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24 results on '"Strohbehn, Samuel"'

1. Synchronized long-read genome, methylome, epigenome and transcriptome profiling resolve a Mendelian condition

Author

Vollger, Mitchell R., Korlach, Jonas, Eldred, Kiara C., Swanson, Elliott, Underwood, Jason G., Bohaczuk, Stephanie C., Mao, Yizi, Cheng, Yong-Han H., Ranchalis, Jane, Blue, Elizabeth E., Schwarze, Ulrike, Munson, Katherine M., Saunders, Christopher T., Wenger, Aaron M., Allworth, Aimee, Chanprasert, Sirisak, Duerden, Brittney L., Glass, Ian, Horike-Pyne, Martha, Kim, Michelle, Leppig, Kathleen A., McLaughlin, Ian J., Ogawa, Jessica, Rosenthal, Elisabeth A., Sheppeard, Sam, Sherman, Stephanie M., Strohbehn, Samuel, Yuen, Amy L., Stacey, Andrew W., Reh, Thomas A., Byers, Peter H., Bamshad, Michael J., Hisama, Fuki M., Jarvik, Gail P., Sancak, Yasemin, Dipple, Katrina M., and Stergachis, Andrew B.

Published
2025
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2. Acute and chronic kidney function decline in patients receiving BRAF/MEK inhibitors for melanoma.

Author

Mistry, Kavita, Zhao, Sophia, Strohbehn, Ian, Wang, Qiyu, Hanna, Paul, Strohbehn, Samuel, Katz-Agranov, Nurit, Sullivan, Ryan J, and Sise, Meghan E

Subjects
BRAF genes, KIDNEY physiology, KIDNEY transplantation, INTERSTITIAL nephritis, MELANOMA
Abstract

This article discusses the potential risk of acute kidney injury (AKI) and chronic kidney disease (CKD) in patients receiving BRAF/MEK inhibitor therapy for melanoma. Real-world data showed higher rates of AKI compared to clinical trials. The study found that patients who received BRAF/MEK inhibitors had a higher risk of CKD compared to a group of patients who underwent surgical resection alone. The study suggests that CKD is an important comorbidity in melanoma patients and further research is needed to understand the mechanisms and develop therapies to slow kidney function decline in these patients. [Extracted from the article]

Published
2024
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3. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition

Author

Vollger, Mitchell R., primary, Korlach, Jonas, additional, Eldred, Kiara C., additional, Swanson, Elliott, additional, Underwood, Jason G., additional, Munson, Katherine M., additional, Cheng, Yong-Han H., additional, Ranchalis, Jane, additional, Mao, Yizi, additional, Blue, Elizabeth E., additional, Schwarze, Ulrike, additional, Saunders, Christopher T., additional, Wenger, Aaron M., additional, Allworth, Aimee, additional, Chanprasert, Sirisak, additional, Duerden, Brittney L., additional, Glass, Ian, additional, Horike-Pyne, Martha, additional, Kim, Michelle, additional, Leppig, Kathleen A., additional, McLaughlin, Ian J., additional, Ogawa, Jessica, additional, Rosenthal, Elisabeth A., additional, Sheppeard, Sam, additional, Sherman, Stephanie M., additional, Strohbehn, Samuel, additional, Yuen, Amy L., additional, Reh, Thomas A., additional, Byers, Peter H., additional, Bamshad, Michael J., additional, Hisama, Fuki M., additional, Jarvik, Gail P., additional, Sancak, Yasemin, additional, Dipple, Katrina M., additional, and Stergachis, Andrew B., additional

Published
2023
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4. Dominant-negative variant in SLC1A4 causes an autosomal dominant epilepsy syndrome

Author

Pujol-Giménez, Jonai, Mirzaa, Ghayda, Blue, Elizabeth E, Albano, Giuseppe, Miller, Danny E, Allworth, Aimee, Bennett, James T, Byers, Peter H, Chanprasert, Sirisak, Chen, Jingheng, Doherty, Daniel, Folta, Andrew B, Gillentine, Madelyn A, Glass, Ian, Hing, Anne, Horike-Pyne, Martha, Leppig, Kathleen A, Parhin, Azma, Ranchalis, Jane, Raskind, Wendy H, Rosenthal, Elisabeth A, Schwarze, Ulrike, Sheppeard, Sam, Strohbehn, Samuel, Sybert, Virginia P, Timms, Andrew, Wener, Mark, Bamshad, Michael J, Hisama, Fuki M, Jarvik, Gail P, Dipple, Katrina M, Hediger, Matthias A., and Stergachis, Andrew B

Subjects
610 Medicine & health
Abstract

SLC1A4 is a trimeric neutral amino acid transporter essential for shuttling L-serine from astrocytes into neurons. Individuals with biallelic variants in SLC1A4 are known to have spastic tetraplegia, thin corpus callosum, and progressive microcephaly (SPATCCM) syndrome, but individuals with heterozygous variants are not thought to have disease. We identify an 8-year-old patient with global developmental delay, spasticity, epilepsy, and microcephaly who has a de novo heterozygous three amino acid duplication in SLC1A4 (L86_M88dup). We demonstrate that L86_M88dup causes a dominant-negative N-glycosylation defect of SLC1A4, which in turn reduces the plasma membrane localization of SLC1A4 and the transport rate of SLC1A4 for L-serine.

Published
2023
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5. Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A

Author

Stergachis, Andrew B., Blue, Elizabeth E., Gillentine, Madelyn A, Wang, Lee-kai, Schwarze, Ulrike, Cortés, Adriana Sedeño, Ranchalis, Jane, Allworth, Aimee, Bland, Austin E., Chanprasert, Sirisak, Chen, Jingheng, Doherty, Daniel, Folta, Andrew B., Glass, Ian, Horike-Pyne, Martha, Huang, Alden Y., Khan, Alyna T., Leppig, Kathleen A., Miller, Danny E., Mirzaa, Ghayda, Parhin, Azma, Raskind, Wendy, Rosenthal, Elisabeth A., Sheppeard, Sam, Strohbehn, Samuel, Sybert, Virginia P., Tran, Thao T., Wener, Mark, Byers, Peter H., Nelson, Stanley F., Bamshad, Michael J., Dipple, Katrina M., Jarvik, Gail P., Hoppins, Suzanne, and Hisama, Fuki M.

Subjects
Article
Abstract

ObjectivesTranscript sequencing of patient derived samples has been shown to improve the diagnostic yield for solving cases of likely Mendelian disorders, yet the added benefit of full-length long-read transcript sequencing is largely unexplored.MethodsWe applied short-read and full-length isoform cDNA sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis.ResultsWe identified an intronic homozygousMFN2c.600-31T>G variant that disrupts a branch point critical for intron 6 spicing. Full-length long-read isoform cDNA sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates five distinct altered splicing transcripts. All five altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-lengthMFN2transcripts are still produced, this branch point variant results in deficient MFN2 protein levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A).DiscussionThis case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A.

Published
2023
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6. Full-length isoform sequencing for resolving the molecular basis of Charcot-Marie-Tooth 2A

Author

Stergachis, Andrew B., primary, Blue, Elizabeth E., additional, Gillentine, Madelyn A, additional, Wang, Lee-kai, additional, Schwarze, Ulrike, additional, Sedeno Cortes, Adriana, additional, Ranchalis, Jane, additional, Allworth, Aimee, additional, Bland, Austin E., additional, Chanprasert, Sirisak, additional, Chen, Jingheng, additional, Doherty, Daniel, additional, Folta, Andrew B., additional, Glass, Ian, additional, Horike-Pyne, Martha, additional, Huang, Alden Y., additional, Khan, Alyna T., additional, Leppig, Kathleen A., additional, Miller, Danny E., additional, Mirzaa, Ghayda, additional, Parhin, Azma, additional, Raskind, Wendy, additional, Rosenthal, Elisabeth A., additional, Sheppeard, Sam, additional, Strohbehn, Samuel, additional, Sybert, Virginia P., additional, Tran, Thao T., additional, Wener, Mark, additional, Byers, Peter H., additional, Nelson, Stanley F., additional, Bamshad, Michael J., additional, Dipple, Katrina M., additional, Jarvik, Gail P., additional, Hoppins, Suzanne, additional, and Hisama, Fuki M., additional

Published
2023
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8. Effect of Cancer Stage on Adverse Kidney Outcomes in Patients Receiving Immune Checkpoint Inhibitors for Melanoma

Author

Wang, Qiyu, primary, Strohbehn, Ian A., additional, Zhao, Sophia, additional, Seethapathy, Harish, additional, Strohbehn, Samuel D., additional, Hanna, Paul, additional, Lee, Meghan, additional, Fadden, Riley, additional, Sullivan, Ryan J., additional, Boland, Genevieve M., additional, Reynolds, Kerry L., additional, and Sise, Meghan E., additional

Published
2022
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9. MO344: Effect of Cancer Stage on Adverse Kidney Outcomes in Patients With Advanced Melanoma Treated With Immune Checkpoint Inhibitors

Author

Wang, Qiyu, primary, Strohbehn, Ian, additional, Strohbehn, Samuel, additional, Lee, Meghan, additional, Seethapathy, Harish, additional, Hanna, Paul, additional, Fadden, Riley, additional, Reynolds, Kerry, additional, Sullivan, Ryan, additional, Zhao, Sophia, additional, Boland, Genevieve, additional, and Sise, Meghan, additional

Published
2022
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10. Dual diagnosis of UQCRFS1-related mitochondrial complex III deficiency and recessive GJA8-related cataracts

Author

Blue, Elizabeth E., Huang, Samuel J., Khan, Alyna, Golden-Grant, Katie, Boyd, Brenna, Rosenthal, Elisabeth A., Gillentine, Madelyn A., Fleming, Leah R., Adams, David R., Wolfe, Lynne, Allworth, Aimee, Bamshad, Michael J., Caruana, Nikeisha J., Chanprasert, Sirisak, Chen, Jingheng, Dargie, Nitsuh, Doherty, Daniel, Friederich, Marisa W., Hisama, Fuki M., Horike-Pyne, Martha, Lee, Jessica C., Donovan, Tonia E., Hock, Daniella H., Leppig, Kathleen A., Miller, Danny E., Mirzaa, Ghayda, Ranchalis, Jane, Raskind, Wendy H., Michel, Cole R., Reisdorph, Richard, Schwarze, Ulrike, Sheppeard, Sam, Strohbehn, Samuel, Stroud, David A., Sybert, Virginia P., Wener, Mark H., Stergachis, Andrew B., Lam, Christina T., Jarvik, Gail P., Dipple, Katrina M., Van Hove, Johan L.K., and Glass, Ian A.

Published
2024
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13. Additional file 3: of Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples

Author

Gorlov, Ivan, Pikielny, Claudio, Hildreth Frost, Her, Stephanie, Cole, Michael, Strohbehn, Samuel, Wallace-Bradley, David, Kimmel, Marek, Gorlova, Olga, and Amos, Christopher

Subjects
animal structures, embryonic structures, human activities
Abstract

The relationship between the proportion of CpG sites and the mutation densities. Proportion of CpGs was computed as the ratio of the number of CpGs in the gene to the gene size in nucleotides. (DOCX 143 kb)

Published
2018
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17. Additional file 2: of Gene characteristics predicting missense, nonsense and frameshift mutations in tumor samples

Author

Gorlov, Ivan, Pikielny, Claudio, Hildreth Frost, Her, Stephanie, Cole, Michael, Strohbehn, Samuel, Wallace-Bradley, David, Kimmel, Marek, Gorlova, Olga, and Amos, Christopher

Abstract

Olfactory genes and densities of missense mutations. First row shows the proportion of olfactory genes in a sliding window of 100 genes, when it moves from lowest to highest nucleotide content. Second row shows the distribution of olfactory (red) and other (blue) genes across mutation densities bins. Olfactory genes have a higher density of missense but not nonsense mutations. Third row shows the effect of excluding of olfactory genes on the relationship between percentage of â Tâ in the gene and density of missense mutations. (DOCX 2413 kb)

Published
2018
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23. Synchronized long-read genome, methylome, epigenome, and transcriptome for resolving a Mendelian condition.

Author

Vollger MR, Korlach J, Eldred KC, Swanson E, Underwood JG, Cheng YH, Ranchalis J, Mao Y, Blue EE, Schwarze U, Munson KM, Saunders CT, Wenger AM, Allworth A, Chanprasert S, Duerden BL, Glass I, Horike-Pyne M, Kim M, Leppig KA, McLaughlin IJ, Ogawa J, Rosenthal EA, Sheppeard S, Sherman SM, Strohbehn S, Yuen AL, Reh TA, Byers PH, Bamshad MJ, Hisama FM, Jarvik GP, Sancak Y, Dipple KM, and Stergachis AB

Abstract

Resolving the molecular basis of a Mendelian condition (MC) remains challenging owing to the diverse mechanisms by which genetic variants cause disease. To address this, we developed a synchronized long-read genome, methylome, epigenome, and transcriptome sequencing approach, which enables accurate single-nucleotide, insertion-deletion, and structural variant calling and diploid de novo genome assembly, and permits the simultaneous elucidation of haplotype-resolved CpG methylation, chromatin accessibility, and full-length transcript information in a single long-read sequencing run. Application of this approach to an Undiagnosed Diseases Network (UDN) participant with a chromosome X;13 balanced translocation of uncertain significance revealed that this translocation disrupted the functioning of four separate genes ( NBEA , PDK3 , MAB21L1 , and RB1 ) previously associated with single-gene MCs. Notably, the function of each gene was disrupted via a distinct mechanism that required integration of the four 'omes' to resolve. These included nonsense-mediated decay, fusion transcript formation, enhancer adoption, transcriptional readthrough silencing, and inappropriate X chromosome inactivation of autosomal genes. Overall, this highlights the utility of synchronized long-read multi-omic profiling for mechanistically resolving complex phenotypes., Competing Interests: Conflicts J.K., J.G.U., C.T.S., A.M.W., M.K. and I.J.M. are full-time employees at PacBio, a company developing single-molecule sequencing technologies. A.B.S. is a co-inventor on a patent relating to the Fiber-seq method (US17/995,058).

Published
2023
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24. Full-length Isoform Sequencing for Resolving the Molecular Basis of Charcot-Marie-Tooth 2A.

Author

Stergachis AB, Blue EE, Gillentine MA, Wang LK, Schwarze U, Cortés AS, Ranchalis J, Allworth A, Bland AE, Chanprasert S, Chen J, Doherty D, Folta AB, Glass I, Horike-Pyne M, Huang AY, Khan AT, Leppig KA, Miller DE, Mirzaa G, Parhin A, Raskind WH, Rosenthal EA, Sheppeard S, Strohbehn S, Sybert VP, Tran TT, Wener MH, Byers PHH, Nelson SF, Bamshad MJ, Dipple KM, Jarvik GP, Hoppins S, and Hisama FM

Abstract

Objectives: Transcript sequencing of patient-derived samples has been shown to improve the diagnostic yield for solving cases of suspected Mendelian conditions, yet the added benefit of full-length long-read transcript sequencing is largely unexplored., Methods: We applied short-read and full-length transcript sequencing and mitochondrial functional studies to a patient-derived fibroblast cell line from an individual with neuropathy that previously lacked a molecular diagnosis., Results: We identified an intronic homozygous MFN2 c.600-31T>G variant that disrupts the branch point critical for intron 6 splicing. Full-length long-read isoform complementary DNA (cDNA) sequencing after treatment with a nonsense-mediated mRNA decay (NMD) inhibitor revealed that this variant creates 5 distinct altered splicing transcripts. All 5 altered splicing transcripts have disrupted open reading frames and are subject to NMD. Furthermore, a patient-derived fibroblast line demonstrated abnormal lipid droplet formation, consistent with MFN2 dysfunction. Although correctly spliced full-length MFN2 transcripts are still produced, this branch point variant results in deficient MFN2 levels and autosomal recessive Charcot-Marie-Tooth disease, axonal, type 2A (CMT2A)., Discussion: This case highlights the utility of full-length isoform sequencing for characterizing the molecular mechanism of undiagnosed rare diseases and expands our understanding of the genetic basis for CMT2A., Competing Interests: The authors report no relevant disclosures. Go to Neurology.org/NG for full disclosures., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.)

Published
2023
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