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1. Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Author

Khan, M., Cornelis, S.S., Pozo-Valero, M.D., Whelan, L., Runhart, E.H., Mishra, K., Bults, F., AlSwaiti, Y., AlTalbishi, A., Baere, E. De, Banfi, S., Banin, E., Bauwens, M., Ben-Yosef, T., Boon, C.J.F., Born, L.I. van den, Defoort, S., Devos, A., Dockery, A., Dudakova, L., Fakin, A., Farrar, G.J., Sallum, J.M.F., Fujinami, K., Gilissen, C., Glavač, D., Gorin, M.B., Greenberg, J., Hayashi, T., Hettinga, Y.M., Hoischen, A., Hoyng, C.B., Hufendiek, K., Jägle, H., Kamakari, S., Karali, M., Kellner, U., Klaver, C.C.W., Kousal, B., Lamey, T.M., MacDonald, I.M., Matynia, A., McLaren, T.L., Mena, M.D., Meunier, I., Miller, R., Newman, H., Ntozini, B., Oldak, M., Pieterse, M., Podhajcer, O.L., Puech, B., Ramesar, R., Rüther, K., Salameh, M., Salles, M.V., Sharon, D., Simonelli, F., Spital, G., Steehouwer, M., Szaflik, J.P., Thompson, J.A., Thuillier, C., Tracewska, A.M., Zweeden, M. van, Vincent, A.L., Zanlonghi, X., Liskova, P., Stöhr, H., Roach, J.N., Ayuso, C., Roberts, L., Weber, B.H.F., Dhaenens, C.M., Cremers, F.P.M., Khan, M., Cornelis, S.S., Pozo-Valero, M.D., Whelan, L., Runhart, E.H., Mishra, K., Bults, F., AlSwaiti, Y., AlTalbishi, A., Baere, E. De, Banfi, S., Banin, E., Bauwens, M., Ben-Yosef, T., Boon, C.J.F., Born, L.I. van den, Defoort, S., Devos, A., Dockery, A., Dudakova, L., Fakin, A., Farrar, G.J., Sallum, J.M.F., Fujinami, K., Gilissen, C., Glavač, D., Gorin, M.B., Greenberg, J., Hayashi, T., Hettinga, Y.M., Hoischen, A., Hoyng, C.B., Hufendiek, K., Jägle, H., Kamakari, S., Karali, M., Kellner, U., Klaver, C.C.W., Kousal, B., Lamey, T.M., MacDonald, I.M., Matynia, A., McLaren, T.L., Mena, M.D., Meunier, I., Miller, R., Newman, H., Ntozini, B., Oldak, M., Pieterse, M., Podhajcer, O.L., Puech, B., Ramesar, R., Rüther, K., Salameh, M., Salles, M.V., Sharon, D., Simonelli, F., Spital, G., Steehouwer, M., Szaflik, J.P., Thompson, J.A., Thuillier, C., Tracewska, A.M., Zweeden, M. van, Vincent, A.L., Zanlonghi, X., Liskova, P., Stöhr, H., Roach, J.N., Ayuso, C., Roberts, L., Weber, B.H.F., Dhaenens, C.M., and Cremers, F.P.M.

Abstract

Contains fulltext : 225504.pdf (Publisher’s version ) (Closed access), PURPOSE: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. METHODS: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. RESULTS: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. CONCLUSION: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.

Published
2020

2. Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Author

Khan, M., Cornelis, S.S., Pozo-Valero, M.D., Whelan, L., Runhart, E.H., Mishra, K., Bults, F., AlSwaiti, Y., AlTalbishi, A., Baere, E. De, Banfi, S., Banin, E., Bauwens, M., Ben-Yosef, T., Boon, C.J.F., Born, L.I. van den, Defoort, S., Devos, A., Dockery, A., Dudakova, L., Fakin, A., Farrar, G.J., Sallum, J.M.F., Fujinami, K., Gilissen, C., Glavač, D., Gorin, M.B., Greenberg, J., Hayashi, T., Hettinga, Y.M., Hoischen, A., Hoyng, C.B., Hufendiek, K., Jägle, H., Kamakari, S., Karali, M., Kellner, U., Klaver, C.C.W., Kousal, B., Lamey, T.M., MacDonald, I.M., Matynia, A., McLaren, T.L., Mena, M.D., Meunier, I., Miller, R., Newman, H., Ntozini, B., Oldak, M., Pieterse, M., Podhajcer, O.L., Puech, B., Ramesar, R., Rüther, K., Salameh, M., Salles, M.V., Sharon, D., Simonelli, F., Spital, G., Steehouwer, M., Szaflik, J.P., Thompson, J.A., Thuillier, C., Tracewska, A.M., Zweeden, M. van, Vincent, A.L., Zanlonghi, X., Liskova, P., Stöhr, H., Roach, J.N., Ayuso, C., Roberts, L., Weber, B.H.F., Dhaenens, C.M., Cremers, F.P.M., Khan, M., Cornelis, S.S., Pozo-Valero, M.D., Whelan, L., Runhart, E.H., Mishra, K., Bults, F., AlSwaiti, Y., AlTalbishi, A., Baere, E. De, Banfi, S., Banin, E., Bauwens, M., Ben-Yosef, T., Boon, C.J.F., Born, L.I. van den, Defoort, S., Devos, A., Dockery, A., Dudakova, L., Fakin, A., Farrar, G.J., Sallum, J.M.F., Fujinami, K., Gilissen, C., Glavač, D., Gorin, M.B., Greenberg, J., Hayashi, T., Hettinga, Y.M., Hoischen, A., Hoyng, C.B., Hufendiek, K., Jägle, H., Kamakari, S., Karali, M., Kellner, U., Klaver, C.C.W., Kousal, B., Lamey, T.M., MacDonald, I.M., Matynia, A., McLaren, T.L., Mena, M.D., Meunier, I., Miller, R., Newman, H., Ntozini, B., Oldak, M., Pieterse, M., Podhajcer, O.L., Puech, B., Ramesar, R., Rüther, K., Salameh, M., Salles, M.V., Sharon, D., Simonelli, F., Spital, G., Steehouwer, M., Szaflik, J.P., Thompson, J.A., Thuillier, C., Tracewska, A.M., Zweeden, M. van, Vincent, A.L., Zanlonghi, X., Liskova, P., Stöhr, H., Roach, J.N., Ayuso, C., Roberts, L., Weber, B.H.F., Dhaenens, C.M., and Cremers, F.P.M.

Abstract

Contains fulltext : 225504.pdf (Publisher’s version ) (Closed access), PURPOSE: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. METHODS: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. RESULTS: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. CONCLUSION: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.

Published
2020

3. Resolving the dark matter of ABCA4 for 1054 Stargardt disease probands through integrated genomics and transcriptomics

Author

Khan, M., Cornelis, S.S., Pozo-Valero, M.D., Whelan, L., Runhart, E.H., Mishra, K., Bults, F., AlSwaiti, Y., AlTalbishi, A., Baere, E. De, Banfi, S., Banin, E., Bauwens, M., Ben-Yosef, T., Boon, C.J.F., Born, L.I. van den, Defoort, S., Devos, A., Dockery, A., Dudakova, L., Fakin, A., Farrar, G.J., Sallum, J.M.F., Fujinami, K., Gilissen, C., Glavač, D., Gorin, M.B., Greenberg, J., Hayashi, T., Hettinga, Y.M., Hoischen, A., Hoyng, C.B., Hufendiek, K., Jägle, H., Kamakari, S., Karali, M., Kellner, U., Klaver, C.C.W., Kousal, B., Lamey, T.M., MacDonald, I.M., Matynia, A., McLaren, T.L., Mena, M.D., Meunier, I., Miller, R., Newman, H., Ntozini, B., Oldak, M., Pieterse, M., Podhajcer, O.L., Puech, B., Ramesar, R., Rüther, K., Salameh, M., Salles, M.V., Sharon, D., Simonelli, F., Spital, G., Steehouwer, M., Szaflik, J.P., Thompson, J.A., Thuillier, C., Tracewska, A.M., Zweeden, M. van, Vincent, A.L., Zanlonghi, X., Liskova, P., Stöhr, H., Roach, J.N., Ayuso, C., Roberts, L., Weber, B.H.F., Dhaenens, C.M., Cremers, F.P.M., Khan, M., Cornelis, S.S., Pozo-Valero, M.D., Whelan, L., Runhart, E.H., Mishra, K., Bults, F., AlSwaiti, Y., AlTalbishi, A., Baere, E. De, Banfi, S., Banin, E., Bauwens, M., Ben-Yosef, T., Boon, C.J.F., Born, L.I. van den, Defoort, S., Devos, A., Dockery, A., Dudakova, L., Fakin, A., Farrar, G.J., Sallum, J.M.F., Fujinami, K., Gilissen, C., Glavač, D., Gorin, M.B., Greenberg, J., Hayashi, T., Hettinga, Y.M., Hoischen, A., Hoyng, C.B., Hufendiek, K., Jägle, H., Kamakari, S., Karali, M., Kellner, U., Klaver, C.C.W., Kousal, B., Lamey, T.M., MacDonald, I.M., Matynia, A., McLaren, T.L., Mena, M.D., Meunier, I., Miller, R., Newman, H., Ntozini, B., Oldak, M., Pieterse, M., Podhajcer, O.L., Puech, B., Ramesar, R., Rüther, K., Salameh, M., Salles, M.V., Sharon, D., Simonelli, F., Spital, G., Steehouwer, M., Szaflik, J.P., Thompson, J.A., Thuillier, C., Tracewska, A.M., Zweeden, M. van, Vincent, A.L., Zanlonghi, X., Liskova, P., Stöhr, H., Roach, J.N., Ayuso, C., Roberts, L., Weber, B.H.F., Dhaenens, C.M., and Cremers, F.P.M.

Abstract

Contains fulltext : 225504.pdf (Publisher’s version ) (Closed access), PURPOSE: Missing heritability in human diseases represents a major challenge, and this is particularly true for ABCA4-associated Stargardt disease (STGD1). We aimed to elucidate the genomic and transcriptomic variation in 1054 unsolved STGD and STGD-like probands. METHODS: Sequencing of the complete 128-kb ABCA4 gene was performed using single-molecule molecular inversion probes (smMIPs), based on a semiautomated and cost-effective method. Structural variants (SVs) were identified using relative read coverage analyses and putative splice defects were studied using in vitro assays. RESULTS: In 448 biallelic probands 14 known and 13 novel deep-intronic variants were found, resulting in pseudoexon (PE) insertions or exon elongations in 105 alleles. Intriguingly, intron 13 variants c.1938-621G>A and c.1938-514G>A resulted in dual PE insertions consisting of the same upstream, but different downstream PEs. The intron 44 variant c.6148-84A>T resulted in two PE insertions and flanking exon deletions. Eleven distinct large deletions were found, two of which contained small inverted segments. Uniparental isodisomy of chromosome 1 was identified in one proband. CONCLUSION: Deep sequencing of ABCA4 and midigene-based splice assays allowed the identification of SVs and causal deep-intronic variants in 25% of biallelic STGD1 cases, which represents a model study that can be applied to other inherited diseases.

Published
2020

4. MED13L-related intellectual disability: involvement of missense variants and delineation of the phenotype

Author

Smol, T., Petit, F., Piton, A., Keren, B., Sanlaville, D., Afenjar, A., Baker, S., Bedoukian, E. C., Bhoj, E. J., Bonneau, D., Boudry-Labis, E., Bouquillon, S., Boute-Benejean, O., Caumes, R., Chatron, N., Colson, C., Coubes, C., Coutton, C., Devillard, F., Dieux-Coeslier, A., Doco-Fenzy, M., Ewans, L. J., Faivre, L., Fassi, E., Field, M., Fournier, C., Francannet, C., Genevieve, D., Giurgea, I., Goldenberg, A., Gréen, Anna, Guerrot, A. M., Heron, D., Isidor, B., Keena, B. A., Krock, B. L., Kuentz, P., Lapi, E., Le Meur, N., Lesca, G., Li, D., Marey, I., Mignot, C., Nava, C., Nesbitt, A., Nicolas, G., Roche-Lestienne, C., Roscioli, T., Satre, V., Santani, A., Stefanova, Margarita, Steinwall Larsen, S., Saugier-Veber, P., Picker-Minh, S., Thuillier, C., Verloes, A., Vieville, G., Wenzel, M., Willems, M., Whalen, S., Zarate, Y. A., Ziegler, A., Manouvrier-Hanu, S., Kalscheuer, V. M., Gerard, B., Ghoumid, Jamal, Smol, T., Petit, F., Piton, A., Keren, B., Sanlaville, D., Afenjar, A., Baker, S., Bedoukian, E. C., Bhoj, E. J., Bonneau, D., Boudry-Labis, E., Bouquillon, S., Boute-Benejean, O., Caumes, R., Chatron, N., Colson, C., Coubes, C., Coutton, C., Devillard, F., Dieux-Coeslier, A., Doco-Fenzy, M., Ewans, L. J., Faivre, L., Fassi, E., Field, M., Fournier, C., Francannet, C., Genevieve, D., Giurgea, I., Goldenberg, A., Gréen, Anna, Guerrot, A. M., Heron, D., Isidor, B., Keena, B. A., Krock, B. L., Kuentz, P., Lapi, E., Le Meur, N., Lesca, G., Li, D., Marey, I., Mignot, C., Nava, C., Nesbitt, A., Nicolas, G., Roche-Lestienne, C., Roscioli, T., Satre, V., Santani, A., Stefanova, Margarita, Steinwall Larsen, S., Saugier-Veber, P., Picker-Minh, S., Thuillier, C., Verloes, A., Vieville, G., Wenzel, M., Willems, M., Whalen, S., Zarate, Y. A., Ziegler, A., Manouvrier-Hanu, S., Kalscheuer, V. M., Gerard, B., and Ghoumid, Jamal

Abstract

Molecular anomalies in MED13L, leading to haploinsufficiency, have been reported in patients with moderate to severe intellectual disability (ID) and distinct facial features, with or without congenital heart defects. Phenotype of the patients was referred to "MED13L haploinsufficiency syndrome." Missense variants in MED13L were already previously described to cause the MED13L-related syndrome, but only in a limited number of patients. Here we report 36 patients with MED13L molecular anomaly, recruited through an international collaboration between centers of expertise for developmental anomalies. All patients presented with intellectual disability and severe language impairment. Hypotonia, ataxia, and recognizable facial gestalt were frequent findings, but not congenital heart defects. We identified seven de novo missense variations, in addition to protein-truncating variants and intragenic deletions. Missense variants clustered in two mutation hot-spots, i.e., exons 15-17 and 25-31. We found that patients carrying missense mutations had more frequently epilepsy and showed a more severe phenotype. This study ascertains missense variations in MED13L as a cause for MED13L-related intellectual disability and improves the clinical delineation of the condition.

Published
2018
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