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Identification of copy number variants by NGS-based NIPT at low sequencing depth. Eur J Obstet Gynecol Reprod Biol 2020; 256:297-301. [PMID: 33310305 DOI: 10.1016/j.ejogrb.2020.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/20/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To explore the clinical utility of detecting chromosome copy number variants (CNVs) in the fetus by noninvasive prenatal testing (NIPT) using the low-pass whole-genome sequencing. METHODS Eight hundred and seventy-three singleton pregnancies with chromosomal microarray analysis (CMA) available between January 2017 to December 2019 and stored enough plasma sample for NIPT testing were included in this study. The CMA results show that forty-eight pregnancies with CNVs and eight hundred and twenty-five pregnancies are normal. Each pregnancy's plasma sample was blindly tested with NIPT at a depth of 0.51-1.19x for CNVs detection. The performance of the NIPT method for CNVs detection compared with the CMA method is evaluated. RESULTS A total of fifty-two CNVs ranging from 0.1-47.3 Mb identified in forty-eight samples were identified by NIPT, of which thirty-four CNVs were consistent with CMA results. Additionally, eighteen CNVs were missed by NIPT. The overall sensitivity and specificity for the detection of CNVs were 65.38% (95% CI: 51.76%-76.89%) and 97.45% (95% CI: 96.12%-98.35%), respectively. However, for the detection of CNVs larger than 2 Mb and CNVs less than 2Mb, the sensitivities were 81.58% (95% CI: 66.27%-91.09%) and 21.43% (95% CI: 6.84%-48.32%), respectively. CONCLUSION Our study demonstrated that the NIPT might be an alternative method for screening CNVs comparable with other studies. However, CNVs less than 2Mb in length shows poor sensitivity by NIPT. Noninvasive CNVs detection based on the NIPT method still needs more clinical validation studies and technical improvement to achieve clinically acceptable accuracy.
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Thiarawat P, Jahromi BR, Kozyrev DA, Intarakhao P, Teo MK, Choque-Velasquez J, Niemelä M, Hernesniemi J. Are Fetal-Type Posterior Cerebral Arteries Associated With an Increased Risk of Posterior Communicating Artery Aneurysms? Neurosurgery 2020; 84:1306-1312. [PMID: 29788502 DOI: 10.1093/neuros/nyy186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 04/11/2018] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Fetal-type posterior cerebral arteries (F-PCAs) might result in alterations in hemodynamic flow patterns and may predispose an individual to an increased risk of posterior communicating artery aneurysms (PCoAAs). OBJECTIVE To determine the association between PCoAAs and the presence of ipsilateral F-PCAs. METHODS We retrospectively reviewed the radiographic findings from 185 patients harboring 199 PCoAAs that were treated at our institution between 2005 and 2015. Our study population consisted of 4 cohorts: (A) patients with 171 internal carotid arteries (ICAs) harboring unilateral PCoAAs; (B) 171 unaffected ICAs in the same patients from the first group; (C) 28 ICAs of 14 patients with bilateral PCoAAs; and (D) 180 ICAs of 90 patients with aneurysms in other locations. We then determined the presence of ipsilateral F-PCAs and recorded all aneurysm characteristics. RESULTS Group A had the highest prevalence of F-PCAs (42%) compared to 19% in group B, 3% in group C, and 14% in group D (odds ratio A : B = 3.041; A : C = 19.626; and A : D = 4.308; P < .001). PCoAAs were associated with larger diameters of the posterior communicating arteries (median value 1.05 vs 0.86 mm; P = .001). The presence of F-PCAs was associated with larger sizes of the aneurysm necks (median value 3.3 vs 3.0 mm; P = .02). CONCLUSION PCoAAs were associated with a higher prevalence of ipsilateral F-PCAs. This variant was associated with larger sizes of the aneurysm necks but was not associated with the sizes of the aneurysm domes or with their rupture statuses.
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Affiliation(s)
- Peeraphong Thiarawat
- Department of Neurosurgery, Helsinki University Hospital, Helsinki, Finland.,De-partment of Surgery, Naresuan University, Phitsanulok, Thailand
| | | | - Danil A Kozyrev
- Department of Neurosurgery, Helsinki University Hospital, Helsinki, Finland.,Department of Paediatric Neurology and Neurosurgery, North-western State Medical University, St. Petersburg, Russia
| | - Patcharin Intarakhao
- Department of Neurosurgery, Helsinki University Hospital, Helsinki, Finland.,Department of Anesthesiology, Naresuan University, Phitsanulok, Thailand
| | - Mario K Teo
- Bristol Institute of Clinical Neurosciences, North Bristol University Hospital, Bristol, United Kingdom
| | | | - Mika Niemelä
- Department of Neurosurgery, Helsinki University Hospital, Helsinki, Finland
| | - Juha Hernesniemi
- Department of Neurosurgery, Helsinki University Hospital, Helsinki, Finland
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Mei C, Junjvlieke Z, Raza SHA, Wang H, Cheng G, Zhao C, Zhu W, Zan L. Copy number variation detection in Chinese indigenous cattle by whole genome sequencing. Genomics 2019; 112:831-836. [PMID: 31145994 DOI: 10.1016/j.ygeno.2019.05.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/25/2019] [Indexed: 12/15/2022]
Abstract
Copy number variation (CNV) refers to a kind of structural variation, having functional and evolutionary effects on phenotypes. Thus far, further elucidation of the CNVs in different Chinese indigenous cattle breeds by whole genome sequencing have yet not been done. In this study, a comprehensive genomic analysis was performed on 75 cattle individuals including six Chinese indigenous cattle breeds and two non-native specialized beef cattle breeds. Based on the 11,486 CNVRs discovered, population analysis was performed, showed that all the cattle breeds clustered in to three clades, consistent with their lineages Bos taurus, Bos taurus × Bos indicus and Bos indicus. Importantly, a set of CNVRs related genes were found to be associated with the traits of interest, which include meat production or quality (CAST, ACTC1, etc.), adaption (BLA-DQB, EGLN2, etc.) and coat color (KIT, MITF, etc.). These results provide valuable full genome variation resources for Chinese bovine genome research and would be helpful for cattle breeding and selection programs in the future.
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Affiliation(s)
- Chugang Mei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zainaguli Junjvlieke
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Chuping Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wenjuan Zhu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Intracranial Aneurysms: Pathology, Genetics, and Molecular Mechanisms. Neuromolecular Med 2019; 21:325-343. [PMID: 31055715 DOI: 10.1007/s12017-019-08537-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/08/2019] [Indexed: 12/14/2022]
Abstract
Intracranial aneurysms (IA) are local dilatations in cerebral arteries that predominantly affect the circle of Willis. Occurring in approximately 2-5% of adults, these weakened areas are susceptible to rupture, leading to subarachnoid hemorrhage (SAH), a type of hemorrhagic stroke. Due to its early age of onset and poor prognosis, SAH accounts for > 25% of years lost for all stroke victims under the age of 65. In this review, we describe the cerebrovascular pathology associated with intracranial aneurysms. To understand IA genetics, we summarize syndromes with elevated incidence, genome-wide association studies (GWAS), whole exome studies on IA-affected families, and recent research that established definitive roles for Thsd1 (Thrombospondin Type 1 Domain Containing Protein 1) and Sox17 (SRY-box 17) in IA using genetically engineered mouse models. Lastly, we discuss the underlying molecular mechanisms of IA, including defects in vascular endothelial and smooth muscle cells caused by dysfunction in mechanotransduction, Thsd1/FAK (Focal Adhesion Kinase) signaling, and the Transforming Growth Factor β (TGF-β) pathway. As illustrated by THSD1 research, cell adhesion may play a significant role in IA.
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Griessenauer CJ, Farrell S, Sarkar A, Zand R, Abedi V, Holland N, Michael A, Cummings CL, Metpally R, Carey DJ, Goren O, Martin N, Hendrix P, Schirmer CM. Genetic susceptibility to cerebrovascular disease: A systematic review. J Cereb Blood Flow Metab 2018; 38:1853-1871. [PMID: 30182779 PMCID: PMC6259318 DOI: 10.1177/0271678x18797958] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Investigation of genetic susceptibility to cerebrovascular disease has been of growing interest. A systematic review of human studies assessing neurogenomic aspects of cerebrovascular disease was performed according to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement. Any association study exploring genetic variants located in the exome associated with one of the major cerebrovascular diseases with at least 500 subjects was eligible for inclusion. Of 6874 manuscripts identified, 35 studies met the inclusion criteria. Most studies of interest focused on ischemic stroke and cerebrovascular occlusive disease. Large cohort genetic association studies on hemorrhagic cerebrovascular disease were less common. In addition to rare, well-established monogenic conditions with significant risk for cerebrovascular disease, a number of genetic variants are also relevant to cerebrovascular pathogenesis as part of a multifactorial process. The 45 polymorphisms identified were located in genes involved in processes related to endothelial and vascular health (15 (33.4%) variants), plasma lipid metabolism (10 (22.2%) variants), inflammation (9 (20%) variants), coagulation (3 (6.7%) variants), and blood pressure modulation (2 (4.4%) variants), and other (6 (13.3%) variants). This work represents a comprehensive overview of genetic variants in the exome relevant to ischemic and hemorrhagic stroke pathophysiology.
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Affiliation(s)
- Christoph J Griessenauer
- 1 Department of Neurosurgery, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA.,2 Research Institute of Neurointervention, Paracelsus Medical University, Salzburg, Austria
| | - Sean Farrell
- 3 Geisinger Commonwealth School of Medicine, Scranton, PA, USA
| | - Atom Sarkar
- 1 Department of Neurosurgery, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
| | - Ramin Zand
- 4 Department of Neurology, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
| | - Vida Abedi
- 5 Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | - Neil Holland
- 4 Department of Neurology, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
| | - Andrew Michael
- 6 Neuroimaging Analytics Laboratory, Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA, USA
| | - Christopher L Cummings
- 4 Department of Neurology, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
| | | | | | - Oded Goren
- 1 Department of Neurosurgery, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
| | - Neil Martin
- 1 Department of Neurosurgery, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
| | - Philipp Hendrix
- 8 Department of Neurosurgery, Saarland University Medical Center and Saarland University Faculty of Medicine, Homburg/Saar, Germany
| | - Clemens M Schirmer
- 1 Department of Neurosurgery, Geisinger Commonwealth School of Medicine, Geisinger, Danville, PA, USA
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Zhou S, Dion PA, Rouleau GA. Genetics of Intracranial Aneurysms. Stroke 2018; 49:780-787. [DOI: 10.1161/strokeaha.117.018152] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/06/2017] [Accepted: 12/20/2017] [Indexed: 01/23/2023]
Affiliation(s)
- Sirui Zhou
- From the Montréal Neurological Institute and Hospital (S.Z., P.A.D., G.A.R.) and Department of Neurology and Neurosurgery (P.A.D., G.A.R.), McGill University, Québec, Canada; and Department of Medicine, Université de Montréal, Québec, Canada (S.Z.)
| | - Patrick A. Dion
- From the Montréal Neurological Institute and Hospital (S.Z., P.A.D., G.A.R.) and Department of Neurology and Neurosurgery (P.A.D., G.A.R.), McGill University, Québec, Canada; and Department of Medicine, Université de Montréal, Québec, Canada (S.Z.)
| | - Guy A. Rouleau
- From the Montréal Neurological Institute and Hospital (S.Z., P.A.D., G.A.R.) and Department of Neurology and Neurosurgery (P.A.D., G.A.R.), McGill University, Québec, Canada; and Department of Medicine, Université de Montréal, Québec, Canada (S.Z.)
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Wang S, Dai D, Kolumam Parameswaran P, Kadirvel R, Ding YH, Robertson AM, Kallmes DF. Rabbit aneurysm models mimic histologic wall types identified in human intracranial aneurysms. J Neurointerv Surg 2017; 10:411-415. [PMID: 28768819 PMCID: PMC5796872 DOI: 10.1136/neurintsurg-2017-013264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/23/2022]
Abstract
Background Semiquantitative scales correlate histopathologic findings in the walls of human aneurysms with rupture status. Objective To apply a semiquantitative scale to the rabbit elastase-induced aneurysm model to determine whether rabbit histologic types mimic the full range of histologic subtypes of humans. Materials and methods Twenty-seven elastase-induced female rabbit aneurysms were studied, harvested at 2 weeks (n=5) and 12 weeks (n=22). Paraffin-embedded sections received hematoxylin-eosin and Verhoeff-Van Gieson staining. Immunohistochemistry was performed for α-smooth muscle actin and CD31 for endothelial cells. A semiquantitative scale was used for scoring based on human aneurysm tissue, divided into four subtypes according to cellular and extracellular matrix findings: type A, linear organized smooth muscle cells (SMCs) and intact endothelium; type B, thickened wall with disorganized, proliferating SMCs; type C, thick, collagenized and hypocellular wall with or without organizing thrombosis, and type D, extremely thin, hypocellular wall. Separate scoring was performed of the aneurysm neck and proximal and distal zones. Results Findings compatible with all subtypes of human aneurysm tissue were identified. Types A and C were found in 13 (48%) and 11 (41%) of 27 aneurysms and in the proximal and distal wall at both time points. Type B was found in 16 aneurysms (59%), exclusively at the neck at both time points; type D, in 14 aneurysms (52%), exclusively at proximal and distal zones of 12-week aneurysms. Conclusions The wall of elastase-induced rabbit aneurysm demonstrates histologic findings similar to the four categories of human cerebral aneurysms based on cellular and extracellular wall content.
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Affiliation(s)
- Shunli Wang
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Pathology, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Daying Dai
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | - Yong-Hong Ding
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Anne M Robertson
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, USA
| | - David F Kallmes
- Department of Radiology, Mayo Clinic, Rochester, Minnesota, USA
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