Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing (2024)

de Lange, I. M., Koudijs, M. J., van 't Slot, R., Sonsma, A. C. M., Mulder, F., Carbo, E. C., van Kempen, M. J. A., Nijman, I. J., Ernst, R. F., Savelberg, S. M. C., Knoers, N. V. A. M., Brilstra, E. H., & Koeleman, B. P. C. (2019). Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing. Journal of Medical Genetics, 56(2), 75-80. https://doi.org/10.1136/jmedgenet-2018-105672

de Lange, Iris M ; Koudijs, Marco J ; van 't Slot, Ruben et al. / Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing. In: Journal of Medical Genetics. 2019 ; Vol. 56, No. 2. pp. 75-80.

@article{268ddd4192e945239dffd387092c1846,

title = "Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing",

abstract = "BACKGROUND: Dravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs in a substantial proportion of families (7%-13%) and has important implications for recurrence risks. However, parental mosaicism can remain undetected by methods regularly used in diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), a technique with high sensitivity for detecting low-grade mosaic variants and high cost-effectiveness, to investigate the incidence of parental mosaicism of SCN1A variants in a cohort of 90 families and assess the feasibility of this technique.METHODS: Deep sequencing of SCN1A was performed using smMIPs. False positive rates for each of the proband's pathogenic variants were determined in 145 unrelated samples. If parents showed corresponding variant alleles at a significantly higher rate than the established noise ratio, mosaicism was confirmed by droplet digital PCR (ddPCR).RESULTS: Sequence coverage of at least 100× at the location of the corresponding pathogenic variant was reached for 80 parent couples. The variant ratio was significantly higher than the established noise ratio in eight parent couples, of which four (5%) were regarded as true mosaics, based on ddPCR results. The false positive rate of smMIP analysis without ddPCR was therefore 50%. Three of these variants had previously been considered de novo in the proband by Sanger sequencing.CONCLUSION: smMIP technology combined withnext generation sequencing (NGS) performs better than Sanger sequencing in the detection of parental mosaicism. Because parental mosaicism has important implications for genetic counselling and recurrence risks, we stress the importance of implementing high-sensitivity NGS-based assays in standard diagnostics.",

author = "{de Lange}, {Iris M} and Koudijs, {Marco J} and {van 't Slot}, Ruben and Sonsma, {Anja C M} and Flip Mulder and Carbo, {Ellen C} and {van Kempen}, {Marjan J A} and Nijman, {Isaac J} and Ernst, {Robert F} and Savelberg, {Sanne M C} and Knoers, {Nine V A M} and Brilstra, {Eva H} and Koeleman, {Bobby P C}",

note = "{\textcopyright} Author(s) (or their employer(s)) 2019. No commercial re-use. See rights and permissions. Published by BMJ.",

year = "2019",

month = feb,

doi = "10.1136/jmedgenet-2018-105672",

language = "English",

volume = "56",

pages = "75--80",

journal = "Journal of Medical Genetics",

issn = "0022-2593",

publisher = "BMJ Publishing Group",

number = "2",

}

de Lange, IM, Koudijs, MJ, van 't Slot, R, Sonsma, ACM, Mulder, F, Carbo, EC, van Kempen, MJA, Nijman, IJ, Ernst, RF, Savelberg, SMC, Knoers, NVAM, Brilstra, EH & Koeleman, BPC 2019, 'Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing', Journal of Medical Genetics, vol. 56, no. 2, pp. 75-80. https://doi.org/10.1136/jmedgenet-2018-105672

Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing. / de Lange, Iris M; Koudijs, Marco J; van 't Slot, Ruben et al.
In: Journal of Medical Genetics, Vol. 56, No. 2, 02.2019, p. 75-80.

Research output: Contribution to journal › Article › Academic › peer-review

TY - JOUR

T1 - Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing

AU - de Lange, Iris M

AU - Koudijs, Marco J

AU - van 't Slot, Ruben

AU - Sonsma, Anja C M

AU - Mulder, Flip

AU - Carbo, Ellen C

AU - van Kempen, Marjan J A

AU - Nijman, Isaac J

AU - Ernst, Robert F

AU - Savelberg, Sanne M C

AU - Knoers, Nine V A M

AU - Brilstra, Eva H

AU - Koeleman, Bobby P C

N1 - © Author(s) (or their employer(s)) 2019. No commercial re-use. See rights and permissions. Published by BMJ.

PY - 2019/2

Y1 - 2019/2

N2 - BACKGROUND: Dravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs in a substantial proportion of families (7%-13%) and has important implications for recurrence risks. However, parental mosaicism can remain undetected by methods regularly used in diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), a technique with high sensitivity for detecting low-grade mosaic variants and high cost-effectiveness, to investigate the incidence of parental mosaicism of SCN1A variants in a cohort of 90 families and assess the feasibility of this technique.METHODS: Deep sequencing of SCN1A was performed using smMIPs. False positive rates for each of the proband's pathogenic variants were determined in 145 unrelated samples. If parents showed corresponding variant alleles at a significantly higher rate than the established noise ratio, mosaicism was confirmed by droplet digital PCR (ddPCR).RESULTS: Sequence coverage of at least 100× at the location of the corresponding pathogenic variant was reached for 80 parent couples. The variant ratio was significantly higher than the established noise ratio in eight parent couples, of which four (5%) were regarded as true mosaics, based on ddPCR results. The false positive rate of smMIP analysis without ddPCR was therefore 50%. Three of these variants had previously been considered de novo in the proband by Sanger sequencing.CONCLUSION: smMIP technology combined withnext generation sequencing (NGS) performs better than Sanger sequencing in the detection of parental mosaicism. Because parental mosaicism has important implications for genetic counselling and recurrence risks, we stress the importance of implementing high-sensitivity NGS-based assays in standard diagnostics.

AB - BACKGROUND: Dravet syndrome is a severe genetic encephalopathy, caused by pathogenic variants in SCN1A. Low-grade parental mosaicism occurs in a substantial proportion of families (7%-13%) and has important implications for recurrence risks. However, parental mosaicism can remain undetected by methods regularly used in diagnostics. In this study, we use single-molecule molecular inversion probes (smMIP), a technique with high sensitivity for detecting low-grade mosaic variants and high cost-effectiveness, to investigate the incidence of parental mosaicism of SCN1A variants in a cohort of 90 families and assess the feasibility of this technique.METHODS: Deep sequencing of SCN1A was performed using smMIPs. False positive rates for each of the proband's pathogenic variants were determined in 145 unrelated samples. If parents showed corresponding variant alleles at a significantly higher rate than the established noise ratio, mosaicism was confirmed by droplet digital PCR (ddPCR).RESULTS: Sequence coverage of at least 100× at the location of the corresponding pathogenic variant was reached for 80 parent couples. The variant ratio was significantly higher than the established noise ratio in eight parent couples, of which four (5%) were regarded as true mosaics, based on ddPCR results. The false positive rate of smMIP analysis without ddPCR was therefore 50%. Three of these variants had previously been considered de novo in the proband by Sanger sequencing.CONCLUSION: smMIP technology combined withnext generation sequencing (NGS) performs better than Sanger sequencing in the detection of parental mosaicism. Because parental mosaicism has important implications for genetic counselling and recurrence risks, we stress the importance of implementing high-sensitivity NGS-based assays in standard diagnostics.

U2 - 10.1136/jmedgenet-2018-105672

DO - 10.1136/jmedgenet-2018-105672

M3 - Article

C2 - 30368457

SN - 0022-2593

VL - 56

SP - 75

EP - 80

JO - Journal of Medical Genetics

JF - Journal of Medical Genetics

IS - 2

ER -

de Lange IM, Koudijs MJ, van 't Slot R, Sonsma ACM, Mulder F, Carbo EC et al. Assessment of parental mosaicism in SCN1A-related epilepsy by single-molecule molecular inversion probes and next-generation sequencing. Journal of Medical Genetics. 2019 Feb;56(2):75-80. doi: 10.1136/jmedgenet-2018-105672