAS
classic 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)
4. To establish genotype-phenotype correlations and
to 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

9. JS + congenital heaptic fibrosis
± ocular colobomas (COACH)
TMEM67
5. To outline the heterogeneity of genetic diseases
i.e. Joubert syndrome (JS)-related disorders sharing the molar tooth sign (MTS) on brain MRI

10. 6a. To identify newborns at risk of developing a RD by ‘genetic screening’
e.g. metabolic disorders benefiting of prompt therapy

11. 6b. To identify at risk individuals by ‘population genetic screening’
e.g. to recognize individuals heterozygous for ß-thalassemia in at risk populations

12. 6c. To identify unaffected at risk individuals by ‘cascade screening’ within a family
e.g. to recognize SMN gene heterozygotes in families segregating spinal muscular atrophy

13. I:1 I:2
II:1 II:6 II:2 II:7 II:3 II:8 II:4 II:9 II:5
III:1 III:2 III:3 III:4 III:5 III:6 III:7 III:8
7. To identify individuals at risk of developing adult onset diseases
e.g.. CTG triplet expansion within DMPK gene in myotonic dystrophy

14. 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
8. To avoid non useful investigations
e.g. genetic testing in families with Adenomatous Polyposis of the Colon (APC gene)

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

16. • 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
10. To improve genetic counseling
e.g. risk assessment in Nablus-syndrome

17. “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

18. Samples with % confirmed
Genetic tests Number of tests clinical
mutations
diagnoses
Williams syndrome 2.628 74 2.82
del7q11.23
DiGeorge/Velo-Cardio-Facial syndrome 3.683 123 3.34
del22q11.2
Fragile X syndrome 5.374 224 4.17
FMR1 mutations
Angelman syndrome 589 52 8.83
del15qmat/pat disomy/UBE3A mutations
Prader-Willi syndrome 639 112 17.53
del15qpat/mat disomy/SNRPN mutations
Achondroplasia 140 51 36.43
FGFR3 mutations
Appropriateness of genetic testing in Italy
Dallapiccola et al., Genet Test Mol Biomarkers. 2010; 14:17-22

19. 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