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4 results on '"Paolicchi, JM"'

1. Association of ultra-rare coding variants with genetic generalized epilepsy: A case–control whole exome sequencing study

Author

Koko, M, Motelow, JE, Stanley, KE, Bobbili, DR, Dhindsa, RS, May, P, Alldredge, BK, Allen, AS, Altmüller, J, Amrom, D, Andermann, E, Auce, P, Avbersek, A, Baulac, S, Bautista, JF, Becker, F, Bellows, Susannah, Berghuis, B, Berkovic, SF, Bluvstein, J, Boro, A, Bridgers, J, Burgess, R, Caglayan, H, Cascino, GD, Cavalleri, GL, Chung, SK, Cieuta-Walti, C, Cloutier, V, Consalvo, D, Cossette, P, Crumrine, P, Delanty, N, Depondt, C, Desbiens, R, Devinsky, O, Dlugos, D, Epstein, MP, Everett, K, Fiol, M, Fountain, NB, Francis, B, French, J, Freyer, C, Friedman, D, Gambardella, A, Geller, EB, Girard, S, Glauser, T, Glynn, S, Goldstein, DB, Gravel, M, Haas, K, Haut, SR, Heinzen, EL, Helbig, I, Hildebrand, MS, Johnson, MR, Jorgensen, A, Joshi, S, Kanner, A, Kirsch, HE, Klein, KM, Knowlton, RC, Koeleman, BPC, Kossoff, EH, Krause, R, Krenn, M, Kunz, WS, Kuzniecky, R, Langley, SR, LeGuern, E, Lehesjoki, AE, Lerche, H, Leu, C, Lortie, A, Lowenstein, DH, Marson, AG, Mebane, C, Mefford, HC, Meloche, C, Moreau, C, Motika, PV, Muhle, H, Møller, RS, Nabbout, R, Nguyen, DK, Nikanorova, M, Novotny, EJ, Nürnberg, P, Ottman, R, O’Brien, TJ, Paolicchi, JM, Parent, JM, Park, K, Peter, S, Petrou, S, Petrovski, S, Pickrell, WO, Poduri, A, Koko, M, Motelow, JE, Stanley, KE, Bobbili, DR, Dhindsa, RS, May, P, Alldredge, BK, Allen, AS, Altmüller, J, Amrom, D, Andermann, E, Auce, P, Avbersek, A, Baulac, S, Bautista, JF, Becker, F, Bellows, Susannah, Berghuis, B, Berkovic, SF, Bluvstein, J, Boro, A, Bridgers, J, Burgess, R, Caglayan, H, Cascino, GD, Cavalleri, GL, Chung, SK, Cieuta-Walti, C, Cloutier, V, Consalvo, D, Cossette, P, Crumrine, P, Delanty, N, Depondt, C, Desbiens, R, Devinsky, O, Dlugos, D, Epstein, MP, Everett, K, Fiol, M, Fountain, NB, Francis, B, French, J, Freyer, C, Friedman, D, Gambardella, A, Geller, EB, Girard, S, Glauser, T, Glynn, S, Goldstein, DB, Gravel, M, Haas, K, Haut, SR, Heinzen, EL, Helbig, I, Hildebrand, MS, Johnson, MR, Jorgensen, A, Joshi, S, Kanner, A, Kirsch, HE, Klein, KM, Knowlton, RC, Koeleman, BPC, Kossoff, EH, Krause, R, Krenn, M, Kunz, WS, Kuzniecky, R, Langley, SR, LeGuern, E, Lehesjoki, AE, Lerche, H, Leu, C, Lortie, A, Lowenstein, DH, Marson, AG, Mebane, C, Mefford, HC, Meloche, C, Moreau, C, Motika, PV, Muhle, H, Møller, RS, Nabbout, R, Nguyen, DK, Nikanorova, M, Novotny, EJ, Nürnberg, P, Ottman, R, O’Brien, TJ, Paolicchi, JM, Parent, JM, Park, K, Peter, S, Petrou, S, Petrovski, S, Pickrell, WO, and Poduri, A

Published
2022

2. Diverse genetic causes of polymicrogyria with epilepsy

Author

Allen, AS, Aggarwal, V, Berkovic, SF, Cossette, P, Delanty, N, Dlugos, D, Eichler, EE, Epstein, MP, Freyer, C, Goldstein, DB, Guerrini, R, Glauser, T, Heinzen, EL, Johnson, MR, Kuzniecky, R, Lowenstein, DH, Marson, AG, Mefford, HC, O'Brien, TJ, Ottman, R, Poduri, A, Petrou, S, Petrovski, S, Ruzzo, EK, Scheffer, IE, Sherr, EH, Abou-Khalil, B, Amrom, D, Andermann, E, Andermann, F, Bluvstein, J, Boro, A, Cascino, G, Consalvo, D, Crumrine, P, Devinsky, O, Fountain, N, Friedman, D, Geller, E, Glynn, S, Haas, K, Haut, S, Joshi, S, Kirsch, H, Knowlton, R, Kossoff, E, Motika, PV, Paolicchi, JM, Parent, JM, Shellhaas, RA, Shih, JJ, Shinnar, S, Singh, RK, Sperling, M, Smith, MC, Sullivan, J, Vining, EPG, Von Allmen, GK, Widdess-Walsh, P, Winawer, MR, Bautista, J, Fiol, M, Hayward, J, Helmers, S, Park, K, Sirven, J, Thio, LL, Venkat, A, Weisenberg, J, Kuperman, R, McGuire, S, Novotny, E, Sadleir, L, Allen, AS, Aggarwal, V, Berkovic, SF, Cossette, P, Delanty, N, Dlugos, D, Eichler, EE, Epstein, MP, Freyer, C, Goldstein, DB, Guerrini, R, Glauser, T, Heinzen, EL, Johnson, MR, Kuzniecky, R, Lowenstein, DH, Marson, AG, Mefford, HC, O'Brien, TJ, Ottman, R, Poduri, A, Petrou, S, Petrovski, S, Ruzzo, EK, Scheffer, IE, Sherr, EH, Abou-Khalil, B, Amrom, D, Andermann, E, Andermann, F, Bluvstein, J, Boro, A, Cascino, G, Consalvo, D, Crumrine, P, Devinsky, O, Fountain, N, Friedman, D, Geller, E, Glynn, S, Haas, K, Haut, S, Joshi, S, Kirsch, H, Knowlton, R, Kossoff, E, Motika, PV, Paolicchi, JM, Parent, JM, Shellhaas, RA, Shih, JJ, Shinnar, S, Singh, RK, Sperling, M, Smith, MC, Sullivan, J, Vining, EPG, Von Allmen, GK, Widdess-Walsh, P, Winawer, MR, Bautista, J, Fiol, M, Hayward, J, Helmers, S, Park, K, Sirven, J, Thio, LL, Venkat, A, Weisenberg, J, Kuperman, R, McGuire, S, Novotny, E, and Sadleir, L

Abstract

OBJECTIVE: We sought to identify novel genes and to establish the contribution of known genes in a large cohort of patients with nonsyndromic sporadic polymicrogyria and epilepsy. METHODS: We enrolled participants with polymicrogyria and their parents through the Epilepsy Phenome/Genome Project. We performed phenotyping and whole exome sequencing (WES), trio analysis, and gene-level collapsing analysis to identify de novo or inherited variants, including germline or mosaic (postzygotic) single nucleotide variants, small insertion-deletion (indel) variants, and copy number variants present in leukocyte-derived DNA. RESULTS: Across the cohort of 86 individuals with polymicrogyria and epilepsy, we identified seven with pathogenic or likely pathogenic variants in PIK3R2, including four germline and three mosaic variants. PIK3R2 was the only gene harboring more than expected de novo variants across the entire cohort, and likewise the only gene that passed the genome-wide threshold of significance in the gene-level rare variant collapsing analysis. Consistent with previous reports, the PIK3R2 phenotype consisted of bilateral polymicrogyria concentrated in the perisylvian region with macrocephaly. Beyond PIK3R2, we also identified one case each with likely causal de novo variants in CCND2 and DYNC1H1 and biallelic variants in WDR62, all genes previously associated with polymicrogyria. Candidate genetic explanations in this cohort included single nucleotide de novo variants in other epilepsy-associated and neurodevelopmental disease-associated genes (SCN2A in two individuals, GRIA3, CACNA1C) and a 597-kb deletion at 15q25, a neurodevelopmental disease susceptibility locus. SIGNIFICANCE: This study confirms germline and postzygotically acquired de novo variants in PIK3R2 as an important cause of bilateral perisylvian polymicrogyria, notably with macrocephaly. In total, trio-based WES identified a genetic diagnosis in 12% and a candidate diagnosis in 6% of our polymicrogyria

Published
2021

3. Copy number variant analysis from exome data in 349 patients with epileptic encephalopathy

Author

Abou-Khalil, B, Alldredge, BK, Allen, AS, Andermann, E, Andermann, F, Amrom, D, Bautista, JF, Berkovic, SF, Boro, A, Cascino, G, Coe, BP, Consalvo, D, Cook, J, Cossette, P, Crumrine, P, Delanty, N, Devinsky, O, Dlugos, D, Eichler, EE, Epstein, MP, Fiol, M, Fountain, NB, French, J, Friedman, D, Geller, EB, Glauser, T, Glynn, S, Goldstein, DB, Haut, SR, Hayward, J, Heinzen, EL, Helmers, SL, Johnson, MR, Joshi, S, Kanner, A, Kirsch, HE, Knowlton, RC, Kossoff, EH, Krumm, N, Kuperman, R, Kuzniecky, R, Lowenstein, DH, Marson, AG, McGuire, SM, Mefford, HC, Motika, PV, Nelson, B, Nieh, SE, Novotny, EJ, O'Brien, TJ, Ottman, R, Paolicchi, JM, Parent, J, Park, K, Petrou, S, Petrovski, S, Poduri, A, Raja, A, Ruzzo, EK, Scheffer, IE, Shellhaas, RA, Sherr, E, Shih, JJ, Singh, R, Sirven, J, Smith, MC, Sullivan, J, Liu, LT, Venkat, A, Vining, EPG, Von Allmen, GK, Weisenberg, JL, Widdess-Walsh, P, Winawer, MR, Abou-Khalil, B, Alldredge, BK, Allen, AS, Andermann, E, Andermann, F, Amrom, D, Bautista, JF, Berkovic, SF, Boro, A, Cascino, G, Coe, BP, Consalvo, D, Cook, J, Cossette, P, Crumrine, P, Delanty, N, Devinsky, O, Dlugos, D, Eichler, EE, Epstein, MP, Fiol, M, Fountain, NB, French, J, Friedman, D, Geller, EB, Glauser, T, Glynn, S, Goldstein, DB, Haut, SR, Hayward, J, Heinzen, EL, Helmers, SL, Johnson, MR, Joshi, S, Kanner, A, Kirsch, HE, Knowlton, RC, Kossoff, EH, Krumm, N, Kuperman, R, Kuzniecky, R, Lowenstein, DH, Marson, AG, McGuire, SM, Mefford, HC, Motika, PV, Nelson, B, Nieh, SE, Novotny, EJ, O'Brien, TJ, Ottman, R, Paolicchi, JM, Parent, J, Park, K, Petrou, S, Petrovski, S, Poduri, A, Raja, A, Ruzzo, EK, Scheffer, IE, Shellhaas, RA, Sherr, E, Shih, JJ, Singh, R, Sirven, J, Smith, MC, Sullivan, J, Liu, LT, Venkat, A, Vining, EPG, Von Allmen, GK, Weisenberg, JL, Widdess-Walsh, P, and Winawer, MR

Abstract

Infantile spasms (IS) and Lennox-Gastaut syndrome (LGS) are epileptic encephalopathies characterized by early onset, intractable seizures, and poor developmental outcomes. De novo sequence mutations and copy number variants (CNVs) are causative in a subset of cases. We used exome sequence data in 349 trios with IS or LGS to identify putative de novo CNVs. We confirm 18 de novo CNVs in 17 patients (4.8%), 10 of which are likely pathogenic, giving a firm genetic diagnosis for 2.9% of patients. Confirmation of exome-predicted CNVs by array-based methods is still required due to false-positive rates of prediction algorithms. Our exome-based results are consistent with recent array-based studies in similar cohorts and highlight novel candidate genes for IS and LGS.

Published
2015

4. De novo mutations in epileptic encephalopathies

Author

Allen, AS, Berkovic, SF, Cossette, P, Delanty, N, Dlugos, D, Eichler, EE, Epstein, MP, Glauser, T, Goldstein, DB, Han, Y, Heinzen, EL, Hitomi, Y, Howell, KB, Johnson, MR, Kuzniecky, R, Lowenstein, DH, Lu, Y-F, Madou, MRZ, Marson, AG, Mefford, HC, Nieh, SE, O'Brien, TJ, Ottman, R, Petrovski, S, Poduri, A, Ruzzo, EK, Scheffer, IE, Sherr, EH, Yuskaitis, CJ, Abou-Khalil, B, Alldredge, BK, Bautista, JF, Boro, A, Cascino, GD, Consalvo, D, Crumrine, P, Devinsky, O, Fiol, M, Fountain, NB, French, J, Friedman, D, Geller, EB, Glynn, S, Haut, SR, Hayward, J, Helmers, SL, Joshi, S, Kanner, A, Kirsch, HE, Knowlton, RC, Kossoff, E, Kuperman, R, McGuire, SM, Motika, PV, Novotny, EJ, Paolicchi, JM, Parent, JM, Park, K, Shellhaas, RA, Shih, JJ, Singh, R, Sirven, J, Smith, MC, Sullivan, J, Thio, LL, Venkat, A, Vining, EPG, Von Allmen, GK, Weisenberg, JL, Widdess-Walsh, P, Winawer, MR, Allen, AS, Berkovic, SF, Cossette, P, Delanty, N, Dlugos, D, Eichler, EE, Epstein, MP, Glauser, T, Goldstein, DB, Han, Y, Heinzen, EL, Hitomi, Y, Howell, KB, Johnson, MR, Kuzniecky, R, Lowenstein, DH, Lu, Y-F, Madou, MRZ, Marson, AG, Mefford, HC, Nieh, SE, O'Brien, TJ, Ottman, R, Petrovski, S, Poduri, A, Ruzzo, EK, Scheffer, IE, Sherr, EH, Yuskaitis, CJ, Abou-Khalil, B, Alldredge, BK, Bautista, JF, Boro, A, Cascino, GD, Consalvo, D, Crumrine, P, Devinsky, O, Fiol, M, Fountain, NB, French, J, Friedman, D, Geller, EB, Glynn, S, Haut, SR, Hayward, J, Helmers, SL, Joshi, S, Kanner, A, Kirsch, HE, Knowlton, RC, Kossoff, E, Kuperman, R, McGuire, SM, Motika, PV, Novotny, EJ, Paolicchi, JM, Parent, JM, Park, K, Shellhaas, RA, Shih, JJ, Singh, R, Sirven, J, Smith, MC, Sullivan, J, Thio, LL, Venkat, A, Vining, EPG, Von Allmen, GK, Weisenberg, JL, Widdess-Walsh, P, and Winawer, MR

Abstract

Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 149) and Lennox-Gastaut syndrome (n = 115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ∼4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 × 10(-3)). Among these are GABRB3, with de novo mutations in four patients, and ALG13, with the same de novo mutation in two patients; both genes show clear statistical evidence of association with epileptic encephalopathy. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are P = 4.1 × 10(-10) and P = 7.8 × 10(-12), respectively. Other genes with de novo mutations in this cohort include CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HNRNPU, IQSEC2, MTOR and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P < 10(-8)), as has been reported previously for autism spectrum disorders.

Published
2013

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