Next Generation Sequencing e sue possibili applicazioni in campo clinico NGS per Diagnostica Eterogeneità Genetica Il concetto classico di Eterogeneità genetica implica il fatto che la stessa condizione può essere causata da mutazioni in geni differenti e questo sta divenendo un problema consistente in Genetica Medica Per alcune malattie il grado di eterogeneità genetica è tale che ci sono più di 100 geni che possono causare la stessa malattia La Retinite Pigmentosa (RP) è un gruppo eterogeneo di malattie ereditarie caratterizzato dalla progressiva perdita della vista, cecità notturna e depositi di pigmento nella retina. NGS per Ricerca Geography of exome sequencing Schinzel-Giedion N a tG e n e t A pr 1 0 Miller syndrome Na t G e ne t N ov 0 9 HPMR N a tG e n e t A u g 1 0 Kabuki syndrome N a tG e n e t A ug 1 0 DFNB82 A m J H u m G e n e t J un 1 0 Perrault syndrome A m J Hu m G e n e t J ul 1 0 Brain Malformation N a tu re A u g 1 0 UNITED WE STAND DE NOVO COMPOUND HETEROZYGOSITY HOMOZYGOSITY Sindromi malformative Malattie Mendeliane non Sindromiche FA2H causes SPG35 and leukodystrophy Two affected sibs from a consanguineous family carry a c.270+3A>T mutation in the FA2H gene exon 1 exon 2 L R G E Q Q G S M E N E P V L R G E Q Q V Q P G R G P P Single Nucleotide Variants SNVs Sib1 Sib 2 Validated 20967 22651 Transition to transversion ratio 2.91 2.89 In dbSNP 19727 (94%) 21237 (94%) Heterozygous in dbSNP 10372 11159 Homozygous in dbSNP 9355 10078 Not in dbSNP 1240 (6%) 1414 (6%) Heterozygous not in dbSNP 1086 1234 Homozygous not in dbSNP 130 154 180 Candidate variants filtering Cumulative total calls: 22711 ROHs in common: 28 No 1000 genomes: 8 NS, in UTRs, SS, nonsense: 28 Cumulative no dbSNPs: 1968 2 NS (1 gene) damaging by at least one prediction tool (SNP&GO, Polyphen, SIFT) 1 altering SS by at least one prediction tool (NetGene2, GDB) +1bp del A novel FA2H c.270+3A>T splice site mutation in an Italian consanguineous pedigree Malattie legate al cromosoma X TARGETED RESEQUENCING OF X CHROMOSOME EXONS Length (Mb) ~ 150 CCDS entries 1153 RefSeq entries 2036 OMIM loci/genes 716 Agilent SureSelect human X chromosome probes 7664 Probe/CCDS genomic regions overlap 95% Probe/RefSeq genomic regions overlap 94% I 1 2 1 2 1 2 1 2 II 1 1 2 1 2 1 2 A CASE STUDIED WITH BOTH “CLASSICAL” AND “NEXT GENERATION” APPROACHES X-linked recurrence of a previously undescribed neurocutaneous phenotype Individuals III-2 and III-4: microcephaly, neurodevelopmental delay, ichthyosis, epilepsy, tetraparesis and ACC Male fetus III-3: ACC callosum and hyperkeratosis of epidermis with desquamation at the autoptic examination after voluntary abortion Individuals I-2, II-2 and II-3: mild ichthyosis limited to the extensor surfaces of Limbs compatible with a balanced chromosome X inactivation pattern POSITIONAL CLONING OF A PAK3 VARIANT . Magini et al., submitted NGS-BASED DETECTION OF A PAK3 VARIANT CHR BAND GEN E hg19 Xp22.31 STS 7268094 . . Xp22.12 MAP3K15 . Xq13.1 STARD8 . Xq23 PAK3 CHANGE 19443659 67940201 110439126 SANGER p.L515 P + LINKAG E ? - p.P477T + - p.G582fs - - p.K389 N + +