Roberto Ciccone, Orsetta Zuffardi Università di Pavia

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1 Roberto Ciccone, Orsetta Zuffardi Università di Pavia XIII Corso di Formazione Malformazioni Congenite dalla Diagnosi Prenatale alla Terapia Postnatale unipv.eu Carrara, 24 ottobre 2014

2 Legend:Bluebars indicate reported CNVs; Redbars indicate reported inversion breakpoints; Greenbars to the left indicate segmental duplications.

3 Structural Variations (SVs) Copy Number Variants (CNVs) Balanced Chromosomal Aberrations (BCAs)

4 Circa 68% del genoma coperto da CNVs > 90% dei trascritti coperti da CNVs > 90% dei geni OMIM coperti da CNVs dgv.tcag.ca/dgv/app/home

5 dgv.tcag.ca/dgv/app/home

6 Common CNVs (MAF > 1%): may determine several multifactorial characters, have numerous alleles, in term of copy number states are involved in sensory perception, immune response, disease susceptibility and drug response Major source of inter-individual genetic variability Rare CNVs (MAF < 1%): often causative of pathological phenotypes have fewer allelic states, usually hemizygous or trisomic are highly penetrant

7

8 Cooper G et al, Nat Genet 2011

9 Size Genomic content (genes, repetitive/unique sequences, regulatory elements) Comparison of CNV with internal and external databases Inheritance/parental origin

10 Gene content When considering the potential phenotypic effect of CNVs it is fundamental to investigate whether the genes in the interval are associated with clinical disorders. However. Genes associated with a clinical phenotype due to haploinsufficiency may have no phenotype associated with a copy number gain. Dosage imbalance does not imply impairment of gene function Copy number gains involving only part of a gene may result in gene disruption or altered coding sequence Single-copy deletions of genes associated with recessive disease may only suggest carrier status for the condition. Small CNVs involving only intronic sequence may have no effect on gene function

11 Recessive coding mutations in PTF1A cause syndromic pancreatic agenesis with neurological features and cerebellar agenesis. However, some families have isolated pancreatic agenesis. Whole Genome Sequencing revealed mutations of a cisregulatory elements of PTF1A

12 16p12.1 recurrent deletion: benign variant or disease causing mutation??

13 16p12.1 recurrent deletion: benign variant or disease causing mutation??

14 Nat. Genet, 2010

15 The frequency of the inherited first hit depends on the purifying selection Milder phenotypes can easily be passed from parent to child Girirajan and Eichler, 2010

16 Clinically relevant CNVs can be identified in 17.6% 22.5% of cases by Chromosomal MicroArray (CMA) Cryptic SVs (CNVs <100 Kb and small balanced rearrangements) can cause pathological phenotypes but cannot be detected by conventional clinical genetic screening Whole-genome sequencing using large-insert jumping libraries allows detection of cryptic and cytogenetically visible SVs

17 These investigations revealed about 200 SVs per subject, the vast majority would be cryptic to conventional CMA

18 Somatic Genomic Alterations Proteus syndrome Proteus syndrome is a severe syndrome characterized by multiple overgrowths of the skin, bone, connective tissue, and other tissues caused by a dominant somatic mutation of the AKT1 gene. Some syndromes caused by germline mutations (i.e. NF1, TSC1 and TSC2..) present characteristics due to additiona somatic mutations.

19 Somatic Genomic Alterations Post-zygotic chromosomal aberrations are very well known cause of syndromic phenotypes (i.e: terminal del/dup mimicking unbalanced translocations) Recently it has been demonstrated that somatic mutations confined at the CNS may cause cortical malformation and neurodegenerative diseases

20 Somatic Activation of AKT3 Causes Hemispheric Developmental Brain Malformations Poduri et al, 2012

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