Targeted massively parallel sequencing of candidate regions on chromosome 22q predisposing to multiple schwannomas: An analysis of 51 individuals in a single-center experience.

التفاصيل البيبلوغرافية
العنوان:	Targeted massively parallel sequencing of candidate regions on chromosome 22q predisposing to multiple schwannomas: An analysis of 51 individuals in a single-center experience.
المؤلفون:	Piotrowski A; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland., Koczkowska M; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.; 3P-Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland.; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland., Poplawski AB; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA., Bartoszewski R; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland., Króliczewski J; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland., Mieczkowska A; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland., Gomes A; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA., Crowley MR; Genomic Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA., Crossman DK; Genomic Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA., Chen Y; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA., Lao P; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA., Serra E; Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain., Llach MC; Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain., Castellanos E; Clinical Genomics Research Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain.; Clinical Genomics Unit, Clinical Genetics Service, Northern Metropolitan Clinical Laboratory, Germans Trias i Pujol University Hospital (HUGTiP), Barcelona, Spain., Messiaen LM; Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
المصدر:	Human mutation [Hum Mutat] 2022 Jan; Vol. 43 (1), pp. 74-84. Date of Electronic Publication: 2021 Nov 15.
نوع المنشور:	Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
اللغة:	English
بيانات الدورية:	Publisher: Wiley-Liss Country of Publication: United States NLM ID: 9215429 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1098-1004 (Electronic) Linking ISSN: 10597794 NLM ISO Abbreviation: Hum Mutat Subsets: MEDLINE
أسماء مطبوعة:	Original Publication: New York : Wiley-Liss, c1992-
مواضيع طبية MeSH:	Neurilemmoma/genetics , Neurilemmoma/pathology , Neurofibromatoses*/genetics, Chromosomes ; High-Throughput Nucleotide Sequencing ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; SMARCB1 Protein/genetics ; Transcription Factors/genetics
مستخلص:	Constitutional LZTR1 or SMARCB1 pathogenic variants (PVs) have been found in ∼86% of familial and ∼40% of sporadic schwannomatosis cases. Hence, we performed massively parallel sequencing of the entire LZTR1, SMARCB1, and NF2 genomic loci in 35 individuals with schwannomas negative for constitutional first-hit PVs in the LZTR1/SMARCB1/NF2 coding sequences; however, with 22q deletion and/or a different NF2 PV in each tumor, including six cases with only one tumor available. Furthermore, we verified whether any other LZTR1/SMARCB1/NF2 (likely) PVs could be found in 16 cases carrying a SMARCB1 constitutional variant in the 3'-untranslated region (3'-UTR) c.17C>T, c.70C>T, or c.82C>T. As no additional variants were found, functional studies were performed to clarify the effect of these 3'-UTR variants on the transcript. The 3'-UTR variants c.17C>T and c.*82C>T showed pathogenicity by negatively affecting the SMARCB1 transcript level. Two novel deep intronic SMARCB1 variants, c.500+883T>G and c.500+887G>A, resulting in out-of-frame missplicing of intron 4, were identified in two unrelated individuals. Further resequencing of the entire repeat-masked genomics sequences of chromosome 22q in individuals negative for PVs in the SMARCB1/LZTR1/NF2 coding- and noncoding regions revealed five potential schwannomatosis-predisposing candidate genes, that is, MYO18B, NEFH, SGSM1, SGSM3, and SBF1, pending further verification. (© 2021 Wiley Periodicals LLC.)
References:	Agnihotri, S., Jalali, S., Wilson, M. R., Danesh, A., Li, M., Klironomos, G., Krieger, J. R., Mansouri, A., Khan, O., Mamatjan, Y., Landon-Brace, N., Tung, T., Dowar, M., Li, T., Bruce, J. P., Burrell, K. E., Tonge, P. D., Alamsahebpour, A., Krischek, B., … Zadeh, G. (2016). The genomic landscape of schwannoma. Nature Genetics, 48, 1339-1348. Bartoszewska, S., Kamysz, W., Jakiela, B., Sanak, M., Kroliczewski, J., Bebok, Z., Bartoszewski, R., & Collawn, J. F. (2017). miR-200b downregulates CFTR during hypoxia in human lung epithelial cells. Cellular and Molecular Biology Letters, 22, 23. Bartoszewski, R., Gebert, M., Janaszak-Jasiecka, A., Cabaj, A., Kroliczewski, J., Bartoszewska, S., Sobolewska, A., Crossman, D. K., Ochocka, R., & Kamysz, W. (2019). Genome-wide mRNA profiling identifies RCAN1 and GADD45A as regulators of the transitional switch from survival to apoptosis during ER stress. FEBS Journal, 287, 2923-2947. Bonfert, T., & Friedel, C. C. (2017). Prediction of poly(A) sites by poly(A) read mapping. PLoS One, 12, e0170914. Castellanos, E., Bielsa, I., Carrato, C., Rosas, I., Solanes, A., Hostalot, C., Amilibia, E., Prades, J., Roca-Ribas, F., Lazaro, C., Blanco, I., & Serra, E. (2015). Segmental neurofibromatosis type 2: Discriminating two hit form four hit in a patient presenting multiple schwannomas confined to one limb. BMC Medical Genomics, 8, 2. Castellanos, E., Rosas, I., Solanes, A., Bielsa, I., Lázaro, C., Carrato, C., Hostalot, C., Prades, P., Roca-Ribas, F., Blanco, I., & Serra, E., NF2 Multidisciplinary Clinics HUGTiP-ICO-IMPPC. (2013). In vitro antisense therapeutics for a deep intronic mutation causing neurofibromatosis type 2. European Journal of Human Genetics, 21, 769-773. Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Cox, A. J., Kruglyak, S., & Saunders, C. T. (2016). Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32, 1220-1222. Cui, Y., Groth, S., Troutman, S., Carlstedt, A., Sperka, T., Riecken, L. B., Kissil, J. L., Jin, H., & Morrison, H. (2019). The NF2 tumor suppressor merlin interacts with Ras and RasGAP, which may modulate Ras signaling. Oncogene, 38, 6370-6381. De Klein, A., Riegman, P. H. J., Bijlsma, E. K., Heldoorn, A., Muijtjens, M., den Bakker, A., Avezaat, C. J., & Zwarthoff, E. C. (1998). A G→A transition creates a branch point sequence and activation of a cryptic exon, resulting in the hereditary disorder neurofibromatosis 2. Human Molecular Genetics, 7, 393-398. Desvignes, J. P., Bartoli, M., Delahue, V., Krahn, M., Miltgen, M., Béroud, C., & Salgado, D. (2018). VarAFT: A variant annotation and filtration system for human next generation sequencing data. Nucleic Acids Research, 46, W545-W553. Evans, D. G., Bowers, N. L., Tobi, S., Hartley, C., Wallace, A. J., King, A. T., Lloyd, S. K. W., Rutherford, S. A., Hammerbeck-Ward, C., Pathmanaban, O. N., Freeman, S. R., Ealing, J., Kellett, M., Laitt, R., Thomas, O., Halliday, D., Ferner, R., Taylor, A., Duff, C., … Smith, M. J. (2018). Schwannomatosis: A genetic and epidemiological study. Journal of Neurology, Neurosurgery and Psychiatry, 89, 1215-1219. Evans, D. G., Hartley, C. L., Smith, P. T., King, A. T., Bowers, N. L., Tobi, S., Wallace, A. J., Perry, M., Anup, R., Lloyd, S. K. W., Rutherford, S. A., Hammerbeck-Ward, C., Pathmanaban, O. N., Stapleton, E., Freeman, S. R., Kellett, M., Halliday, D., Parry, A., Gair, J. J., … Smith, M. J. (2020). Incidence of mosaicism in 1055 de novo NF2 cases: Much higher than previous estimates with high utility of next-generation sequencing. Genetics in Medicine, 22, 53-59. Ewing, A. D., Ballinger, T. J., Earl, D., Harris, C. C., Wilson, R. K., Ding, L., & Haussler, D., Broad Institute Genome Sequencing and Analysis Program and Platform. (2013). Retrotransposition of gene transcript leads to structural variation in mammalian genomes. Genome Biology, 14, R22. Hadfield, K. D., Newman, W. G., Bowers, N. L., Wallace, A., Bolger, C., Colley, A., McCann, E., Trump, D., Prescott, T., & Evans, D. G. (2008). Molecular characterization of SMARCB1 and NF2 familial and sporadic schwannomatosis. Journal of Medical Genetics, 45, 3332-339. Hulsebos, T. J. M., Plomp, A. S., Wolterman, R. A., Robanus-Maandag, E. C., Baas, F., & Wesseling, P. (2007). Germline mutation of INI1/SMARCB1 in familial schwannomatosis. American Journal of Human Genetics, 80, 805-810. Johnston, J. J., van der Smagt, J. J., Rosenfeld, J. A., Pagnamenta, A. T., Alswaid, A., Baker, E. H., Blair, E., Borck, G., Brinkmann, J., Craigen, W., Dung, V. C., Emrick, L., Everman, D. B., van Gassen, K. L., Gulsuner, S., Harr, M. H., Jain, M., Kuechler, A., Leppig, K. A., … Biesecker, L. G. (2018). Autosomal recessive Noonan syndrome associated with biallelic LZTR1 variants. Genetics in Medicine, 20, 1175-1185. Kehrer-Sawatzki, H., Farschtschi, S., Mautner, V. F., & Cooper, D. N. (2017). The molecular pathogenesis of schwannomatosis, a paradigm for the co-involvement of multiple tumour suppresor genes in tumorigenesis. Human Genetics, 136, 129-148. Larionov, A., Krause, A., & Miller, W. (2005). A standard curve based method for relative real time PCR data processing. BMC Bioinformatics, 136(6), 62. Lee, I. K., Kim, K. S., Kim, H., Lee, J. Y., Ryu, C. H., Chun, H. J., Lee, K. U., Lim, Y., Kim, Y. H., Huh, P. W., Lee, K. H., Han, S. I., Jun, T. Y., & Rha, H. K. (2004). MAP, a protein interacting with a tumor suppressor, merlin, through the run domain. Biochemical and Biophysical Research Communications, 325, 774-783. Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Horner, N., Marth, G., Abecasis, G., & Durbin, R., 1000 genome project data processing subgroup. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079. Louvrier, C., Pasmant, E., Briand-Suleau, Cohen, J., Nitschké, P., Nectoux, J., Orhant, L., Zordan, C., Goizet, C., & Goutagny, S. (2018). Targeted next-generation sequencing for differential diagnosis of neurofibromastosis and meningiomatosis. Neuro-Oncology, 20, 917-929. Madanecki, P., Balut, M., Buckley, P. G., Ochocka, J. R., Bartoszewski, R., Crossman, D. K., Messiaen, L. M., & Piotrowski, A. (2018). High-throughput tabular data processor-Platform independent graphical tool for processing large data sets. PLoS One, 13, e0192858. Mansouri, S., Suppiah, S., Mamatjan, Y., Paganini, I., Liu, J. C., Karimi, S., Patil, V., Nassiri, F., Singh, O., Sundaravadanam, Y., Rath, P., Sestini, R., Gensini, F., Agnihotri, S., Blakeley, J., Ostrow, K., Largaespada, D., Plotkin, S. R., Stemmer-Rachamimov, A., … Zadeh, G. (2020). Epigenomic, genomic, and transcriptomic landscape of schwannomatosis. Acta Neuropathologica, 141, 101-116. Mayr, C. (2017). Regulation by 3′-untranslanted regions. Annual Review of Genetics, 51, 171-194. Messiaen, L. M., Callens, T., Mortier, G., Beysen, D., Vandenbroucke, I., Van Roy, N., Speleman, F., & Paepe, A. D. (2000). Exhaustive mutation analysis of the NF1 gene allows identification of 95% of mutations and reveals a high frequency of unusual splicing defects. Human Mutation, 15, 541-555. Piotrowski, A., Xie, J., Liu, Y. F., Poplawski, A. B., Gomes, A. R., Madanecki, P., Fu, C., Crowley, M. R., Crossman, D. K., Armstrong, L., Babovic-Vuksanovic, D., Bergner, A., Blakeley, J. O., Blumenthal, A. L., Daniels, M. S., Feit, H., Gardner, K., Hurst, S., Kobelka, C., … Messiaen, L. M. (2014). Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas. Nature Genetics, 46, 182-187. Richards, S., Aziz, N., Bale, S., Bick, D., Das, S., Gastier-Foster, J., Grody, W. W., Hegde, M., Lyon, E., Spector, E., Voelkerding, K., Rehm, H. L., & ACMG Laboratory Quality Assurance Committee. (2015). Standards and guidelines for the interpretation of sequence variants: A joint consensus of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 17, 405-424. Rimmer, A., Phan, H., Mathieson, I., Iqbal, Z., Twigg, S. R. F., WGS500 Consortium, Wilkie, A. O. M., McVean, G., & Lunter, G. (2014). Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nature Genetics, 46, 912-918. Rivera, B., Nadaf, J., Fahiminiya, S., Apellaniz-Ruiz, M., Saskin, A., Chong, A. S., Sharma, S., Wagener, R., Revil, T., Condello, V., Harra, Z., Hamel, N., Sabbaghian, N., Muchantef, K., Thomas, C., de Kock, L., Hébert-Blouin, M. N., Bassenden, A. V., Rabenstein, H., … Foulkes, W. D. (2020). DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis. Journal of Clinical Investigation, 130, 1479-1490. Schrider, D. R., Navarro, F. C. P., Galante, P. A. F., Parmigiani, R. B., Camargo, A. A., Hahn, M. W., & de Souza, S. J. (2013). Gene copy-number polymorphism caused by retrotransposition in humans. PLoS Genetics, 9, e1003242. Schulz, A., Büttner, R., Toledo, A., Baader, S. L., von Maltzahn, J., Irintchev, A., Bauer, R., & Morrison, H. (2016). Neuron-specific deletion of the NF2 tumor suppressor impairs functional nerve regeneration. PLoS One, 11, e0159718. Scott, P., Bruwer, Z., Al-Kharusi, K., Meftah, D., & Al-Murshedi, F. (2016). Ocurence of optic neuritis and cervical cord schwannoma with Charcot-Marie-Tooth type 4B1 disease. Oman Medical Journal, 31, 227-230. Sestini, R., Bacci, C., Provenzano, A., Genuardi, M., & Papi, L. (2008). Evidence of a four-hit mechanism involving SMARCB1 and Nf2 in schwannomatosis-associated schwannomas. Human Mutation, 29, 227-231. Sherf, B. A., Navarro, S. L., & Wood, K. V. (1996). Dual-luciferase TM reporter assay: an advanced co-reporter technology integrating firefly and Renilla luciferase assays. Promega Notes, 57, 2-8. Smith, M. J., Bowers, N. L., Banks, C., Coates-Brown, R., Morris, K. A., Ewans, L., Wilson, M., Pinner, J., Bhaskar, S. S., Cammarata-Scalisi, F., Wallace, A. J., & Evans, D. (2020). A deep intronic SMARCB1 variant associated with schwannomatosis. Clinical Genetics, 97, 376-377. Smith, M. J., Walker, J. A., Shen, Y., Stemmer-Rachamimov, A., Gusella, J. F., & Plotkin, S. R. (2012). Expression of SMARCB1 (INI1) mutations in familial schwannomatosis. Human Molecular Genetics, 21, 5239-5245. Thung, D. T., de Ligt, J., Vissers, L. E. M., Steehouwer, M., Kroon, M., de Vries, P., Slagboom, E. P., Ye, K., Veltman, J. A., & Hehir-Kwa, J. Y. (2014). Mobster: accurate detection of mobile element insertions in next generation sequencing data. Genome Biology, 15, 488. Truty, R., Paul, J., Kennemer, M., Lincoln, S. E., Olivares, E., Nussbaum, R. L., & Aradhya, S. (2019). Prevalence and properties of intragenic copy-number variation in Mendelian disease genes. Genetics in Medicine, 21, 114-123. Watson, C. J., Gaunt, L., Evans, G., Patel, K., Harris, R., & Strachan, T. (1993). A disease-associated germline deletion maps the type 2 neurofibromatosis (NF2) gene between the Ewing sarcoma region and the leukemia inhibitory factor locus. Human Molecular Genetics, 2, 701-704. Wong, K., Adams, D. J., & Keane, T. M. (2013). Go retro and get a GRIP. Genome Biology, 14, 108. Yang, X., Ren, H., Guo, X., Hu, C., & Fu, J. (2020). The expressions and mechanism of sarcomeric proteins in cancers. Disease Markers, 2020, 8885286. Yang, H., Sasaki, T., Minoshima, S., & Shimizu, N. (2007). Identification of three novel proteins (SGSM1,2,3) which modulate small G protein (RAP and RAB)-mediated signaling pathway. Genomics, 90, 249-260. Zhang, K., Lin, J. W., Wang, J., Wu, X., Gao, H., Hsieh, Y. C., Hwu, P., Liu, Y. R., Su, L., Chiou, H. Y., Wang, D., Yuan, Y. C., Whang-Peng, J., Chiu, W. T., & Yen, Y. (2014). A germline missense mutation in COQ6 is associated with susceptibility to familial schwannomatosis. Genetics in Medicine, 16, 787-792.
فهرسة مساهمة:	Keywords: LZTR1; MYO18B; NEFH; NF2; SBF1; SGSM1; SGSM3; SMARCB1; deep intronic variant; low level mosaicism; massively parallel sequencing; schwannomatosis
المشرفين على المادة:	0 (Intracellular Signaling Peptides and Proteins) 0 (LZTR1 protein, human) 0 (SMARCB1 Protein) 0 (Transcription Factors)
تواريخ الأحداث:	Date Created: 20211108 Date Completed: 20220331 Latest Revision: 20240109
رمز التحديث:	20240109
DOI:	10.1002/humu.24294
PMID:	34747535
قاعدة البيانات:	MEDLINE

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تدمد:	1098-1004
DOI:	10.1002/humu.24294