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Koczkowska M, Chen Y, Xie J, Callens T, Gomes A, Wimmer K, Messiaen LM. Analysis of 200 unrelated individuals with a constitutional NF1 deep intronic pathogenic variant reveals that variants flanking the alternatively spliced NF1 exon 31 [23a] cause a classical neurofibromatosis type 1 phenotype while altering predominantly NF1 isoform type II. Hum Genet 2023:10.1007/s00439-023-02555-z. [PMID: 37186028 DOI: 10.1007/s00439-023-02555-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Neurofibromatosis type 1 results from loss-of-function NF1 pathogenic variants (PVs). Up to 30% of all NF1 PVs disrupt mRNA splicing, including deep intronic variants. Here, we retrospectively investigated the spectrum of NF1 deep intronic PVs in a cohort of 8,090 unrelated individuals from the University of Alabama at Birmingham (UAB) dataset with a molecularly confirmed neurofibromatosis type 1. All variants were identified through their effect on the NF1 transcript, followed by variant characterization at the DNA-level. A total of 68 distinct variants, which were ≥ 20 nucleotides away from the closest exon-intron junction, were identified in 2.5% unrelated individuals with NF1 (200/8,090). Nine different pathogenic splice variants, identified in 20 probands, led to exonization of different parts of intron 30 [23.2] or 31 [23a]. The two major NF1 transcript isoforms, distinguished by the absence (type I) or presence (type II) of the alternatively spliced cassette exon 31 [23a], are equally expressed in blood in control individuals without NF1 or NF1-affected individuals carrying their PV not in the introns flanking exon 31 [23a]. By fragment and cloning analysis we demonstrated that the exonization of intron 31 [23a] sequences due to deep intronic PV predominantly affects the NF1 isoform II. Seven additional (likely) pathogenic NF1 deep intronic variants not observed in the UAB dataset were found by classification of 36 variants identified by a literature search. Hence, the unique list of these 75 deep intronic (likely) PVs should be included in any comprehensive NF1 testing strategy.
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Affiliation(s)
- Magdalena Koczkowska
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
- 3P-Medicine Laboratory, Medical University of Gdansk, 80-211, Gdansk, Poland.
| | - Yunjia Chen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jing Xie
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Natera, Inc., San Carlos, CA, USA
| | - Tom Callens
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Alicia Gomes
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, 6020, Innsbruck, Austria
| | - Ludwine M Messiaen
- Medical Genomics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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2
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Mohammadi E, Chojnowska K, Bieńkowski M, Kostecka A, Koczkowska M, Żmijewski MA, Jąkalski M, Ingelsson M, Filipowicz N, Olszewski P, Davies H, Wierzbicka JM, Hyman BT, Dumanski JP, Piotrowski A, Mieczkowski J. Size matters: the impact of nucleus size on results from spatial transcriptomics. J Transl Med 2023; 21:270. [PMID: 37081484 PMCID: PMC10120157 DOI: 10.1186/s12967-023-04129-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/12/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Visium Spatial Gene Expression (ST) is a method combining histological spatial information with transcriptomics profiles directly from tissue sections. The use of spatial information has made it possible to discover new modes of gene expression regulations. However, in the ST experiment, the nucleus size of cells may exceed the thickness of a tissue slice. This may, in turn, negatively affect comprehensive capturing the transcriptomics profile in a single slice, especially for tissues having large differences in the size of nuclei. METHODS Here, we defined the effect of Consecutive Slices Data Integration (CSDI) on unveiling accurate spot clustering and deconvolution of spatial transcriptomic spots in human postmortem brains. By considering the histological information as reference, we assessed the improvement of unsupervised clustering and single nuclei RNA-seq and ST data integration before and after CSDI. RESULTS Apart from the escalated number of defined clusters representing neuronal layers, the pattern of clusters in consecutive sections was concordant only after CSDI. Besides, the assigned cell labels to spots matches the histological pattern of tissue sections after CSDI. CONCLUSION CSDI can be applied to investigate consecutive sections studied with ST in the human cerebral cortex, avoiding misinterpretation of spot clustering and annotation, increasing accuracy of cell recognition as well as improvement in uncovering the layers of grey matter in the human brain.
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Affiliation(s)
- Elyas Mohammadi
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | | | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | - Anna Kostecka
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | | | - Michał A Żmijewski
- Department of Histology, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | - Marcin Jąkalski
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences, Geriatrics, Rudbeck Laboratory, Uppsala University, 751 85, Uppsala, Sweden
- Krembil Brain Institute, University Health Network, Toronto, ON, M5G 2C4, Canada
- Department of Medicine and Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | - Paweł Olszewski
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | | | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Massachusetts Alzheimer's Disease Research Center, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | | | - Jakub Mieczkowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, 80 210, Gdańsk, Poland.
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3
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Jasiak A, Koczkowska M, Stukan M, Wydra D, Biernat W, Izycka-Swieszewska E, Buczkowski K, Eccles MR, Walker L, Wasag B, Ratajska M. Analysis of BRCA1 and BRCA2 alternative splicing in predisposition to ovarian cancer. Exp Mol Pathol 2023; 130:104856. [PMID: 36791903 DOI: 10.1016/j.yexmp.2023.104856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 01/25/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023]
Abstract
BACKGROUND The mRNA splicing is regulated on multiple levels, resulting in the proper distribution of genes' transcripts in each cell and maintaining cell homeostasis. At the same time, the expression of alternative transcripts can change in response to underlying genetic variants, often missed during routine diagnostics. AIM The main aim of this study was to define the frequency of aberrant splicing in BRCA1 and BRCA2 genes in blood RNA extracted from ovarian cancer patients who were previously found negative for the presence of pathogenic alterations in the 25 most commonly analysed ovarian cancer genes, including BRCA1 and BRCA2. MATERIAL AND METHODS Frequency and spectrum of splicing alterations in BRCA1 and BRCA2 genes were analysed in blood RNA from 101 ovarian cancer patients and healthy controls (80 healthy women) using PCR followed by gel electrophoresis and Sanger sequencing. The expression of splicing events was examined using RT-qPCR. RESULTS We did not identify any novel, potentially pathogenic splicing alterations. Nevertheless, we detected six naturally occurring transcripts, named BRCA1ΔE9-10, BRCA1ΔE11, BRCA1ΔE11q, and BRCA2ΔE3, BRCA2ΔE12 and BRCA2ΔE17-18 of which three (BRCA1ΔE11q, BRCA1ΔE11 and BRCA2ΔE3) were significantly higher expressed in the ovarian cancer cohort than in healthy controls (p ≤ 0.0001). CONCLUSIONS This observation indicates that the upregulation of selected naturally occurring transcripts can be stimulated by non-genetic mechanisms and be a potential systemic response to disease progression and/or treatment. However, this hypothesis requires further examination.
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Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland.
| | - Magdalena Koczkowska
- 3P Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland; Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Maciej Stukan
- Department of Gynecologic Oncology, Gdynia Oncology Center, Pomeranian Hospitals, Gdynia, Poland; Department Oncological Propedeutics, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wydra
- Department of Gynaecology, Gynaecological Oncology and Gynaecological Endocrinology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, Gdansk, Poland
| | | | - Kamil Buczkowski
- Department of Pathology & Neuropathology, Medical University of Gdansk, Gdansk, Poland
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Logan Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Bartosz Wasag
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Laboratory of Clinical Genetics, University Clinical Centre, Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland; Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand.
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4
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Kostecka A, Nowikiewicz T, Olszewski P, Koczkowska M, Horbacz M, Heinzl M, Andreou M, Salazar R, Mair T, Madanecki P, Gucwa M, Davies H, Skokowski J, Buckley PG, Pęksa R, Śrutek E, Szylberg Ł, Hartman J, Jankowski M, Zegarski W, Tiemann-Boege I, Dumanski JP, Piotrowski A. High prevalence of somatic PIK3CA and TP53 pathogenic variants in the normal mammary gland tissue of sporadic breast cancer patients revealed by duplex sequencing. NPJ Breast Cancer 2022; 8:76. [PMID: 35768433 PMCID: PMC9243094 DOI: 10.1038/s41523-022-00443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
The mammary gland undergoes hormonally stimulated cycles of proliferation, lactation, and involution. We hypothesized that these factors increase the mutational burden in glandular tissue and may explain high cancer incidence rate in the general population, and recurrent disease. Hence, we investigated the DNA sequence variants in the normal mammary gland, tumor, and peripheral blood from 52 reportedly sporadic breast cancer patients. Targeted resequencing of 542 cancer-associated genes revealed subclonal somatic pathogenic variants of: PIK3CA, TP53, AKT1, MAP3K1, CDH1, RB1, NCOR1, MED12, CBFB, TBX3, and TSHR in the normal mammary gland at considerable allelic frequencies (9 × 10-2- 5.2 × 10-1), indicating clonal expansion. Further evaluation of the frequently damaged PIK3CA and TP53 genes by ultra-sensitive duplex sequencing demonstrated a diversified picture of multiple low-level subclonal (in 10-2-10-4 alleles) hotspot pathogenic variants. Our results raise a question about the oncogenic potential in non-tumorous mammary gland tissue of breast-conserving surgery patients.
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Affiliation(s)
- Anna Kostecka
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
| | - Tomasz Nowikiewicz
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland.
- Department of Breast Cancer and Reconstructive Surgery, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland.
| | - Paweł Olszewski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Koczkowska
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Horbacz
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Monika Heinzl
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Maria Andreou
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
| | - Renato Salazar
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Theresa Mair
- Institute of Biophysics, Johannes Kepler University, Linz, Austria
| | - Piotr Madanecki
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Magdalena Gucwa
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdansk, Gdansk, Poland
| | | | - Rafał Pęksa
- Department of Patomorphology, Medical University of Gdansk, Gdansk, Poland
| | - Ewa Śrutek
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology, Prof. F. Lukaszczyk Oncology Center, Bydgoszcz, Poland
- Department of Perinatology, Gynaecology and Gynaecologic, Oncology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Johan Hartman
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
- MedTech Labs, Bioclinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Michał Jankowski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | - Wojciech Zegarski
- Department of Surgical Oncology, Ludwik Rydygier's Collegium Medicum UMK, Bydgoszcz, Poland
| | | | - Jan P Dumanski
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arkadiusz Piotrowski
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland.
- 3P Medicine Lab, Medical University of Gdansk, Gdansk, Poland.
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5
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Piotrowski A, Koczkowska M, Poplawski AB, Bartoszewski R, Króliczewski J, Mieczkowska A, Gomes A, Crowley MR, Crossman DK, Chen Y, Lao P, Serra E, Llach MC, Castellanos E, Messiaen LM. Targeted massively parallel sequencing of candidate regions on chromosome 22q predisposing to multiple schwannomas: An analysis of 51 individuals in a single-center experience. Hum Mutat 2022; 43:74-84. [PMID: 34747535 DOI: 10.1002/humu.24294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 01/07/2023]
Abstract
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.
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Affiliation(s)
- Arkadiusz Piotrowski
- 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
| | - Magdalena Koczkowska
- 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
| | - Andrzej B Poplawski
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rafał Bartoszewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Jarosław Króliczewski
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Alina Mieczkowska
- Department of Biology and Pharmaceutical Botany, Medical University of Gdansk, Gdansk, Poland
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael R Crowley
- Genomic Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David K Crossman
- Genomic Core Facility, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ping Lao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Eduard Serra
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Meritxell C Llach
- Hereditary Cancer Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Elisabeth Castellanos
- 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
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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6
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Koczkowska M, Callens T, Chen Y, Gomes A, Hicks AD, Sharp A, Johns E, Uhas KA, Armstrong L, Bosanko KA, Babovic‐Vuksanovic D, Baker L, Basel DG, Bengala M, Bennett JT, Chambers C, Clarkson LK, Clementi M, Cortés FM, Cunningham M, D'Agostino MD, Delatycki MB, Digilio MC, Dosa L, Esposito S, Fox S, Freckmann M, Fauth C, Giugliano T, Giustini S, Goetsch A, Goldberg Y, Greenwood RS, Griffis C, Gripp KW, Gupta P, Haan E, Hachen RK, Haygarth TL, Hernández‐Chico C, Hodge K, Hopkin RJ, Hudgins L, Janssens S, Keller K, Kelly‐Mancuso G, Kochhar A, Korf BR, Lewis AM, Liebelt J, Lichty A, Listernick RH, Lyons MJ, Maystadt I, Martinez Ojeda M, McDougall C, McGregor LK, Melis D, Mendelsohn N, Nowaczyk MJ, Ortenberg J, Panzer K, Pappas JG, Pierpont ME, Piluso G, Pinna V, Pivnick EK, Pond DA, Powell CM, Rogers C, Ruhrman Shahar N, Rutledge SL, Saletti V, Sandaradura SA, Santoro C, Schatz UA, Schreiber A, Scott DA, Sellars EA, Sheffer R, Siqveland E, Slopis JM, Smith R, Spalice A, Stockton DW, Streff H, Theos A, Tomlinson GE, Tran G, Trapane PL, Trevisson E, Ullrich NJ, Van den Ende J, Schrier Vergano SA, Wallace SE, Wangler MF, Weaver DD, Yohay KH, Zackai E, Zonana J, Zurcher V, Claes KBM, Eoli M, Martin Y, Wimmer K, De Luca A, Legius E, Messiaen LM. Clinical spectrum of individuals with pathogenic NF1 missense variants affecting p.Met1149, p.Arg1276, and p.Lys1423: genotype-phenotype study in neurofibromatosis type 1. Hum Mutat 2020; 41:299-315. [PMID: 31595648 PMCID: PMC6973139 DOI: 10.1002/humu.23929] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/03/2019] [Accepted: 10/02/2019] [Indexed: 12/15/2022]
Abstract
We report 281 individuals carrying a pathogenic recurrent NF1 missense variant at p.Met1149, p.Arg1276, or p.Lys1423, representing three nontruncating NF1 hotspots in the University of Alabama at Birmingham (UAB) cohort, together identified in 1.8% of unrelated NF1 individuals. About 25% (95% confidence interval: 20.5-31.2%) of individuals heterozygous for a pathogenic NF1 p.Met1149, p.Arg1276, or p.Lys1423 missense variant had a Noonan-like phenotype, which is significantly more compared with the "classic" NF1-affected cohorts (all p < .0001). Furthermore, p.Arg1276 and p.Lys1423 pathogenic missense variants were associated with a high prevalence of cardiovascular abnormalities, including pulmonic stenosis (all p < .0001), while p.Arg1276 variants had a high prevalence of symptomatic spinal neurofibromas (p < .0001) compared with "classic" NF1-affected cohorts. However, p.Met1149-positive individuals had a mild phenotype, characterized mainly by pigmentary manifestations without externally visible plexiform neurofibromas, symptomatic spinal neurofibromas or symptomatic optic pathway gliomas. As up to 0.4% of unrelated individuals in the UAB cohort carries a p.Met1149 missense variant, this finding will contribute to more accurate stratification of a significant number of NF1 individuals. Although clinically relevant genotype-phenotype correlations are rare in NF1, each affecting only a small percentage of individuals, together they impact counseling and management of a significant number of the NF1 population.
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Affiliation(s)
| | - Tom Callens
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Yunjia Chen
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Alicia Gomes
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Alesha D. Hicks
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Angela Sharp
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Eric Johns
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | | | - Linlea Armstrong
- Department of Medical Genetics, BC Women's HospitalUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Katherine Armstrong Bosanko
- Division of Clinical Genetics and Metabolism, Arkansas Children's HospitalUniversity of Arkansas for Medical SciencesLittle RockArkansas
| | | | - Laura Baker
- Division of Medical GeneticsAl DuPont Hospital for ChildrenWilmingtonDelaware
| | | | - Mario Bengala
- U.O.C Laboratorio di Genetica Medica, Dipartimento di OncoematologiaFondazione Policlinico di Tor VergataRomeItaly
| | - James T. Bennett
- Division of Genetic Medicine, Department of PediatricsUniversity of WashingtonSeattleWashington
| | - Chelsea Chambers
- Department of NeurologyUniversity of Virginia Medical CenterCharlottesvilleVirginia
| | | | - Maurizio Clementi
- Clinical Genetics Unit, Department of Women's and Children's HealthUniversity of PadovaPadovaItaly
| | | | - Mitch Cunningham
- Division of Genetic, Genomic, and Metabolic Disorders, Detroit Medical CenterChildren's Hospital of MichiganDetroitMichigan
| | | | - Martin B. Delatycki
- Bruce Lefroy Centre for Genetic Health ResearchMurdoch Childrens Research InstituteParkvilleVictoriaAustralia
| | - Maria C. Digilio
- Medical Genetics Unit, Bambino Gesù Children's HospitalIRCCSRomeItaly
| | - Laura Dosa
- SOC Genetica MedicaAOU MeyerFlorenceItaly
| | - Silvia Esposito
- Developmental Neurology UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Stephanie Fox
- Division of Medical GeneticsMcGill University Health CentreMontréalQuebecCanada
| | - Mary‐Louise Freckmann
- Department of Clinical GeneticsRoyal North Shore HospitalSt LeonardsNew South WalesAustralia
| | - Christine Fauth
- Division of Human GeneticsMedical University of InnsbruckInnsbruckAustria
| | - Teresa Giugliano
- Department of Precision MedicineUniversità degli Studi della Campania “Luigi Vanvitelli”NaplesItaly
| | - Sandra Giustini
- Department of Dermatology and Venereology, Policlinico Umberto ISapienza University of RomeRomeItaly
| | - Allison Goetsch
- Department of PediatricsNorthwestern University Feinberg School of MedicineChicagoIllinois
| | - Yael Goldberg
- The Raphael Recanati Genetics InstituteRabin Medical CenterPetah TikvaIsrael
| | - Robert S. Greenwood
- Division of Child NeurologyUniversity of North Carolina School of MedicineChapel HillNorth Carolina
| | | | - Karen W. Gripp
- Division of Medical GeneticsAl DuPont Hospital for ChildrenWilmingtonDelaware
| | - Punita Gupta
- Neurofibromatosis Diagnostic and Treatment ProgramSt. Joseph's Children's HospitalPatersonNew Jersey
| | - Eric Haan
- Adult Genetics UnitRoyal Adelaide HospitalAdelaideSouth AustraliaAustralia
| | - Rachel K. Hachen
- Neurofibromatosis ProgramChildren's Hospital of PhiladelphiaPhiladelphiaPennsylvania
| | - Tamara L. Haygarth
- Carolinas HealthCare SystemLevine Children's Specialty CenterCharlotteNorth Carolina
| | - Concepción Hernández‐Chico
- Department of Genetics, Hospital Universitario Ramón y CajalInstitute of Health Research (IRYCIS) and Center for Biomedical Research‐Network of Rare Diseases (CIBERER)MadridSpain
| | - Katelyn Hodge
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndiana
| | - Robert J. Hopkin
- Division of Human GeneticsCincinnati Children's Hospital Medical CenterCincinnatiOhio
| | - Louanne Hudgins
- Division of Medical GeneticsStanford University School of MedicineStanfordCalifornia
| | - Sandra Janssens
- Center for Medical GeneticsGhent University HospitalGhentBelgium
| | - Kory Keller
- Department of Molecular and Medical GeneticsOregon Health and Science UniversityPortlandOregon
| | | | - Aaina Kochhar
- Department of Medical Genetics and MetabolismValley Children's HealthcareMaderaCalifornia
| | - Bruce R. Korf
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Andrea M. Lewis
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Jan Liebelt
- The South Australian Clinical Genetics Service at the Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | | | - Robert H. Listernick
- Department of PediatricsNorthwestern University Feinberg School of MedicineChicagoIllinois
| | | | - Isabelle Maystadt
- Center for Human GeneticsInstitute of Pathology and Genetics (IPG)GosseliesBelgium
| | | | - Carey McDougall
- Division of Human Genetics, Children's Hospital of PhiladelphiaUniversity of Pennsylvania School of MedicinePhiladelphiaPennsylvania
| | - Lesley K. McGregor
- The South Australian Clinical Genetics Service at the Women's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Daniela Melis
- Section of Pediatrics, Department of Translational Medical SciencesFederico II UniversityNaplesItaly
| | - Nancy Mendelsohn
- Genomics Medicine ProgramChildren's Hospital MinnesotaMinneapolisMinnesota
| | | | - June Ortenberg
- Division of Medical GeneticsMcGill University Health CentreMontréalQuebecCanada
| | - Karin Panzer
- University of Iowa Stead Family Children's HospitalIowa CityIowa
| | - John G. Pappas
- Division of Clinical Genetic Services, Department of PediatricsNYU School of MedicineNew YorkNew York
| | - Mary Ella Pierpont
- Department of Pediatrics and OpthalmologyUniversity of MinnesotaMinneapolisMinnesota
| | - Giulio Piluso
- Department of Precision MedicineUniversità degli Studi della Campania “Luigi Vanvitelli”NaplesItaly
| | - Valentina Pinna
- Molecular Genetics UnitIRCCS Casa Sollievo della SofferenzaSan Giovanni RotondoFoggiaItaly
| | - Eniko K. Pivnick
- Department of Pediatrics and Department of OphthalmologyUniversity of Tennessee Health Science CenterMemphisTennessee
| | - Dinel A. Pond
- Genomics Medicine ProgramChildren's Hospital MinnesotaMinneapolisMinnesota
| | - Cynthia M. Powell
- Department of Genetics and Department of PediatricsUniversity of North Carolina School of MedicineChapel HillNorth Carolina
| | - Caleb Rogers
- Department of Molecular and Medical GeneticsOregon Health and Science UniversityPortlandOregon
| | - Noa Ruhrman Shahar
- The Raphael Recanati Genetics InstituteRabin Medical CenterPetah TikvaIsrael
| | - S. Lane Rutledge
- Department of GeneticsUniversity of Alabama at BirminghamBirminghamAlbama
| | - Veronica Saletti
- Developmental Neurology UnitFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Sarah A. Sandaradura
- Division of Clinical Genetics, Department of Paediatrics and Child Health, Children's Hospital at WestmeadUniversity of SydneySydneyNew South WalesAustralia
| | - Claudia Santoro
- Specialistic and General Surgery Unit, Department of Woman and Child, Referral Centre of NeurofibromatosisUniversità degli Studi della Campania “Luigi Vanvitelli”NaplesItaly
| | - Ulrich A. Schatz
- Division of Human GeneticsMedical University of InnsbruckInnsbruckAustria
| | | | - Daryl A. Scott
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Elizabeth A. Sellars
- Division of Clinical Genetics and Metabolism, Arkansas Children's HospitalUniversity of Arkansas for Medical SciencesLittle RockArkansas
| | - Ruth Sheffer
- Department of Genetics and Metabolic DiseasesHadassah‐Hebrew University Medical CenterJerusalemIsrael
| | | | - John M. Slopis
- Department of Neuro‐OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Rosemarie Smith
- Division of Genetics, Department of PediatricsMaine Medical CenterPortlandMaine
| | - Alberto Spalice
- Child Neurology Division, Department of PediatricsSapienza University of RomeRomeItaly
| | - David W. Stockton
- Division of Genetic, Genomic, and Metabolic Disorders, Detroit Medical CenterChildren's Hospital of MichiganDetroitMichigan
| | - Haley Streff
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Amy Theos
- Department of DermatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Gail E. Tomlinson
- Division of Pediatric Hematology–Oncology, Greehey Children's Cancer Research InstituteThe University of Texas Health Science CenterSan AntonioTexas
| | - Grace Tran
- Department of Clinical Cancer GeneticsThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | - Pamela L. Trapane
- Division of Pediatric Genetics, Department of PediatricsUniversity of Florida College of MedicineJacksonvilleFlorida
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women's and Children's HealthUniversity of PadovaPadovaItaly
| | - Nicole J. Ullrich
- Department of NeurologyBoston Children's HospitalBostonMassachusetts
| | - Jenneke Van den Ende
- Center for Medical GeneticsUniversity of Antwerp and Antwerp University HospitalAntwerpBelgium
| | | | - Stephanie E. Wallace
- Division of Genetic Medicine, Department of PediatricsUniversity of WashingtonSeattleWashington
| | - Michael F. Wangler
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - David D. Weaver
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndiana
| | - Kaleb H. Yohay
- Department of Neurology, New York University School of MedicineLangone Medical CenterNew YorkNew York
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of PhiladelphiaUniversity of Pennsylvania School of MedicinePhiladelphiaPennsylvania
| | - Jonathan Zonana
- Department of Molecular and Medical GeneticsOregon Health and Science UniversityPortlandOregon
| | | | | | - Marica Eoli
- Division of Molecular Neuro‐OncologyFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Yolanda Martin
- Department of Genetics, Hospital Universitario Ramón y CajalInstitute of Health Research (IRYCIS) and Center for Biomedical Research‐Network of Rare Diseases (CIBERER)MadridSpain
| | - Katharina Wimmer
- Division of Human GeneticsMedical University of InnsbruckInnsbruckAustria
| | - Alessandro De Luca
- Molecular Genetics UnitIRCCS Casa Sollievo della SofferenzaSan Giovanni RotondoFoggiaItaly
| | - Eric Legius
- Department of Human GeneticsKU LeuvenLeuvenBelgium
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7
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Wiczling P, Daghir-Wojtkowiak E, Kaliszan R, Markuszewski MJ, Limon J, Koczkowska M, Stukan M, Kuźniacka A, Ratajska M. Bayesian multilevel model of micro RNA levels in ovarian-cancer and healthy subjects. PLoS One 2019; 14:e0221764. [PMID: 31465488 PMCID: PMC6715278 DOI: 10.1371/journal.pone.0221764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
In transcriptomics, micro RNAs (miRNAs) has gained much interest especially as potential disease indicators. However, apart from holding a great promise related to their clinical application, a lot of inconsistent results have been published. Our aim was to compare the miRNA expression levels in ovarian cancer and healthy subjects using the Bayesian multilevel model and to assess their potential usefulness in diagnosis. We have analyzed a case-control observational data on expression profiling of 49 preselected miRNA-based ovarian cancer indicators in 119 controls and 59 patients. A Bayesian multilevel model was used to characterize the effect of disease on miRNA levels controlling for differences in age and body weight. The difference between the miRNA level and health status of the patient on the scale of the data variability were discussed in the context of their potential usefulness in diagnosis. Additionally, the cross-validated area under the ROC curve (AUC) was used to assess the expected out-of-sample discrimination index of a different sets of miRNAs. The proposed model allowed us to describe the set of miRNA levels in patients and controls. Three highly correlated miRNAs: miR-101-3p, miR-142-5p, miR-148a-3p rank the highest with almost identical effect sizes that ranges from 0.45 to 1.0. For those miRNAs the credible interval for AUC ranged from 0.63 to 0.67 indicating their limited discrimination potential. A little benefit in adding information from other miRNAs was observed. There were several miRNAs in the dataset (miR-604, hsa-miR-221-5p) for which inferences were uncertain. For those miRNAs more experimental effort is needed to fully assess their effect in the context of new hits discovery and usefulness as disease indicators. The proposed multilevel Bayesian model can be used to characterize the panel of miRNA profile and to assess the difference in expression levels between healthy and cancer individuals.
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Affiliation(s)
- Paweł Wiczling
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
- * E-mail:
| | - Emilia Daghir-Wojtkowiak
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Roman Kaliszan
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Michał Jan Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Gen. J. Hallera, Gdańsk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| | - Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| | - Maciej Stukan
- Department of Gynecological Oncology, Gdynia Oncology Centre, Powstania Styczniowego, Gdynia, Poland
| | - Alina Kuźniacka
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
| | - Magdalena Ratajska
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki, Gdańsk, Poland
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8
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Koczkowska M, Callens T, Gomes A, Sharp A, Chen Y, Hicks AD, Aylsworth AS, Azizi AA, Basel DG, Bellus G, Bird LM, Blazo MA, Burke LW, Cannon A, Collins F, DeFilippo C, Denayer E, Digilio MC, Dills SK, Dosa L, Greenwood RS, Griffis C, Gupta P, Hachen RK, Hernández-Chico C, Janssens S, Jones KJ, Jordan JT, Kannu P, Korf BR, Lewis AM, Listernick RH, Lonardo F, Mahoney MJ, Ojeda MM, McDonald MT, McDougall C, Mendelsohn N, Miller DT, Mori M, Oostenbrink R, Perreault S, Pierpont ME, Piscopo C, Pond DA, Randolph LM, Rauen KA, Rednam S, Rutledge SL, Saletti V, Schaefer GB, Schorry EK, Scott DA, Shugar A, Siqveland E, Starr LJ, Syed A, Trapane PL, Ullrich NJ, Wakefield EG, Walsh LE, Wangler MF, Zackai E, Claes KBM, Wimmer K, van Minkelen R, De Luca A, Martin Y, Legius E, Messiaen LM. Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype-phenotype correlation. Genet Med 2019; 21:867-876. [PMID: 30190611 PMCID: PMC6752285 DOI: 10.1038/s41436-018-0269-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 07/31/2018] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Neurofibromatosis type 1 (NF1) is characterized by a highly variable clinical presentation, but almost all NF1-affected adults present with cutaneous and/or subcutaneous neurofibromas. Exceptions are individuals heterozygous for the NF1 in-frame deletion, c.2970_2972del (p.Met992del), associated with a mild phenotype without any externally visible tumors. METHODS A total of 135 individuals from 103 unrelated families, all carrying the constitutional NF1 p.Met992del pathogenic variant and clinically assessed using the same standardized phenotypic checklist form, were included in this study. RESULTS None of the individuals had externally visible plexiform or histopathologically confirmed cutaneous or subcutaneous neurofibromas. We did not identify any complications, such as symptomatic optic pathway gliomas (OPGs) or symptomatic spinal neurofibromas; however, 4.8% of individuals had nonoptic brain tumors, mostly low-grade and asymptomatic, and 38.8% had cognitive impairment/learning disabilities. In an individual with the NF1 constitutional c.2970_2972del and three astrocytomas, we provided proof that all were NF1-associated tumors given loss of heterozygosity at three intragenic NF1 microsatellite markers and c.2970_2972del. CONCLUSION We demonstrate that individuals with the NF1 p.Met992del pathogenic variant have a mild NF1 phenotype lacking clinically suspected plexiform, cutaneous, or subcutaneous neurofibromas. However, learning difficulties are clearly part of the phenotypic presentation in these individuals and will require specialized care.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Angela Sharp
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Alesha D Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arthur S Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Amedeo A Azizi
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Donald G Basel
- Children's Hospital of Wisconsin, Milwaukee, Wisconsin, USA
| | - Gary Bellus
- Department of Clinical Genetics and Metabolism, Children's Hospital, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego; Division of Genetics/Dysmorphology, Rady Children's Hospital, San Diego, California, USA
| | | | - Leah W Burke
- Clinical Genetics Program, University of Vermont Medical Center, Burlington, Vermont, USA
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Felicity Collins
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Colette DeFilippo
- Department of Pediatrics, Division of Genomic Medicine, UC Davis MIND Institute, Sacramento, California, USA
| | - Ellen Denayer
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Maria C Digilio
- Medical Genetics Unit, Bambino Gesù Children's, IRCCS, Rome, Italy
| | | | - Laura Dosa
- SOC Genetica Medica, AOU Meyer, Florence, Italy
| | - Robert S Greenwood
- Department of Neurology, Division of Child Neurology, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Punita Gupta
- Neurofibromatosis Diagnostic & Treatment Program, St. Joseph's Children's Hospital, Paterson, New Jersey, USA
| | - Rachel K Hachen
- Neurofibromatosis Program, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Concepción Hernández-Chico
- Department of Genetics, Hospital Universitario Ramón y Cajal, Institute of Health Research (IRYCIS), Madrid, Spain
- Center for Biomedical Research-Network of Rare Diseases (CIBERER), Madrid, Spain
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kristi J Jones
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Justin T Jordan
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Robert H Listernick
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - Maurice J Mahoney
- Department of Genetics, Yale University, New Haven, Connecticut, USA
| | - Mayra Martinez Ojeda
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Nancy Mendelsohn
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, Minnesota, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Mari Mori
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, Rhode Island, USA
| | - Rianne Oostenbrink
- Department of General Pediatrics, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Sebastién Perreault
- CHU Sainte-Justine, Mother and Child University Hospital Center, Montréal, Québec, Canada
| | - Mary Ella Pierpont
- Department of Pediatrics and Ophthalmology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Carmelo Piscopo
- U.O.S.C. Medical Genetics, A.O.R.N. "A. Cardarelli", Naples, Italy
| | - Dinel A Pond
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, Minnesota, USA
| | - Linda M Randolph
- Division of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Katherine A Rauen
- Department of Pediatrics, Division of Genomic Medicine, UC Davis MIND Institute, Sacramento, California, USA
| | - Surya Rednam
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Veronica Saletti
- Developmental Neurology Unit, IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - G Bradley Schaefer
- Division of Medical Genetics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Elizabeth K Schorry
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Andrea Shugar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth Siqveland
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, Minnesota, USA
| | - Lois J Starr
- Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ashraf Syed
- DCH Regional Medical Center and Northport Medical Center, Northport, Alabama, USA
| | - Pamela L Trapane
- Stead Family Department of Pediatrics, University of Iowa Hospitals & Clinics, Iowa City, Iowa, USA
| | - Nicole J Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Emily G Wakefield
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Laurence E Walsh
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Katharina Wimmer
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alessandro De Luca
- IRCCS Casa Sollievo della Sofferenza, Molecular Genetics Unit, San Giovanni Rotondo, Foggia, Italy
| | - Yolanda Martin
- Department of Genetics, Hospital Universitario Ramón y Cajal, Institute of Health Research (IRYCIS), Madrid, Spain
- Center for Biomedical Research-Network of Rare Diseases (CIBERER), Madrid, Spain
| | - Eric Legius
- Department of Human Genetics, KU Leuven-University of Leuven, Leuven, Belgium
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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9
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Koczkowska M, Callens T, Gomes A, Sharp A, Chen Y, Hicks AD, Aylsworth AS, Azizi AA, Basel DG, Bellus G, Bird LM, Blazo MA, Burke LW, Cannon A, Collins F, DeFilippo C, Denayer E, Digilio MC, Dills SK, Dosa L, Greenwood RS, Griffis C, Gupta P, Hachen RK, Hernández-Chico C, Janssens S, Jones KJ, Jordan JT, Kannu P, Korf BR, Lewis AM, Listernick RH, Lonardo F, Mahoney MJ, Ojeda MM, McDonald MT, McDougall C, Mendelsohn N, Miller DT, Mori M, Oostenbrink R, Perreault S, Pierpont ME, Piscopo C, Pond DA, Randolph LM, Rauen KA, Rednam S, Rutledge SL, Saletti V, Schaefer GB, Schorry EK, Scott DA, Shugar A, Siqveland E, Starr LJ, Syed A, Trapane PL, Ullrich NJ, Wakefield EG, Walsh LE, Wangler MF, Zackai E, Claes KBM, Wimmer K, van Minkelen R, De Luca A, Martin Y, Legius E, Messiaen LM. Correction: Expanding the clinical phenotype of individuals with a 3-bp in-frame deletion of the NF1 gene (c.2970_2972del): an update of genotype-phenotype correlation. Genet Med 2019; 21:764-765. [PMID: 30275510 PMCID: PMC7608433 DOI: 10.1038/s41436-018-0326-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
A correction has been published to this Article. The PDF and HTML have been updated accordingly.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Angela Sharp
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alesha D Hicks
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Arthur S Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amedeo A Azizi
- Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Gary Bellus
- Department of Clinical Genetics and Metabolism, Children's Hospital, University of Colorado School of Medicine, Denver, Aurora, CO, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego; Division of Genetics/Dysmorphology, Rady Children's Hospital, San Diego, CA, USA
| | | | - Leah W Burke
- Clinical Genetics Program, University of Vermont Medical Center, Burlington, VT, USA
| | - Ashley Cannon
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Felicity Collins
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Colette DeFilippo
- Department of Pediatrics, Division of Genomic Medicine, UC Davis MIND Institute, Sacramento, CA, USA
| | - Ellen Denayer
- Department of Human Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Maria C Digilio
- Medical Genetics Unit, Bambino Gesù Children's, IRCCS, Rome, Italy
| | | | - Laura Dosa
- SOC Genetica Medica, AOU Meyer, Florence, Italy
| | - Robert S Greenwood
- Department of Neurology, Division of Child Neurology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | | | - Punita Gupta
- Neurofibromatosis Diagnostic & Treatment Program, St. Joseph's Children's Hospital, Paterson, NJ, USA
| | - Rachel K Hachen
- Neurofibromatosis Program, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Concepción Hernández-Chico
- Department of Genetics, Hospital Universitario Ramón y Cajal, Institute of Health Research (IRYCIS), Madrid, Spain
- Center for Biomedical Research-Network of Rare Diseases (CIBERER), Valencia, Spain
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Kristi J Jones
- Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Justin T Jordan
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Peter Kannu
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Robert H Listernick
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | | | | | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Nancy Mendelsohn
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Mari Mori
- Department of Pediatrics, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Rianne Oostenbrink
- Department of General Pediatrics, Erasmus MC-Sophia, Rotterdam, The Netherlands
| | - Sebastién Perreault
- CHU Sainte-Justine, Mother and Child University Hospital Center, Montréal, QC, Canada
| | - Mary Ella Pierpont
- Department of Pediatrics and Ophthalmology, University of Minnesota, Minneapolis, MN, USA
| | - Carmelo Piscopo
- U.O.S.C. Medical Genetics, A.O.R.N. "A. Cardarelli", Naples, Italy
| | - Dinel A Pond
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN, USA
| | - Linda M Randolph
- Division of Medical Genetics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Katherine A Rauen
- Department of Pediatrics, Division of Genomic Medicine, UC Davis MIND Institute, Sacramento, CA, USA
| | - Surya Rednam
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Veronica Saletti
- Developmental Neurology Unit, IRCCS Foundation, Carlo Besta Neurological Institute, Milan, Italy
| | - G Bradley Schaefer
- Division of Medical Genetics, University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Little Rock, AR, USA
| | - Elizabeth K Schorry
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Shugar
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elizabeth Siqveland
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN, USA
| | - Lois J Starr
- Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ashraf Syed
- DCH Regional Medical Center and Northport Medical Center, Northport, AL, USA
| | - Pamela L Trapane
- Stead Family Department of Pediatrics, University of Iowa Hospitals & Clinics, Iowa City, IA, USA
| | - Nicole J Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Emily G Wakefield
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Laurence E Walsh
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Katharina Wimmer
- Division of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alessandro De Luca
- IRCCS Casa Sollievo della Sofferenza, Molecular Genetics Unit, San Giovanni Rotondo, Foggia, Italy
| | - Yolanda Martin
- Department of Genetics, Hospital Universitario Ramón y Cajal, Institute of Health Research (IRYCIS), Madrid, Spain
- Center for Biomedical Research-Network of Rare Diseases (CIBERER), Valencia, Spain
| | - Eric Legius
- Department of Human Genetics, KU Leuven - University of Leuven, Leuven, Belgium
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA.
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10
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Koczkowska M, Chen Y, Callens T, Gomes A, Sharp A, Johnson S, Hsiao MC, Chen Z, Balasubramanian M, Barnett CP, Becker TA, Ben-Shachar S, Bertola DR, Blakeley JO, Burkitt-Wright EMM, Callaway A, Crenshaw M, Cunha KS, Cunningham M, D'Agostino MD, Dahan K, De Luca A, Destrée A, Dhamija R, Eoli M, Evans DGR, Galvin-Parton P, George-Abraham JK, Gripp KW, Guevara-Campos J, Hanchard NA, Hernández-Chico C, Immken L, Janssens S, Jones KJ, Keena BA, Kochhar A, Liebelt J, Martir-Negron A, Mahoney MJ, Maystadt I, McDougall C, McEntagart M, Mendelsohn N, Miller DT, Mortier G, Morton J, Pappas J, Plotkin SR, Pond D, Rosenbaum K, Rubin K, Russell L, Rutledge LS, Saletti V, Schonberg R, Schreiber A, Seidel M, Siqveland E, Stockton DW, Trevisson E, Ullrich NJ, Upadhyaya M, van Minkelen R, Verhelst H, Wallace MR, Yap YS, Zackai E, Zonana J, Zurcher V, Claes K, Martin Y, Korf BR, Legius E, Messiaen LM. Genotype-Phenotype Correlation in NF1: Evidence for a More Severe Phenotype Associated with Missense Mutations Affecting NF1 Codons 844-848. Am J Hum Genet 2018; 102:69-87. [PMID: 29290338 PMCID: PMC5777934 DOI: 10.1016/j.ajhg.2017.12.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023] Open
Abstract
Neurofibromatosis type 1 (NF1), a common genetic disorder with a birth incidence of 1:2,000-3,000, is characterized by a highly variable clinical presentation. To date, only two clinically relevant intragenic genotype-phenotype correlations have been reported for NF1 missense mutations affecting p.Arg1809 and a single amino acid deletion p.Met922del. Both variants predispose to a distinct mild NF1 phenotype with neither externally visible cutaneous/plexiform neurofibromas nor other tumors. Here, we report 162 individuals (129 unrelated probands and 33 affected relatives) heterozygous for a constitutional missense mutation affecting one of five neighboring NF1 codons-Leu844, Cys845, Ala846, Leu847, and Gly848-located in the cysteine-serine-rich domain (CSRD). Collectively, these recurrent missense mutations affect ∼0.8% of unrelated NF1 mutation-positive probands in the University of Alabama at Birmingham (UAB) cohort. Major superficial plexiform neurofibromas and symptomatic spinal neurofibromas were more prevalent in these individuals compared with classic NF1-affected cohorts (both p < 0.0001). Nearly half of the individuals had symptomatic or asymptomatic optic pathway gliomas and/or skeletal abnormalities. Additionally, variants in this region seem to confer a high predisposition to develop malignancies compared with the general NF1-affected population (p = 0.0061). Our results demonstrate that these NF1 missense mutations, although located outside the GAP-related domain, may be an important risk factor for a severe presentation. A genotype-phenotype correlation at the NF1 region 844-848 exists and will be valuable in the management and genetic counseling of a significant number of individuals.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tom Callens
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alicia Gomes
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Angela Sharp
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Sherrell Johnson
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meng-Chang Hsiao
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zhenbin Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK
| | | | - Troy A Becker
- Medical Genetics, John Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Shay Ben-Shachar
- The Genetic Institute, Tel-Aviv Sourasky Medical Center and Sackler Faculty of Medicine, Tel-Aviv 6997801, Israel
| | - Debora R Bertola
- Department of Pediatrics, University of São Paulo, São Paulo 05403-000, Brazil
| | - Jaishri O Blakeley
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Emma M M Burkitt-Wright
- Genomic Medicine, Division of Evolution and Genomic Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury SP2 8BJ, UK
| | - Melissa Crenshaw
- Medical Genetics, John Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Karin S Cunha
- Department of Pathology, School of Medicine, Universidade Federal Fluminense, Niterói 24220-900, Brazil
| | - Mitch Cunningham
- Division of Genetic, Genomic and Metabolic Disorders, Children's Hospital of Michigan, Detroit Medical Center, Detroit, MI 48201, USA
| | - Maria D D'Agostino
- Department of Medical Genetics, McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Karin Dahan
- Center for Human Genetics, Institute of Pathology and Genetics (IPG), Gosselies 6041, Belgium
| | - Alessandro De Luca
- Molecular Genetics Unit, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo 71013, Italy
| | - Anne Destrée
- Center for Human Genetics, Institute of Pathology and Genetics (IPG), Gosselies 6041, Belgium
| | - Radhika Dhamija
- Department of Clinical Genomics and Neurology, Mayo Clinic, Phoenix, AZ 85259, USA
| | - Marica Eoli
- Unit of Molecular Neuro-Oncology, IRCCS Foundation, Carlo Besta Neurological Institute, Milan 20133, Italy
| | - D Gareth R Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, Manchester Academic Health Sciences Centre, University of Manchester, Central Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | | | | | - Karen W Gripp
- Division of Medical Genetics, Al DuPont Hospital for Children, Wilmington, DE 19803, USA
| | - Jose Guevara-Campos
- Pediatrics Service, Felipe Guevara Rojas Hospital, University of Oriente, El Tigre-Anzoátegui, Venezuela 6034, Spain
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Concepcion Hernández-Chico
- Department of Genetics, Hospital Universitario Ramón y Cayal, Institute of Health Research (IRYCIS), Madrid 28034, Spain and Center for Biomedical Research-Network of Rare Diseases (CIBERER)
| | - LaDonna Immken
- Dell Children's Medical Center of Central Texas, Austin, TX 78723, USA
| | - Sandra Janssens
- Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium
| | - Kristi J Jones
- Department of Clinical Genetics, the Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Beth A Keena
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Aaina Kochhar
- Department of Genetics, Valley Children's Healthcare, Madera, CA 93636, USA
| | - Jan Liebelt
- Women's and Children's Hospital/SA Pathology, North Adelaide, SA 5006, Australia
| | - Arelis Martir-Negron
- Division of Clinical Genetics, Center for Genomic Medicine, Miami Cancer Institute, Miami, FL 33176, USA
| | | | - Isabelle Maystadt
- Center for Human Genetics, Institute of Pathology and Genetics (IPG), Gosselies 6041, Belgium
| | - Carey McDougall
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Meriel McEntagart
- St George's University Hospitals NHS Foundation Trust, London SW17 0QT, UK
| | - Nancy Mendelsohn
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN 55404, USA
| | - David T Miller
- Multidisciplinary Neurofibromatosis Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Geert Mortier
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp 2650, Belgium
| | - Jenny Morton
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham B15 2TG, UK
| | - John Pappas
- Department of Pediatrics, Clinical Genetic Services, NYU School of Medicine, New York, NY 10016, USA
| | - Scott R Plotkin
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dinel Pond
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN 55404, USA
| | - Kenneth Rosenbaum
- Division of Genetics and Metabolism, Children's National Health System, Washington, DC 20010, USA
| | - Karol Rubin
- University of Minnesota Health, Minneapolis, MN 55404, USA
| | - Laura Russell
- Department of Medical Genetics, McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Lane S Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Veronica Saletti
- Developmental Neurology Unit, IRCCS Foundation, Carlo Besta Neurological Institute, Milan 20133, Italy
| | - Rhonda Schonberg
- Division of Genetics and Metabolism, Children's National Health System, Washington, DC 20010, USA
| | - Allison Schreiber
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Meredith Seidel
- Department of Neurology and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elizabeth Siqveland
- Genomics Medicine Program, Children's Hospital Minnesota, Minneapolis, MN 55404, USA
| | - David W Stockton
- Division of Genetic, Genomic and Metabolic Disorders, Children's Hospital of Michigan, Detroit Medical Center, Detroit, MI 48201, USA
| | - Eva Trevisson
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padova, Italy and Italy Istituto di Ricerca Pediatria, IRP, Città della Speranza, Padova 35128, Italy
| | - Nicole J Ullrich
- Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Meena Upadhyaya
- Division of Cancer and Genetics, Cardiff University, Cardiff CF14 4XN, UK
| | - Rick van Minkelen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam 3015 GE, the Netherlands
| | - Helene Verhelst
- Department of Paediatrics, Division of Paediatric Neurology, Ghent University Hospital, Ghent 9000, Belgium
| | - Margaret R Wallace
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL 32610, USA
| | - Yoon-Sim Yap
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore; Faculty of Health Sciences, School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan Zonana
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Vickie Zurcher
- Genomic Medicine Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kathleen Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent 9000, Belgium
| | - Yolanda Martin
- Department of Genetics, Hospital Universitario Ramón y Cayal, Institute of Health Research (IRYCIS), Madrid 28034, Spain and Center for Biomedical Research-Network of Rare Diseases (CIBERER)
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Eric Legius
- Department of Human Genetics, KU Leuven - University of Leuven, Leuven 3000, Belgium
| | - Ludwine M Messiaen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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11
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Koczkowska M, Lipska-Ziętkiewicz BS, Iliszko M, Ryś J, Miettinen M, Lasota J, Biernat W, Harazin-Lechowska A, Kruczak A, Limon J. Application of high-resolution genomic profiling in the differential diagnosis of liposarcoma. Mol Cytogenet 2017; 10:7. [PMID: 28331547 PMCID: PMC5356274 DOI: 10.1186/s13039-017-0309-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/06/2017] [Indexed: 01/04/2023] Open
Abstract
Background Rarity and heterogeneity of liposarcomas (LPS) make their diagnosis difficult even for sarcoma-experts pathologists. The molecular mechanism underlying the development and progression of liposarcomas (LPS) remains only partially known. In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes. Results Copy number aberrations (CNAs) were identified in 98% of WDLPS and DDLPS and in 95% of MLPS cases. The minimal common region of amplification at 12q14.1q21.1 was observed in 96% of WDLPS and DDLPS cases. Four regions of CNAs, including losses of chromosome 6, 11 and 13 and gains of chromosome 14 were classified as recurrent in DDLPS; at least one was identified in 74% of DDLPS tumors. The DDLPS-associated losses were much more common in tumors with increased genomic complexity. In MLPS, the most frequent CNAs were losses of chromosome 6 (40%) and gains of chromosome 1 (30%), with the minimal overlapping regions 6q14.1q22.31 and 1q25.1q32.2, respectively. Conclusions Our findings show that the application of array-CGH allows to delineate clearly the genomic profiles of WDLPS, DDLPS and MLPS that reflect biological differences between these tumors. Although CNAs varied widely, the subtypes of tumors have characteristic genomic profiles that could facilitate the differential diagnosis of LPS subtypes, especially between WDLPS and DDLPS. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0309-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211 Gdansk, Poland
| | | | - Mariola Iliszko
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211 Gdansk, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, M. Sklodowska-Curie Memorial Institute of Oncology, 11 Garncarska Street, 31-115 Krakow, Poland
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, Building 10, Room B1B47, 10 Center Drive, Bethesda, 20892 MD USA
| | - Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, Building 10, Room B1B47, 10 Center Drive, Bethesda, 20892 MD USA
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, 17 Smoluchowskiego Street, 80-214 Gdansk, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, M. Sklodowska-Curie Memorial Institute of Oncology, 11 Garncarska Street, 31-115 Krakow, Poland
| | - Anna Kruczak
- Department of Tumor Pathology, M. Sklodowska-Curie Memorial Institute of Oncology, 11 Garncarska Street, 31-115 Krakow, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211 Gdansk, Poland
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12
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Jankauskienė A, Koczkowska M, Bjerre A, Bernaciak J, Schaefer F, Lipska-Ziętkiewicz BS. Erratum to: Glomerulopathy in patients with distal duplication of chromosome 6p. BMC Nephrol 2016; 17:43. [PMID: 27117553 PMCID: PMC4847247 DOI: 10.1186/s12882-016-0255-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 04/14/2016] [Indexed: 11/10/2022] Open
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13
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Koczkowska M, Wierzba J, Śmigiel R, Sąsiadek M, Cabała M, Ślężak R, Iliszko M, Kardaś I, Limon J, Lipska-Ziętkiewicz BS. Genomic findings in patients with clinical suspicion of 22q11.2 deletion syndrome. J Appl Genet 2016; 58:93-98. [PMID: 27629806 PMCID: PMC5243916 DOI: 10.1007/s13353-016-0366-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/15/2016] [Accepted: 08/29/2016] [Indexed: 12/13/2022]
Abstract
Chromosome 22q11.2 deletion syndrome, one of the most common human genomic syndromes, has highly heterogeneous clinical presentation. Patients usually harbor a 1.5 to 3 Mb hemizygous deletion at chromosome 22q11.2, resulting in pathognomic TBX1, CRKL and/or MAPK1 haploinsufficiency. However, there are some individuals with clinical features resembling the syndrome who are eventually diagnosed with genomic disorders affecting other chromosomal regions. The objective of this study was to evaluate the additive value of high-resolution array-CGH testing in the cohort of 41 patients with clinical features of 22q11.2 deletion syndrome and negative results of standard cytogenetic diagnostic testing (karyotype and FISH for 22q11.2 locus). Array-CGH analysis revealed no aberrations at chromosomes 22 or 10 allegedly related to the syndrome. Five (12.2 %) patients were found to have other genomic imbalances, namely 17q21.31 microdeletion syndrome (MIM#610443), 1p36 deletion syndrome (MIM#607872), NF1 microduplication syndrome (MIM#613675), chromosome 6pter-p24 deletion syndrome (MIM#612582) and a novel interstitial deletion at 3q26.31 of 0.65 Mb encompassing a dosage-dependent gene NAALADL2. Our study demonstrates that the implementation of array-CGH into the panel of classic diagnostic procedures adds significantly to their efficacy. It allows for detection of constitutional genomic imbalances in 12 % of subjects with negative result of karyotype and FISH targeted for 22q11.2 region. Moreover, if used as first-tier genetic test, the method would provide immediate diagnosis in ∼40 % phenotypic 22q11.2 deletion subjects.
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MESH Headings
- Abnormalities, Multiple/diagnosis
- Abnormalities, Multiple/genetics
- Chromosome Deletion
- Chromosome Disorders/diagnosis
- Chromosome Disorders/genetics
- Chromosome Duplication/genetics
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 6/genetics
- Comparative Genomic Hybridization
- DiGeorge Syndrome/diagnosis
- DiGeorge Syndrome/genetics
- Eye Abnormalities/diagnosis
- Eye Abnormalities/genetics
- Facies
- Female
- Hearing Loss/diagnosis
- Hearing Loss/genetics
- Heart Defects, Congenital/diagnosis
- Heart Defects, Congenital/genetics
- Humans
- Hypertelorism/diagnosis
- Hypertelorism/genetics
- In Situ Hybridization, Fluorescence
- Intellectual Disability/diagnosis
- Intellectual Disability/genetics
- Karyotyping
- Male
- Neurofibromatoses/diagnosis
- Neurofibromatoses/genetics
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Affiliation(s)
- Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland
| | - Jolanta Wierzba
- General Nursery, Medical University of Gdansk, 7 Debinki Street, 80-211, Gdansk, Poland
| | - Robert Śmigiel
- Department of Social Pediatrics, Wroclaw Medical University, 5 Bartla Street, 51-618, Wroclaw, Poland
| | - Maria Sąsiadek
- Department of Genetics, Wroclaw Medical University, 1 Marcinkowskiego Street, 50-368, Wroclaw, Poland
| | - Magdalena Cabała
- Department of Social Pediatrics, Wroclaw Medical University, 5 Bartla Street, 51-618, Wroclaw, Poland
| | - Ryszard Ślężak
- Department of Genetics, Wroclaw Medical University, 1 Marcinkowskiego Street, 50-368, Wroclaw, Poland
| | - Mariola Iliszko
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland
| | - Iwona Kardaś
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland
| | - Beata S Lipska-Ziętkiewicz
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211, Gdansk, Poland.
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14
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Majak P, Jerzyńska J, Bojo M, Brzozowska A, Koczkowska M, Sielski P, Stelmach W, Stelmach R, Janas A, Stelmach I. Cytokine profiling in exhaled breath condensate after exercise challenge in asthmatic children with post-exercise symptoms. Arch Med Sci 2016; 12:778-84. [PMID: 27478459 PMCID: PMC4947605 DOI: 10.5114/aoms.2015.48547] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/21/2014] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Markers of exhaled breath condensate (EBC) correlate with lung function impairment, airway remodeling and different aspects of the disease such as exercise-induced bronchoconstriction (EIB). Aim of the study was to determine the cytokine profile in EBC of children with asthma after an exercise treadmill challenge in order to obtain clinically useful information about mechanisms of EIB; also, to assess correlations between cytokine concentrations in EBC and clinical characteristics of the patients. MATERIAL AND METHODS The study population consisted of 25 randomly selected children, aged 8 to 19 years, with asthma and EIB symptoms despite the use of control medications. Patients on the day of the study visit underwent fractional exhaled nitric oxide measurement (FeNO) and baseline spirometry, performed an exercise treadmill challenge (ETC), and EBC samples were obtained at the end of the ETC. RESULTS In asthmatic children with positive ETC, monocyte hemotactic protein-1 (MCP-1) and IL-16 adjusted to pre-EBC forced expiratory volume in 1 s (FEV1) were significantly higher compared to children with negative ETC (p = 0.022 and p = 0.017 respectively). After adjustment to pre-EBC FEV1 other cytokines (IL-4, IL-5, IL-6, IL-8, MIG, TNF-α) were not related to post-exercise changes in FEV1. CONCLUSIONS We observed a specific inflammatory profile in the airways of asthmatic children with bronchoconstriction induced by exercise. The concentration of cytokines in EBC depended on the post-exercise decrease in FEV1, which was measured by the area under the curve (AUC). MCP-1 and IL-16, adjusted to pre-EBC FEV1, were significantly higher in children with a positive exercise challenge compared to those with a negative one.
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Affiliation(s)
- Paweł Majak
- Department of Internal Medicine, Asthma and Allergy, Barlicki University Hospital, Medical University of Lodz, Lodz, Poland
| | - Joanna Jerzyńska
- Department of Paediatrics and Allergy, Medical University of Lodz, Lodz, Poland
| | - Magdalena Bojo
- Department of Paediatrics and Allergy, Medical University of Lodz, Lodz, Poland
| | | | - Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Sielski
- Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland
| | - Włodzimierz Stelmach
- Department of Social and Preventive Medicine, Medical University of Lodz, Lodz, Poland
| | - Rafał Stelmach
- Institute of Dental Surgery, Faculty of Medicine and Dentistry, Medical University of Lodz, Lodz, Poland
| | - Anna Janas
- Institute of Dental Surgery, Faculty of Medicine and Dentistry, Medical University of Lodz, Lodz, Poland
| | - Iwona Stelmach
- Department of Paediatrics and Allergy, Medical University of Lodz, Lodz, Poland
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15
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Koczkowska M, Zuk M, Gorczynski A, Ratajska M, Lewandowska M, Biernat W, Limon J, Wasag B. Detection of somatic BRCA1/2 mutations in ovarian cancer - next-generation sequencing analysis of 100 cases. Cancer Med 2016; 5:1640-6. [PMID: 27167707 PMCID: PMC4867663 DOI: 10.1002/cam4.748] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/18/2016] [Accepted: 04/03/2016] [Indexed: 12/22/2022] Open
Abstract
The overall prevalence of germline BRCA1/2 mutations is estimated between 11% and 15% of all ovarian cancers. Individuals with germline BRCA1/2 alterations treated with the PARP1 inhibitors (iPARP1) tend to respond better than patients with wild-type BRCA1/2. Additionally, also somatic BRCA1/2 alterations induce the sensitivity to iPARP1. Therefore, the detection of both germline and somatic BRCA1/2 mutations is required for effective iPARP1 treatment. The aim of this study was to identify the frequency and spectrum of germline and somatic BRCA1/2 alterations in a group of Polish patients with ovarian serous carcinoma. In total, 100 formalin-fixed paraffin-embedded (FFPE) ovarian serous carcinoma tissues were enrolled to the study. Mutational analysis of BRCA1/2 genes was performed by using next-generation sequencing. The presence of pathogenic variants was confirmed by Sanger sequencing. In addition, to confirm the germline or somatic status of the mutation, the nonneoplastic tissue was analyzed by bidirectional Sanger sequencing. In total, 27 (28% of patient samples) mutations (20 in BRCA1 and 7 in BRCA2) were identified. For 22 of 27 patients, nonneoplastic cells were available and sequencing revealed the somatic character of two BRCA1 (2/16; 12.5%) and two BRCA2 (2/6; 33%) mutations. Notably, we identified six novel frameshift or nonsense BRCA1/2 mutations. The heterogeneity of the detected mutations confirms the necessity of simultaneous analysis of BRCA1/2 genes in all patients diagnosed with serous ovarian carcinoma. Moreover, the use of tumor tissue for mutational analysis allowed the detection of both somatic and germline BRCA1/2 mutations.
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Affiliation(s)
| | - Monika Zuk
- Department of Biology and GeneticsMedical University of GdanskGdanskPoland
| | - Adam Gorczynski
- Department of PathologyMedical University of GdanskGdanskPoland
| | - Magdalena Ratajska
- Department of Biology and GeneticsMedical University of GdanskGdanskPoland
| | - Marzena Lewandowska
- Molecular Oncology and Genetics DepartmentInnovative Medical ForumThe Franciszek Lukaszczyk Oncology CenterBydgoszczPoland
- Department of Thoracic Surgery and TumorsLudwik Rydygier Medical College in BydgoszczNicolaus Copernicus University in TorunBydgoszczPoland
| | | | - Janusz Limon
- Department of Biology and GeneticsMedical University of GdanskGdanskPoland
| | - Bartosz Wasag
- Department of Biology and GeneticsMedical University of GdanskGdanskPoland
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16
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Jankauskienė A, Koczkowska M, Bjerre A, Bernaciak J, Schaefer F, Lipska-Ziętkiewicz BS. Glomerulopathy in patients with distal duplication of chromosome 6p. BMC Nephrol 2016; 17:32. [PMID: 27000031 PMCID: PMC4802583 DOI: 10.1186/s12882-016-0246-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background Duplication of the distal part of chromosome 6p is a rare genetic syndrome. Renal involvement has been reported in the majority of patients, including a wide range of congenital abnormalities of kidney and urinary tract and, occasionally, a proteinuric glomerulopathy. Case presentation Here, we report a 13-year-old girl with 6p25.3p22.1 duplication who presented with proteinuria in infancy, was later diagnosed as focal segmental glomerulosclerosis, progressed to end-stage renal disease and was successfully transplanted. Conclusion A systematic literature review suggests that 15–20 % of individuals with distal 6p duplication develop progressive proteinuric glomerulopathy. Monitoring of kidney function should be recommended in all cases. Electronic supplementary material The online version of this article (doi:10.1186/s12882-016-0246-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Augustina Jankauskienė
- Vilnius University, Children hospital affiliate of Vilnius university hospital "Santariskiu klinikos", Santariskiu 4, LT-08406, Vilnius, Lithuania.
| | - Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdańsk, Dębinki 1, 80211, Gdańsk, Poland
| | - Anna Bjerre
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Franz Schaefer
- Division of Pediatric Nephrology, Center for Pediatrics and Adolescent Medicine, Heidelberg, Germany
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17
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Hogendorf A, Lipska-Zietkiewicz BS, Szadkowska A, Borowiec M, Koczkowska M, Trzonkowski P, Drozdz I, Wyka K, Limon J, Mlynarski W. Chromosome 18q deletion syndrome with autoimmune diabetes mellitus: putative genomic loci for autoimmunity and immunodeficiency. Pediatr Diabetes 2016; 17:153-9. [PMID: 25403779 DOI: 10.1111/pedi.12235] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/09/2014] [Accepted: 10/10/2014] [Indexed: 01/16/2023] Open
Abstract
A girl with 18q deletion syndrome was diagnosed with autoimmune diabetes mellitus and Hashimoto's thyroiditis at the age of 3 yr. In addition, the girl suffered from recurrent infections due to immunoglobulin A and IgG4 deficiency. She was also found to have CD3+CD4+FoxP3+, CD3+CD4+FoxP3+CD25+, and CD3+CD4+CD25+CD127 regulatory T cells deficiency. The exceptional coincidence of the two autoimmune disorders occurring at an early age, and associated with immune deficiency, implies that genes located on deleted 19.4 Mbp region at 18q21.32-q23 (chr18:58,660,699-78,012,870) might play a role in the pathogenesis of autoimmunity leading to β cell destruction and diabetes.
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Affiliation(s)
- Anna Hogendorf
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | | | - Agnieszka Szadkowska
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Maciej Borowiec
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland.,Department of Clinical Genetics, Medical University of Lodz, Lodz, Poland
| | - Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Piotr Trzonkowski
- Clinical Immunology and Transplantology Unit at the Department of Immunology, Medical University of Gdansk, Gdansk, Poland
| | - Izabela Drozdz
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Krystyna Wyka
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Mlynarski
- Department of Pediatrics, Oncology, Hematology and Diabetology, Medical University of Lodz, Lodz, Poland
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18
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Lipska BS, Koczkowska M, Wierzba J, Ploszynska A, Iliszko M, Izycka-Swieszewska E, Adamkiewicz-Drozynska E, Limon J. On the significance of germline cytogenetic rearrangements at MYCN locus in neuroblastoma. Mol Cytogenet 2013; 6:43. [PMID: 24131700 PMCID: PMC3819649 DOI: 10.1186/1755-8166-6-43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023] Open
Abstract
Background MYCN oncogene amplification is the most important prognostic factor in neuroblastoma. 25% neuroblastoma tumors have somatic amplifications at this locus but little is known about its constitutional aberrations and their potential role in carcinogenesis. Here, we have performed an array-CGH and qPCR characterization of two patients with constitutional partial 2p trisomy including MYCN genomic region. Results One of the patients had congenital neuroblastoma and showed presence of minute areas of gains and losses within the common fragile site FRA2C at 2p24 encompassing MYCN. The link between 2p24 germline rearrangements and neuroblastoma development was reassessed by reviewing similar cases in the literature. Conclusions It appears that constitutional rearrangements involving chromosome 2p24 may play role in NB development.
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Affiliation(s)
- Beata S Lipska
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1str, 80211 Gdansk, Poland.
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19
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Kuzniacka A, Wierzba J, Ratajska M, Lipska BS, Koczkowska M, Malinowska M, Limon J. Erratum to: Spectrum of NIPBL gene mutations in Polish patients with Cornelia de Lange syndrome. J Appl Genet 2013. [PMCID: PMC4079576 DOI: 10.1007/s13353-013-0138-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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20
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Kuzniacka A, Wierzba J, Ratajska M, Lipska BS, Koczkowska M, Malinowska M, Limon J. Spectrum of NIPBL gene mutations in Polish patients with Cornelia de Lange syndrome. J Appl Genet 2013; 54:27-33. [PMID: 23254390 PMCID: PMC3548104 DOI: 10.1007/s13353-012-0126-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 11/14/2012] [Accepted: 11/15/2012] [Indexed: 02/04/2023]
Abstract
Cornelia de Lange syndrome (CdLS) is a rare multi-system genetic disorder characterised by growth and developmental delay, distinctive facial dysmorphism, limb malformations and multiple organ defects. The disease is caused by mutations in genes responsible for the formation and regulation of cohesin complex. About half of the cases result from mutations in the NIPBL gene coding delangin, a protein regulating the initialisation of cohesion. To date, approximately 250 point mutations have been identified in more than 300 CdLS patients worldwide. In the present study, conducted on a group of 64 unrelated Polish CdLS patients, 25 various NIPBL sequence variants, including 22 novel point mutations, were detected. Additionally, large genomic deletions on chromosome 5p13 encompassing the NIPBL gene locus were detected in two patients with the most severe CdLS phenotype. Taken together, 42 % of patients were found to have a deleterious alteration affecting the NIPBL gene, by and large private ones (89 %). The review of the types of mutations found so far in Polish patients, their frequency and correlation with the severity of the observed phenotype shows that Polish CdLS cases do not significantly differ from other populations.
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Affiliation(s)
- Alina Kuzniacka
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1 str., 80211 Gdansk, Poland
| | - Jolanta Wierzba
- Department of Pediatrics, Hematology, Oncology and Endocrinology, Department of General Nursery, Medical University of Gdansk, Debinki 7 str., 80211 Gdansk, Poland
| | - Magdalena Ratajska
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1 str., 80211 Gdansk, Poland
| | - Beata S. Lipska
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1 str., 80211 Gdansk, Poland
| | - Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1 str., 80211 Gdansk, Poland
| | - Monika Malinowska
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1 str., 80211 Gdansk, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1 str., 80211 Gdansk, Poland
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