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Skvortsova L, Abdikerim S, Yergali K, Mit N, Perfilyeva A, Omarbayeva N, Zhunussova A, Kachiyeva Z, Sadykova T, Bekmanov B, Kaidarova D, Djansugurova L, Zhunussova G. Association of Genetic Markers with the Risk of Early-Onset Breast Cancer in Kazakh Women. Genes (Basel) 2024; 15:108. [PMID: 38254997 PMCID: PMC10815330 DOI: 10.3390/genes15010108] [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] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Breast cancer is a global health problem. It is an age-dependent disease, but cases of early-onset breast cancer (eBC) are gradually increasing. There are many unresolved questions regarding eBC risk factors, mechanisms of development and screening. Only 10% of eBC cases are due to mutations in the BRCA1/BRCA2 genes, and 90% have a more complex genetic background. This poses a significant challenge to timely cancer detection in young women and highlights the need for research and awareness. Therefore, identifying genetic risk factors for eBC is essential to solving these problems. This study represents an association analysis of 144 eBC cases and 163 control participants to identify genetic markers associated with eBC risks in Kazakh women. We performed a two-stage approach in association analysis to assess genetic predisposition to eBC. First-stage genome-wide association analysis revealed two risk intronic loci in the CHI3L2 gene (p = 5.2 × 10-6) and MGAT5 gene (p = 8.4 × 10-6). Second-stage exonic polymorphisms haplotype analysis showed significant risks for seven haplotypes (p < 9.4 × 10-4). These results point to the importance of studying medium- and low-penetrant genetic markers in their haplotype combinations for a detailed understanding of the role of detected genetic markers in eBC development and prediction.
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Affiliation(s)
- Liliya Skvortsova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Anastassiya Perfilyeva
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Nazgul Omarbayeva
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
| | - Zulfiya Kachiyeva
- Research Institute of Applied and Fundamental Medicine, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan;
| | - Tolkyn Sadykova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Bakhytzhan Bekmanov
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Dilyara Kaidarova
- Breast Cancer Department, Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan; (N.O.); (T.S.); (D.K.)
- Oncology Department, Asfendiyarov Kazakh National Medical University, Almaty 050012, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
- Department of Molecular Biology and Genetics, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan
| | - Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan; (L.S.); (S.A.); (K.Y.); (N.M.); (A.P.); (A.Z.); (B.B.); (L.D.)
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Altynova N, Khamdiyeva O, Garshin A, Baratzhanova G, Amirgaliyeva A, Seisenbayeva A, Abylkassymova G, Yergali K, Tolebaeva A, Skvortsova L, Zhunussova G, Bekmanov B, Cakir-Kiefer C, Djansugurova L. Case-Control Study of the Association between Single Nucleotide Polymorphisms of Genes Involved in Xenobiotic Detoxification and Antioxidant Protection with the Long-Term Influence of Organochlorine Pesticides on the Population of the Almaty Region. Toxics 2023; 11:948. [PMID: 38133349 PMCID: PMC10747153 DOI: 10.3390/toxics11120948] [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] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
The association of genetic polymorphisms with the individual sensitivity of humans to the action of pesticide pollution is being actively studied in the world. The aim of this study was a molecular epidemiological analysis of candidate polymorphisms of genes involved in pesticide metabolism, detoxification, and antioxidant protection. Some of the selected polymorphisms also relate to susceptibility to cancer and cardiovascular, respiratory, and immune system diseases in individuals exposed to pesticides for a long time. For a case-control study of a unique cohort of people exposed to organochlorine pesticides for 10 years or more were chosen, a control cohort was selected that matched with the experimental group by the main population characteristics. PCR-PRLF and genome-wide microarray genotyping (GWAS) methods were used. We identified 17 polymorphisms of xenobiotic detoxification genes and 27 polymorphisms of antioxidant defense genes, which had a significantly high statistical association with the negative impact of chronic pesticide intoxication on human health. We also found 17 polymorphisms of xenobiotic detoxification genes and 12 polymorphisms of antioxidant defense genes that have a protective effect. Data obtained added to the list of potential polymorphisms that define a group at high risk or resistant to the negative effects of pesticides.
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Affiliation(s)
- Nazym Altynova
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan
| | - Ozada Khamdiyeva
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Aleksandr Garshin
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan
| | - Gulminyam Baratzhanova
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan
- INRAE, UR AFPA, USC 340, University of Lorraine, Nancy F-54000, France;
| | - Almira Amirgaliyeva
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Akerke Seisenbayeva
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Gulnar Abylkassymova
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Kanagat Yergali
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Anar Tolebaeva
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Liliya Skvortsova
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Gulnur Zhunussova
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
| | - Bakhytzhan Bekmanov
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan
| | | | - Leyla Djansugurova
- Institute of Genetics and Physiology, Al-Farabi Avenue 93, Almaty 050060, Kazakhstan; (N.A.); (A.G.); (A.A.); (A.S.); (G.A.); (K.Y.); (A.T.); (L.S.); (G.Z.); (B.B.)
- Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Avenue 71, Almaty 050040, Kazakhstan
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Amandykova M, Akhatayeva Z, Kozhakhmet A, Kapassuly T, Orazymbetova Z, Yergali K, Khamzin K, Iskakov K, Dossybayev K. Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat-Wool Sheep Breed. Genes (Basel) 2023; 14:1988. [PMID: 38002931 PMCID: PMC10671688 DOI: 10.3390/genes14111988] [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] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat-wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat-wool sheep using the Illumina iScan® system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat-wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH1-2 Mb were much higher than ROH2-4 Mb and ROH8-16 Mb in the three sheep populations. Most of individuals had small number of ROH>16 Mb. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated FROH presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (BMP2, BMPR2, BMPRIB, CLOCK, KDM2B, TIAM1, TASP1, MYBPC1, MYOM1, and CACNA2D1), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat-wool sheep breed.
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Affiliation(s)
- Makpal Amandykova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zhanerke Akhatayeva
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Altynay Kozhakhmet
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Tilek Kapassuly
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
| | - Zarina Orazymbetova
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
| | - Kanagat Yergali
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kadyrzhan Khamzin
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Iskakov
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
| | - Kairat Dossybayev
- Laboratory of Animal Genetics and Cytogenetics, Institute of Genetics and Physiology SC MSHE RK, Al-Farabi Ave. 93, Almaty 050060, Kazakhstan; (M.A.); (Z.A.); (A.K.); (T.K.); (Z.O.); (K.Y.); (K.I.)
- Department of Molecular Biology and Genetics, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi Ave. 71, Almaty 050042, Kazakhstan
- Laboratory of Molecular Genetics, Kazakh Research Institute of Livestock and Fodder Production, Zhandosov Str. 51, Almaty 050035, Kazakhstan;
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Zhunussova G, Omarbayeva N, Kaidarova D, Abdikerim S, Mit N, Kisselev I, Yergali K, Zhunussova A, Goncharova T, Abdrakhmanova A, Djansugurova L. Determination of genetic predisposition to early breast cancer in women of Kazakh ethnicity. Oncotarget 2023; 14:860-877. [PMID: 37791908 PMCID: PMC10549772 DOI: 10.18632/oncotarget.28518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 05/06/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023] Open
Abstract
Breast cancer (BC) is the most common type of cancer among women in Kazakhstan. To date, little data are available on the spectrum of genetic variation in Kazakh women with BC. We aimed to identify population-specific genetic markers associated with the risk of developing early-onset BC and test their association with clinical and prognostic factors. The study included 224 Kazakh women diagnosed with BC (≤40 age). Entire coding regions (>1700 exons) and the flanking noncoding regions of 94 cancer-associated genes were sequenced from blood DNA using MiSeq platform. We identified 38 unique pathogenic variants (PVs) in 13 different cancer-predisposing genes among 57 patients (25.4%), of which 6 variants were novel. In total, 12 of the 38 distinct PVs were detected recurrently, including BRCA1 c.5266dup, c.5278-2del, and c.2T>C, and BRCA2 c.9409dup and c.9253del that may be founder in this population. BRCA1 carriers were significantly more likely to develop triple-negative BC (OR = 6.61, 95% CI 2.44-17.91, p = 0.0002) and have family history of BC (OR = 3.17, 95% CI 1.14-8.76, p = 0.03) compared to non-carriers. This study allowed the identification of PVs specific to early-onset BC, which may be used as a foundation to develop regional expertise and diagnostic tools for early detection of BC in young Kazakh women.
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Affiliation(s)
- Gulnur Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
- Al-Farabi Kazakh National University, Almaty 050060, Kazakhstan
| | - Nazgul Omarbayeva
- Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty 050060, Kazakhstan
| | - Dilyara Kaidarova
- Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty 050060, Kazakhstan
| | - Saltanat Abdikerim
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
- Al-Farabi Kazakh National University, Almaty 050060, Kazakhstan
| | - Natalya Mit
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | - Ilya Kisselev
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | - Kanagat Yergali
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | - Aigul Zhunussova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
| | | | - Aliya Abdrakhmanova
- Kazakh Institute of Oncology and Radiology, Almaty 050060, Kazakhstan
- Asfendiyarov Kazakh National Medical University, Almaty 050060, Kazakhstan
| | - Leyla Djansugurova
- Laboratory of Molecular Genetics, Institute of Genetics and Physiology, Almaty 050060, Kazakhstan
- Al-Farabi Kazakh National University, Almaty 050060, Kazakhstan
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Altynova N, Khamdiyeva O, Zhaniyazov Z, Garshin A, Baratzhanova G, Amirgalieva A, Yergali K, Artygaliyeva D, Talgatbekova D, Tokmurzina S, Abdullayeva M, Zhunussova G, Djansugurova L. A genome-wide association study for different types allergic diseases. ijbch 2022. [DOI: 10.26577/ijbch.2022.v15.i2.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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