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Hu Y, Li K, Swahn H, Ordoukhanian P, Head SR, Natarajan P, Woods AK, Joseph SB, Johnson KA, Lotz MK. Transcriptomic analyses of joint tissues during osteoarthritis development in a rat model reveal dysregulated mechanotransduction and extracellular matrix pathways. Osteoarthritis Cartilage 2023; 31:199-212. [PMID: 36354073 PMCID: PMC9892293 DOI: 10.1016/j.joca.2022.10.003] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/20/2022] [Accepted: 10/03/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Transcriptomic changes in joint tissues during the development of osteoarthritis (OA) are of interest for the discovery of biomarkers and mechanisms of disease. The objective of this study was to use the rat medial meniscus transection (MMT) model to discover stage and tissue-specific transcriptomic changes. DESIGN Sham or MMT surgeries were performed in mature rats. Cartilage, menisci and synovium were scored for histopathological changes at 2, 4 and 6 weeks post-surgery and processed for RNA-sequencing. Differentially expressed genes (DEG) were used to identify pathways and mechanisms. Published transcriptomic datasets from animal models and human OA were used to confirm and extend present findings. RESULTS The total number of DEGs was already high at 2 weeks (723 in meniscus), followed by cartilage (259) and synovium (42) and declined to varying degrees in meniscus and synovium but increased in cartilage at 6 weeks. The most upregulated genes included tenascins. The 'response to mechanical stimulus' and extracellular matrix-related pathways were enriched in both cartilage and meniscus. Pathways that were enriched in synovium at 4 weeks indicate processes related to synovial hyperplasia and fibrosis. Synovium also showed upregulation of IL-11 and several MMPs. The mechanical stimulus pathway included upregulation of the mechanoreceptors PIEZO1, PIEZO2 and TRPV4 and nerve growth factor. Analysis of data from prior RNA-sequencing studies of animal models and human OA support these findings. CONCLUSION These results indicate several shared pathways that are affected during OA in cartilage and meniscus and support the role of mechanotransduction and other pathways in OA pathogenesis.
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Affiliation(s)
- Y Hu
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA; Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - K Li
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - H Swahn
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA
| | - P Ordoukhanian
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, CA, 92037, USA
| | - S R Head
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, CA, 92037, USA
| | - P Natarajan
- Center for Computational Biology & Bioinformatics and Genomics Core, Scripps Research, La Jolla, CA, 92037, USA
| | - A K Woods
- Calibr, a Division of Scripps Research, La Jolla, CA, 92037, USA
| | - S B Joseph
- Calibr, a Division of Scripps Research, La Jolla, CA, 92037, USA
| | - K A Johnson
- Calibr, a Division of Scripps Research, La Jolla, CA, 92037, USA
| | - M K Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, 92037, USA.
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2
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Modena BD, Kurian SM, Gaber LW, Waalen J, Su AI, Gelbart T, Mondala TS, Head SR, Papp S, Heilman R, Friedewald JJ, Flechner S, Marsh CL, Sung RS, Shidban H, Chan L, Abecassis MM, Salomon DR. Gene Expression in Biopsies of Acute Rejection and Interstitial Fibrosis/Tubular Atrophy Reveals Highly Shared Mechanisms That Correlate With Worse Long-Term Outcomes. Am J Transplant 2016; 16:1982-98. [PMID: 26990570 PMCID: PMC5501990 DOI: 10.1111/ajt.13728] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [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: 09/04/2015] [Revised: 01/08/2016] [Accepted: 01/13/2016] [Indexed: 01/25/2023]
Abstract
Interstitial fibrosis and tubular atrophy (IFTA) is found in approximately 25% of 1-year biopsies posttransplant. It is known that IFTA correlates with decreased graft survival when histological evidence of inflammation is present. Identifying the mechanistic etiology of IFTA is important to understanding why long-term graft survival has not changed as expected despite improved immunosuppression and dramatically reduced rates of clinical acute rejection (AR) (Services UDoHaH. http://www.ustransplant.org/annual_reports/current/509a_ki.htm). Gene expression profiles of 234 graft biopsy samples were obtained with matching clinical and outcome data. Eighty-one IFTA biopsies were divided into subphenotypes by degree of histological inflammation: IFTA with AR, IFTA with inflammation, and IFTA without inflammation. Samples with AR (n = 54) and normally functioning transplants (TX; n = 99) were used in comparisons. A novel analysis using gene coexpression networks revealed that all IFTA phenotypes were strongly enriched for dysregulated gene pathways and these were shared with the biopsy profiles of AR, including IFTA samples without histological evidence of inflammation. Thus, by molecular profiling we demonstrate that most IFTA samples have ongoing immune-mediated injury or chronic rejection that is more sensitively detected by gene expression profiling. These molecular biopsy profiles correlated with future graft loss in IFTA samples without inflammation.
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Affiliation(s)
- B. D. Modena
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - S. M. Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA,DNA Microarray and Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA
| | - L. W. Gaber
- Department of Pathology, The Methodist Hospital, Houston, TX
| | - J. Waalen
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - A. I. Su
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - T. Gelbart
- DNA Microarray and Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA
| | - T. S. Mondala
- DNA Microarray and Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA
| | - S. R. Head
- DNA Microarray and Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA
| | - S. Papp
- DNA Microarray and Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA
| | - R. Heilman
- Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Department of Transplant Nephrology, Mayo Clinic, Phoenix, AZ
| | - J. J. Friedewald
- Northwestern Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - S.M. Flechner
- Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Glickman Urology and Kidney Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - C. L. Marsh
- Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Scripps Center for Organ and Cell Transplantation, Scripps Health, La Jolla, CA
| | - R. S. Sung
- Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Section of Transplant Surgery, University of Michigan, Ann Arbor, MI
| | - H. Shidban
- Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Department of Surgery, St Vincent Medical Center, Los Angeles, CA
| | - L. Chan
- Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Department of Transplant/Nephrology, University of Colorado, Aurora, CO
| | - M. M. Abecassis
- Northwestern Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - D. R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA,DNA Microarray and Next Generation Sequencing Core, The Scripps Research Institute, La Jolla, CA,Transplant Genomics Collaborative Group (TGCG), La Jolla, CA,Corresponding author: Daniel R. Salomon,
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3
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Kurian SM, Williams AN, Gelbart T, Campbell D, Mondala TS, Head SR, Horvath S, Gaber L, Thompson R, Whisenant T, Lin W, Langfelder P, Robison EH, Schaffer RL, Fisher JS, Friedewald J, Flechner SM, Chan LK, Wiseman AC, Shidban H, Mendez R, Heilman R, Abecassis MM, Marsh CL, Salomon DR. Molecular classifiers for acute kidney transplant rejection in peripheral blood by whole genome gene expression profiling. Am J Transplant 2014; 14:1164-72. [PMID: 24725967 PMCID: PMC4439107 DOI: 10.1111/ajt.12671] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [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: 09/09/2013] [Revised: 12/30/2013] [Accepted: 01/15/2014] [Indexed: 01/25/2023]
Abstract
There are no minimally invasive diagnostic metrics for acute kidney transplant rejection (AR), especially in the setting of the common confounding diagnosis, acute dysfunction with no rejection (ADNR). Thus, though kidney transplant biopsies remain the gold standard, they are invasive, have substantial risks, sampling error issues and significant costs and are not suitable for serial monitoring. Global gene expression profiles of 148 peripheral blood samples from transplant patients with excellent function and normal histology (TX; n = 46), AR (n = 63) and ADNR (n = 39), from two independent cohorts were analyzed with DNA microarrays. We applied a new normalization tool, frozen robust multi-array analysis, particularly suitable for clinical diagnostics, multiple prediction tools to discover, refine and validate robust molecular classifiers and we tested a novel one-by-one analysis strategy to model the real clinical application of this test. Multiple three-way classifier tools identified 200 highest value probesets with sensitivity, specificity, positive predictive value, negative predictive value and area under the curve for the validation cohort ranging from 82% to 100%, 76% to 95%, 76% to 95%, 79% to 100%, 84% to 100% and 0.817 to 0.968, respectively. We conclude that peripheral blood gene expression profiling can be used as a minimally invasive tool to accurately reveal TX, AR and ADNR in the setting of acute kidney transplant dysfunction.
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Affiliation(s)
- S. M. Kurian
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - A. N. Williams
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - T. Gelbart
- DNA Array Core, The Scripps Research Institute, La Jolla, CA
| | - D. Campbell
- DNA Array Core, The Scripps Research Institute, La Jolla, CA
| | - T. S. Mondala
- DNA Array Core, The Scripps Research Institute, La Jolla, CA
| | - S. R. Head
- DNA Array Core, The Scripps Research Institute, La Jolla, CA
| | - S. Horvath
- Department of Biostatistics, University of California, Los Angeles, CA
| | - L. Gaber
- The Texas Medical Center, Houston, TX
| | - R. Thompson
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - T. Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - W. Lin
- Department of Biostatistics, University of California, Los Angeles, CA
| | - P. Langfelder
- Department of Biostatistics, University of California, Los Angeles, CA
| | - E. H. Robison
- DNA Array Core, The Scripps Research Institute, La Jolla, CA
| | - R. L. Schaffer
- Scripps Center for Organ Transplantation, Scripps Health, La Jolla, CA
| | - J. S. Fisher
- Scripps Center for Organ Transplantation, Scripps Health, La Jolla, CA
| | - J. Friedewald
- Northwestern Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - S. M. Flechner
- Glickman Urological Institute, The Cleveland Clinic, Cleveland, OH
| | - L. K. Chan
- University of Colorado Hospital, Transplant Services, Aurora, CO
| | - A. C. Wiseman
- University of Colorado Hospital, Transplant Services, Aurora, CO
| | - H. Shidban
- St. Vincent Medical Center, Kidney Transplantation, Los Angeles, CA
| | - R. Mendez
- St. Vincent Medical Center, Kidney Transplantation, Los Angeles, CA
| | - R. Heilman
- Department of Medicine, Mayo Clinic Arizona and Mayo Clinic College of Medicine, Phoenix, AZ
| | - M. M. Abecassis
- Northwestern Comprehensive Transplant Center, Northwestern University, Chicago, IL
| | - C. L. Marsh
- Scripps Center for Organ Transplantation, Scripps Health, La Jolla, CA
| | - D. R. Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA,Scripps Center for Organ Transplantation, Scripps Health, La Jolla, CA,Corresponding author: Daniel R. Salomon,
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Kunicki TJ, Williams SA, Salomon DR, Harrison P, Crisler P, Nakagawa P, Mondala TS, Head SR, Nugent DJ. Genetics of platelet reactivity in normal, healthy individuals. J Thromb Haemost 2009; 7:2116-22. [PMID: 19740098 DOI: 10.1111/j.1538-7836.2009.03610.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
BACKGROUND The Platelet Function Analyzer-100 (PFA-100) is widely used to measure platelet reactivity in whole blood under high shear. OBJECTIVE To characterize the genetic component of platelet reactivity among normal individuals, using the PFA-100. METHODS We compared baseline platelet reactivity with sex, age, platelet count, hematocrit, plasma von Willebrand factor antigen (VWF:Ag), and alleles of seven candidate genes: integrin subunits alpha2 (ITGA2) and beta3 (ITGB3), platelet glycoproteins GPIbalpha (GP1BA) and GPVI (GP6), purinogenic receptors (P2RY1 and P2RY12) and cyclooxygenase-1 (COX1). RESULTS Based on linear and logistic regression models, we report an inverse correlation between baseline closure time (CT) initiated by collagen plus epinephrine (CEPI) and plasma VWF:Ag level, ITGA2 807T and P2RY1 893C, and an inverse correlation between baseline CT initiated by collagen plus adenosine diphosphate (CADP) and P2RY1 893C or GP1BA -5C. CONCLUSIONS These results indicate that genetic polymorphisms in ITGA2 and P2RY1 combine with plasma VWF:Ag levels to modulate baseline platelet reactivity in response to collagen plus EPI, while genetic differences in P2RY1 and GP1BA significantly effect platelet responses to collagen plus ADP. Our results demonstrate that the PFA-100 can be used to evaluate the effects of genetic predictors of platelet function.
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Affiliation(s)
- T J Kunicki
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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5
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Kunicki TJ, Baronciani L, Canciani MT, Gianniello F, Head SR, Mondala TS, Salomon DR, Federici AB. An association of candidate gene haplotypes and bleeding severity in von Willebrand disease type 2A, 2B, and 2M pedigrees. J Thromb Haemost 2006; 4:137-47. [PMID: 16409463 DOI: 10.1111/j.1538-7836.2005.01675.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
We analyzed the association of bleeding severity with candidate gene haplotypes within pedigrees of 11 index cases of von Willebrand disease (VWD) type 2 (two type 2A, three type 2B and six type 2M), using the QTL Association model (MENDEL 5.5). In addition to the 11 index cases, these pedigrees included 47 affected and 49 unaffected relatives, as defined by VWF mutations and/or phenotype. A bleeding severity score was derived from a detailed history and adjusted for age. Donors were genotyped using a primer extension method, and eight candidate genes were selected for analysis. VWF antigen (or ristocetin cofactor activity) levels had the strongest influence on bleeding severity score. After Bonferroni correction for multiple testing, only ITGA2 promoter haplotype -52T was associated with an increased bleeding severity score (P < 0.01). This association remained statistically significant when the three type 2B pedigrees were excluded (P = 0.012) or when gender-specific bleeding categories were excluded (P < 0.01). The major haplotypes of seven other candidate genes, GP1BA, ITGA2B, ITGB3, GP6, VWF, FGB, and IL6, were not associated with bleeding severity. These results establish that genetic differences in the expression of the integrin subunit alpha2 can influence the bleeding phenotype of VWD type 2 and complement our previous findings in VWD type 1. Genetically controlled attenuation of platelet collagen receptor expression can influence risk for morbidity in clinical settings where hemostasis is compromised.
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Affiliation(s)
- T J Kunicki
- Department of Molecular and Experimental Medicine, The Division of Experimental Hemostasis and Thrombosis, The Scripps Research Institute, La Jolla, CA 92037, USA.
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6
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Chismar JD, Mondala T, Fox HS, Roberts E, Langford D, Masliah E, Salomon DR, Head SR. Analysis of result variability from high-density oligonucleotide arrays comparing same-species and cross-species hybridizations. Biotechniques 2002; 33:516-8, 520, 522 passim. [PMID: 12238761 DOI: 10.2144/02333st01] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
There exists a significant limitation in the variety of organismsfor which microarrays have been developed because of a lack of genomic sequence data. A near-term solution to this limitation is to use microarrays designed for one species to analyze RNA samples from closely related species. The assumption is that conservation of gene sequences between species will be sufficient to generate a reasonable amount of good-quality data. While there have been relatively few published reports describing the use of microarrays for cross-species hybridizations, this technique is potentially a powerful tool for understanding genomics in model organisms such as nonhuman primates. Here we describe the analysis and comparison of hybridization characteristics and data variability from a set of cross-species (rhesus macaque) and same-species (human) hybridization experiments using human high-density Affymetrix oligonucleotide arrays. The data reveal that a large fraction of probe sets are effective at transcript detection in the cross-species hybridization, validating the application of cross-species hybridizations for nonhuman primate genomics research.
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Affiliation(s)
- J D Chismar
- Department of Shared Services, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Abstract
DNA chip arrays hold considerable promise for diagnostic sequencing of polymerase chain reaction (PCR) products. To date, however, arrays have been relatively expensive, complex to use and difficult to interpret, preventing their adaptation to the clinical lab. A moderate density array method has been developed that enables efficient, easy-to-interpret and robust solid-phase PCR product sequencing. Here, the results of Mycobacterium tuberculosis rifampin resistance mutation detection by primer-extension-based sequence scanning of the rpo B gene of M. tuberculosis are presented. Rifampin resistant clinical isolates were identified in as little as 1 h post PCR amplification with visual results detection.
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Affiliation(s)
- S R Head
- Alpha Center, Orchid Biocomputer, Inc., Hopkins Bayview Research Campus, 5210 Eastern Avenue, Baltimore, Maryland, 21224, USA
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Head SR, Rogers YH, Parikh K, Lan G, Anderson S, Goelet P, Boyce-Jacino MT. Nested genetic bit analysis (N-GBA) for mutation detection in the p53 tumor suppressor gene. Nucleic Acids Res 1997; 25:5065-71. [PMID: 9396817 PMCID: PMC147127 DOI: 10.1093/nar/25.24.5065] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
There is a growing and significant demand for reliable, simple and sensitive methods for repeated scanning of a given gene or gene fragment for detection and characterization of mutations. Solid-phase sequencing by single base primer extension of nested GBATM primers on miniaturized DNA arrays can be used to effectively scan targeted sequences for missense, insertion and deletion mutations. This paper describes the use of N-GBA arrays designed to scan the sequence of a 33 base region of exon 8 of the p53 gene (codons 272-282) encompassing a hot spot for mutations associated with the development of cancer. Synthetic DNA templates containing various missense, insertion and deletion mutations, as well as DNA prepared from pancreatic and biliary tumor cells, were genotyped using the exon 8 arrays.
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Affiliation(s)
- S R Head
- Molecular Tool, Inc., Alpha Center, Hopkins Bayview Research Campus, 5210 Eastern Avenue, Baltimore, MD 21224, USA.
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Head SR, Grimberg B, Chesar J, Soudry M. [Magnuson-Stack operation for chronic anterior shoulder instability]. Harefuah 1996; 130:300-4, 358. [PMID: 8707170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Between the years 1975-1992 we operated on 30 cases of recurrent anterior dislocation of the shoulder by the Magnuson-Stack procedure, using the subscapularis tendon. 23 patients (25 shoulders) have since been followed for an average of 5 years. We developed a comprehensive shoulder rating scale to evaluate functional status of involved shoulders. By this rating system the results were excellent in 73.9% of the cases, good in 17.4% and fair in 8.7%. The operation is technically simple, rapid, had no complications and is at least as effective as other operations.
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Affiliation(s)
- S R Head
- Dept. of Orthopedic Surgery and Traumatology, Western Galilee Medical Center, Nahariya and Technion Faculty of Medicine, Haifa
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