Contributions
Abstract: EP1463
Type: Poster Sessions
Abstract Category: Pathology and pathogenesis of MS - Genetics/Epigenetics
Introduction: Multiple Sclerosis (MS) is a multifactorial inflammatory and neurodegenerative disease in which both genetic and environmental factors contribute to the pathogenesis. More than 200 common variants have been already identified to be associated to MS susceptibility, however it is still unclear the role of rare/private variants in raising disease risk.
Aim: to explore the role of rare functional variants in MS by studying multiplex families.
Methods: We recruited a total of 29 families with ≥ 3 affected relatives (2 of them with first-degree relationship). Whole exome sequencing (WES) was performed on Illumina Hiseq2500 platform.
An internal pipeline based on BWA aligner and GATK UnifiedGenotyper was used for alignment and calling steps, while variant annotation was performed using SnpEff suite.
For each family with at least two sequenced cases (24 families) we selected variants with: (a) High or moderate impact, (b) allele frequency (AF) ≤ 5% according to public databases and (c) AF≤10% in Italian population according to our internal database of healthy controls (HC).
For each family we generated lists of genes according to two different strategies:
(i) “sharing model” including genes with at least one variant shared by all affected members in at least one family followed by comparison across families; (ii) “segregation model” including genes with at least one variant that segregates according to family's pedigree. Pathway analysis was then performed within each model using WebGestalt tool.
Results: A preliminary analysis on 12 families (37 MS and 30 HC) allowed to identify:
(i) 2130 genes containing variants in at least one family, 119 of which were present in at least 3 families;
(ii) 359 genes harbouring variants present in at least one family, of which 11 in common between at least two families.
In either model pathway analysis showed an enrichment of genes involved in immunity (i.e. Th1 and Th2 cell differentiation (FDR=0.018 and 0.065 respectively in sharing and segregation model), Cell adhesion molecules (CAMs) (FDR=0.095 and 0.065 respectively in sharing and segregation model)).
Analyses on the overall cohort are ongoing.
Conclusions: The application of WES in familial cases can be useful in identifying rare variants potentially contributing to the disease and in unravelling novel genes, pathways and mechanisms involved in MS pathophysiology.
Disclosure: E. Mascia, A. Zauli, C. Guaschino, L. Ferrè, M. Sorosina, A.M. Osiceanu, S. Santoro, S. Peroni, D. Biancolini, S. Bonfiglio, D. Lazarevic, N. Barizzone, C. Basagni, M. Zuccalà, D. Vecchio, M. Liguori, F.M. Guerini, D. Caputo, G. Tonon, S. D'Alfonso : nothing to disclose.
G. Meola: Advisory Board Lupin
V. Martinelli: received honoraria from Biogen-Idec, Merck, Bayer, TEVA, Novartis and Genzyme.
G. Comi: received compensation for consulting services and/or speaking activities with Novartis, Teva, Sanofi, Genzyme, Merck, Biogen, Excemed, Roche, Almirall, Chugai, Receptos, Forward Pharma.
F. Esposito: received honoraria from Almirall and Genzyme.
F. Martinelli Boneschi: received honoraria for consulting, research grant and travel expenses from TEVA neuroscience, Biogen IDEC, Merck Serono, Roche and Sanofi-Genzyme.
Abstract: EP1463
Type: Poster Sessions
Abstract Category: Pathology and pathogenesis of MS - Genetics/Epigenetics
Introduction: Multiple Sclerosis (MS) is a multifactorial inflammatory and neurodegenerative disease in which both genetic and environmental factors contribute to the pathogenesis. More than 200 common variants have been already identified to be associated to MS susceptibility, however it is still unclear the role of rare/private variants in raising disease risk.
Aim: to explore the role of rare functional variants in MS by studying multiplex families.
Methods: We recruited a total of 29 families with ≥ 3 affected relatives (2 of them with first-degree relationship). Whole exome sequencing (WES) was performed on Illumina Hiseq2500 platform.
An internal pipeline based on BWA aligner and GATK UnifiedGenotyper was used for alignment and calling steps, while variant annotation was performed using SnpEff suite.
For each family with at least two sequenced cases (24 families) we selected variants with: (a) High or moderate impact, (b) allele frequency (AF) ≤ 5% according to public databases and (c) AF≤10% in Italian population according to our internal database of healthy controls (HC).
For each family we generated lists of genes according to two different strategies:
(i) “sharing model” including genes with at least one variant shared by all affected members in at least one family followed by comparison across families; (ii) “segregation model” including genes with at least one variant that segregates according to family's pedigree. Pathway analysis was then performed within each model using WebGestalt tool.
Results: A preliminary analysis on 12 families (37 MS and 30 HC) allowed to identify:
(i) 2130 genes containing variants in at least one family, 119 of which were present in at least 3 families;
(ii) 359 genes harbouring variants present in at least one family, of which 11 in common between at least two families.
In either model pathway analysis showed an enrichment of genes involved in immunity (i.e. Th1 and Th2 cell differentiation (FDR=0.018 and 0.065 respectively in sharing and segregation model), Cell adhesion molecules (CAMs) (FDR=0.095 and 0.065 respectively in sharing and segregation model)).
Analyses on the overall cohort are ongoing.
Conclusions: The application of WES in familial cases can be useful in identifying rare variants potentially contributing to the disease and in unravelling novel genes, pathways and mechanisms involved in MS pathophysiology.
Disclosure: E. Mascia, A. Zauli, C. Guaschino, L. Ferrè, M. Sorosina, A.M. Osiceanu, S. Santoro, S. Peroni, D. Biancolini, S. Bonfiglio, D. Lazarevic, N. Barizzone, C. Basagni, M. Zuccalà, D. Vecchio, M. Liguori, F.M. Guerini, D. Caputo, G. Tonon, S. D'Alfonso : nothing to disclose.
G. Meola: Advisory Board Lupin
V. Martinelli: received honoraria from Biogen-Idec, Merck, Bayer, TEVA, Novartis and Genzyme.
G. Comi: received compensation for consulting services and/or speaking activities with Novartis, Teva, Sanofi, Genzyme, Merck, Biogen, Excemed, Roche, Almirall, Chugai, Receptos, Forward Pharma.
F. Esposito: received honoraria from Almirall and Genzyme.
F. Martinelli Boneschi: received honoraria for consulting, research grant and travel expenses from TEVA neuroscience, Biogen IDEC, Merck Serono, Roche and Sanofi-Genzyme.