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Azarsiz E, Karaca N, Karaca E, Aksu G, Genel F, Gulez N, Ozen S, Kutukculer N. Eight years of follow-up experience in children with mendelian susceptibility to mycobacterial disease and review of the literature. Asian Pac J Allergy Immunol 2023; 41:372-378. [PMID: 33638623 DOI: 10.12932/ap-271219-0726] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Mendelian susceptibility to mycobacterial disease (MSMD) is a rare primary immunodeficiency, caused by non-tuberculous mycobacteria or Bacillus Calmette-Guerin (BCG) vaccine and characterized by severe diseases in childhood. OBJECTIVE In this study, we examined eight years followed-up 12 Turkish children with genetically proven MSMD and we tried to evaluate the survival rate with succesfull disease management, rate of consanguinity, molecular, cellular and clinical features of patients. In addition, we wanted to emphasize the importance of early diagnosis before administration of BCG vaccine in countries where this vaccine is routinely used. METHODS Twelve patients diagnosed with molecular studies [IFNγR1 complete (n = 1), IFNγR2 partial (n = 3), IL12Rβ1 (n = 6), NEMO (n = 1), STAT1 mutation (n = 1)] were included. RESULTS Ten patients (83%) were born from consanguineous parents and frequency of family history for the primary immunodeficiency was 58% (n = 7). All the cases had been immunized with BCG vaccine (Mycobacterium bovis) due to lack of early diagnosis. Two patients had BCG-itis and four patients had "BCG-osis". Survival rate was 75% after successful disease management with antibiotics, anti-tuberculous agents and recombinant IFN-γ. CONCLUSIONS It was concluded that MSMD must be differentiated from different forms of primary immunodeficiencies, so clinicians should be aware of MSMD especially in patients with BCG vaccine complications and non-tuberculous mycobacterial infection.
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Affiliation(s)
- Elif Azarsiz
- Department of Clinical Biochemistry, Ege University, Izmir, Turkey
| | - Neslihan Karaca
- Department of Pediatric Allergy and Immunology, Ege University, Izmir, Turkey
| | - Emin Karaca
- Department of Genetics, Ege University, Izmir, Turkey
| | - Guzide Aksu
- Department of Pediatric Allergy and Immunology, Ege University, Izmir, Turkey
| | - Ferah Genel
- Department of Pediatric Allergy and Immunology, Dr Behcet Uz Children's Hospital, Izmir, Turkey
| | - Nesrin Gulez
- Department of Pediatric Allergy and Immunology, Dr Behcet Uz Children's Hospital, Izmir, Turkey
| | - Selime Ozen
- Department of Pediatric Allergy and Immunology, Dr Behcet Uz Children's Hospital, Izmir, Turkey
| | - Necil Kutukculer
- Department of Pediatric Allergy and Immunology, Ege University, Izmir, Turkey
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Yıldırım AT, Gülen H, Türkmen H, Özek G, Oymak Y, Durmaz B, Karaca E. Successful Treatment of a Child with Hemoglobin Hammersmith with Hematopoietic Stem Cell Transplantation. Hemoglobin 2023; 47:137-139. [PMID: 37605549 DOI: 10.1080/03630269.2023.2219007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 05/22/2023] [Indexed: 08/23/2023]
Abstract
Hemoglobin (Hb) Hammersmith, formed by serine substitution for phenylalanine at residue 42 in the beta-globin chain, is a very rare variant of unstable hemoglobin with low oxygen affinity. For patients with hemoglobinopathies, it is well-established that hematopoietic stem cell transplantation provides a complete cure, but the literature on its role for those with Hb Hammersmith is limited. A seven-month-old girl who was examined for anemia and splenomegaly was followed up for congenital hemolytic anemia. The patient with visible cyanosis of the lips and whose p50 was low in blood gas was diagnosed with Hb Hammersmith through the DNA sequence analysis. During the follow-up, frequent blood transfusions had to be given due to anemia aggravated by infections. Following a successful hematopoietic stem cell transplant from an HLA-matched sibling, the patient completely recovered from Hb Hammersmith. The case is presented because of its rarity.
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Affiliation(s)
- Ayşen Türedi Yıldırım
- Department of Pediatric Hematology and Oncology, Manisa Celal Bayar University, Manisa, Turkey
| | - Hüseyin Gülen
- Department of Pediatric Hematology and Oncology, Manisa Celal Bayar University, Manisa, Turkey
| | - Hülya Türkmen
- Department of Pediatric Hematology and Oncology, Manisa Celal Bayar University, Manisa, Turkey
| | - Gülcihan Özek
- Department of Pediatric Hematology and Oncology, Pediatric Bone Marrow Transplant Unit, Ege University, İzmir, Turkey
| | - Yeşim Oymak
- Department of Pediatric Hematology and Oncology, Pediatric Bone Marrow Transplant Unit, Ege University, İzmir, Turkey
| | - Burak Durmaz
- Department of Medical Genetics, Ege University, İzmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Ege University, İzmir, Turkey
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Karaca E, Byrne PJP, Hasnip PJ, Probert MIJ. Cr[Formula: see text]AlN and the search for the highest temperature superconductor in the M[Formula: see text]AX family. Sci Rep 2023; 13:6576. [PMID: 37085557 PMCID: PMC10121671 DOI: 10.1038/s41598-023-33517-0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023] Open
Abstract
We have developed a high-throughput computational method to predict the superconducting transition temperature in stable hexagonal M[Formula: see text]AX phases, and applied it to all the known possible choices for M (M: Sc, Ti, V, Cr, Mn, Fe, Y, Zr, Nb, Mo, Lu, Hf and Ta). We combine this with the best candidates for A (A: Al, Cu, Ge and Sn ) and X (X: C and N) from our previous work, and predict T[Formula: see text] for 60 M[Formula: see text]AX-phase materials, 53 of which have never been studied before. From all of these, we identify Cr[Formula: see text]AlN as the best candidate for the highest T[Formula: see text], and confirm its high T[Formula: see text] with more detailed density functional theory electron-phonon coupling calculations. Our detailed calculations predict [Formula: see text] = 14.8 K for Cr[Formula: see text]AlN, which is significantly higher than any [Formula: see text] value known or predicted for any material in the M[Formula: see text]AX family to date.
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Affiliation(s)
- E. Karaca
- Department of Physics, University of York, York, YO10 5DD UK
- Sakarya University, Biomedical, Magnetic and Semiconductor Materials Research Center (BIMAS-RC), 54187 Sakarya, Turkey
| | - P. J. P. Byrne
- Department of Physics, University of York, York, YO10 5DD UK
| | - P. J. Hasnip
- Department of Physics, University of York, York, YO10 5DD UK
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Demir D, Hekimgil M, Karaca E, Ulusoy Y, Özdemir HH, Saydam G, Durmaz B, Akın H, Çetingül N, Tombuloğlu M, Özsan N. Clinicopathological characteristics, genetics and prognosis of patients with myeloid sarcoma: a single-center study. J Clin Pathol 2023; 76:244-251. [PMID: 35927017 DOI: 10.1136/jcp-2021-208000] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 07/12/2022] [Indexed: 11/04/2022]
Abstract
AIM Myeloid sarcoma (MS) is a rare tumour comprising myeloid blasts occurring at an anatomical site other than the bone marrow. We sought to investigate both paediatric and adult patients with MS diagnosed at our institution and determine possible correlations among their clinicopathological, phenotypic, molecular and prognostic features. METHODS This study retrospectively evaluated the data of 45 patients diagnosed with MS at Ege University Faculty of Medicine Hospital, Turkey, over a 17-year period. RESULTS The male-to-female ratio was 1.5:1, and the median age was 39.12 years. The most commonly involved sites were the skin, lymph nodes, soft tissues and bone. Immunohistochemically, CD68-KP1 was the most commonly expressed marker, followed by CD33, myeloperoxidase, CD117, lysozyme, CD68-PGM1 and CD34. Of the patients, 26 (57.7%) presented with de novo MS, 7 (15.5%) had simultaneous acute myeloid leukaemia and 12 (26.8%) had a previous history of haematological disorders. Kaplan-Meier survival analysis revealed that the 2-year and 5-year overall survival (OS) rates were 46.4% and 39.8%, respectively; the median OS duration was 11 months. Increasing age had a negative prognostic relationship with survival (p = 0.04). Chromosomal abnormalities were detected in approximately 6/10 (60%) of paediatric patients and 6/9 (66.7%) of adult patients. t(8;21)(q22;q22) translocation was identified in 20% of paediatric patients. CONCLUSIONS MS diagnosis is usually challenging; an expanded immunohistochemical panel should be used for an accurate diagnosis. Although MS generally has a poor prognosis, increasing age appears to be associated with a worse outcome.
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Affiliation(s)
- Derya Demir
- Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Mine Hekimgil
- Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Emin Karaca
- Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Yusuf Ulusoy
- Internal Medicine, Division of Hematology, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | | | - Güray Saydam
- Internal Medicine, Division of Hematology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Burak Durmaz
- Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Haluk Akın
- Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Nazan Çetingül
- Pediatric Hematology-Oncology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Murat Tombuloğlu
- Internal Medicine, Division of Hematology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Nazan Özsan
- Pathology, Ege University Faculty of Medicine, Izmir, Turkey
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Aksoy E, Cogulu O, Pariltay E, Ozen S, Ata A, Karaca E, Darcan S. Association between clinical variations and copy number variations in cases with Turner syndrome. J Pediatr Endocrinol Metab 2022; 35:1161-1168. [PMID: 35953302 DOI: 10.1515/jpem-2022-0153] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 07/14/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Turner syndrome (TS) is one of the most common chromosomal abnormalities with an incidence of approximately one in 2,500 live births. Short stature and primary ovarian insufficiency are two most important characteristic findings of TS. Turner syndrome karyotypes include monosomy X, mosaic structure and X chromosome structural anomalies. Genotypic and phenotypic characteristics vary among cases. This study aimed to evaluate the clinical variations observed in TS cases with the copy number variations (CNV) detected by microarray study. METHODS Fifty-three patients diagnosed with TS, between the ages of 0-18 were included in the study. Peripheral blood samples were taken from 36 cases for microarray study. RESULTS Karyotypes were as follows: thirty-three of cases were 45,X, 7 were 45,X/46,XX, 6 were 45,X/46,Xi(Xq), 2 were 46,Xi(Xq), 2 were 45,X/46,r(X), 1 was 45,X/46,Xi(Xp), 1 was 45,X/46,XY and 1 was 45,X/46,X+mar(idicY) karyotype. A significant correlation was found between karyotype groups and FSH values of the cases (p=0.034). In monosomy X and mosaic isochromosome Xq cases, the FSH value was found to be significantly higher than those with 45,X/46,XX mosaic karyotype. CNVs were found in 8 (22.2%) out of 36 cases whose microarray study was performed. Unexpected atypical findings were discussed in the light of the characteristics of CNVs. CONCLUSIONS In conclusion, the microarray method has a great contribution in explaining many unexpected findings in TS cases. Moreover, those CNV findings may contribute for the explanation of the underlying mechanisms of those anomalies.
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Affiliation(s)
- Ezgi Aksoy
- Department of Child Health and Diseases, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Ozgur Cogulu
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Erhan Pariltay
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Samim Ozen
- Department of Pediatric Endocrinology and Diabetes, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Aysun Ata
- Department of Pediatric Endocrinology and Diabetes, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Sukran Darcan
- Department of Pediatric Endocrinology and Diabetes, Faculty of Medicine, Ege University, Izmir, Turkey
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Kahya Eren N, Karaca E, Şirin FB, Levent F, Gündüz C, Özdemir E, Nazlı C, Cogulu O, Ergene AO, Ergene AO. Does MicroRNA Profile Differ in Early Onset Coronary Artery Disease? Turk Kardiyol Dern Ars 2022; 50:407-414. [PMID: 36068979 DOI: 10.5543/tkda.2022.22408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE MicroRNAs have been explored as potential biomarkers for many pathological processes including coronary artery disease. In this study, we aimed to compare the circulating levels of selected atherosclerosis-associated miRNAs in patients with a history of early-onset coronary artery disease with that of age- and sex-matched healthy controls and older patients with late-onset coronary artery disease. METHODS Study population consisted of 30 patients with early onset coronary artery disease, 31 age- and sex-matched healthy controls, and 30 patients with late-onset coronary artery disease. Plasma levels of 13 microRNAs (endothelial cell-related miR-126, -92a/b; vascular smooth muscle cell-related miR-145; inflammation-related miR-16, -21, -125b, -146a/b, -147b, -150, -155; lipometabolism-related miR-27b, -122, -370) were evaluated by using real-time polymerase chain reaction. RESULTS In patients with early onset coronary artery disease, plasma expressions of the lipometabolism-related miR-27b, miR-122; inflammation-related miR-125b, miR-146a/b, miR-147b, miR-150, miR-155; and VSMC-related miR-145 were significantly downregulated and endothelial cell-related miR-126 was significantly upregulated compared to age- and sexmatched healthy controls. Circulating microRNA profile of patients with early onset coronary artery disease was also different from that of older patients with late-onset coronary artery disease. Plasma levels of miR-21, miR-27b, miR-122, miR-125b, miR-146b, miR-147b, and miR-155 were lower and plasma levels of miR-16 and miR-92a were higher in patients with early onset coronary artery disease compared to older patients with late-onset coronary artery disease. CONCLUSION MicroRNAs are promising biomarkers for early onset coronary artery disease.
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Affiliation(s)
- Nihan Kahya Eren
- Department of Cardiology, Faculty of Medicine, Katip Çelebi University, İzmir, Turkey
| | - Emin Karaca
- Department of Medical Biology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Fevziye Burcu Şirin
- Department of Biochemistry, Faculty of Medicine, Süleyman Demirel University, Isparta, Turkey
| | - Fatih Levent
- Department of Cardiology, Bursa Yüksek İhtisas Training and Research Hospital, Bursa, Turkey
| | - Cumhur Gündüz
- Department of Medical Biology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Emre Özdemir
- Department of Cardiology, Faculty of Medicine, Katip Çelebi University, İzmir, Turkey
| | - Cem Nazlı
- Department of Cardiology, Faculty of Medicine, Katip Çelebi University, İzmir, Turkey
| | - Ozgur Cogulu
- Department of Medical Biology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Asım Oktay Ergene
- Department of Cardiology, Faculty of Medicine, Dokuz Eylül University, İzmir, Turkey
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Karaca E, Byrne PJP, Hasnip PJ, Probert MIJ. Prediction of phonon-mediated superconductivity in new Ti-based M[Formula: see text]AX phases. Sci Rep 2022; 12:13198. [PMID: 35915155 PMCID: PMC9343435 DOI: 10.1038/s41598-022-17539-8] [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: 06/09/2022] [Accepted: 07/27/2022] [Indexed: 11/09/2022] Open
Abstract
A high-throughput computational method is used to predict 39 new superconductors in the Ti-based M[Formula: see text]AX phases, and the best candidates are then studied in more detail using density functional theory electron-phonon coupling calculations. The detailed calculations agree with the simple predictions, and Ti[Formula: see text]AlX (X: B, C and N) materials are predicted to have higher values of [Formula: see text] than any currently known hexagonal M[Formula: see text]AX phases. The electronic states at the Fermi level are dominated by the Ti 3d states. The choice of X (X: B, C and N) has a significant impact on the electronic density of states but not on the phonon characteristics. The electron-phonon coupling parameter for Ti[Formula: see text]AlX (X: B, C and N) was determined to be 0.685, 0.743 and 0.775 with a predicted [Formula: see text] of 7.8 K, 10.8 K and 13.0 K, respectively.
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Affiliation(s)
- E. Karaca
- Department of Physics, University of York, York, YO10 5DD UK
- Biomedical, Magnetic and Semiconductor Materials Research Center (BIMAS-RC), Sakarya University, 54187 Sakarya, Turkey
| | - P. J. P. Byrne
- Department of Physics, University of York, York, YO10 5DD UK
| | - P. J. Hasnip
- Department of Physics, University of York, York, YO10 5DD UK
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Acet F, Sahin G, Uçar AAO, Emirdar V, Karaca E, Durmaz B, Goker ENT, Tavmergen E. In vitro fertilization and preimplantation genetic diagnosis outcomes in mosaic Turner's Syndrome: A retrospective cohort study from a single referral center experience. J Gynecol Obstet Hum Reprod 2022; 51:102405. [DOI: 10.1016/j.jogoh.2022.102405] [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] [Received: 12/24/2021] [Revised: 04/14/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022]
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Kok Kilic G, Pariltay E, Karaca E, Durmaz B, Ekici H, Imamoglu M, Okmen F, Akin H, Cogulu O. Prenatal diagnosis of a case with tetrasomy 9p confirmed by cytogenetics, FISH, microarray analysis and review. Taiwan J Obstet Gynecol 2022; 61:122-126. [PMID: 35181020 DOI: 10.1016/j.tjog.2021.10.003] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2021] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVE Tetrasomy 9p is a rare fetal condition. Cases are usually mosaic. Here, we present a non-mosaic tetrasomy 9p case with cytogenetic analysis, fluorescence in situ hybridization, microarray data, ultrasound findings, and phenotypic presentation. CASE REPORT A pregnancy was referred to cytogenetic analysis because of increased nuchal translucency in prenatal ultrasound at 13 weeks of gestation. Prenatal laboratory analysis revealed an extra marker chromosome with a non-mosaic pattern. Ultrasonographic findings were unilateral cleft lip and palate, micrognathia, and atrioventricular septal defect at the 17th week; additionally, ventriculomegaly, left axis deviation of the fetal heart, and a single umbilical artery were determined at the 23rd week. CONCLUSION Phenotypic severity in non-mosaic tetrasomy 9p widely differs depending on the chromosomal content. We recommend performing appropriate genetic tests in those pregnancies with the suspicion of tetrasomy 9p, evaluating the mosaic state, and following those cases with detailed ultrasonographic examinations.
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Affiliation(s)
- Gizem Kok Kilic
- Ege University, School of Medicine, Department of Medical Genetics, Izmir, Turkey.
| | - Erhan Pariltay
- Ege University, School of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Emin Karaca
- Ege University, School of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Burak Durmaz
- Ege University, School of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Huseyin Ekici
- Ege University, School of Medicine, Department of Obstetrics and Gynecology, Izmir, Turkey
| | - Metehan Imamoglu
- Ege University, School of Medicine, Department of Obstetrics and Gynecology, Izmir, Turkey
| | - Firat Okmen
- Ege University, School of Medicine, Department of Obstetrics and Gynecology, Izmir, Turkey
| | - Haluk Akin
- Ege University, School of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Ozgur Cogulu
- Ege University, School of Medicine, Department of Medical Genetics, Izmir, Turkey; Ege University, School of Medicine, Department of Pediatrics, Izmir, Turkey
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Dundar M, Fahrioglu U, Yildiz SH, Bakir-Gungor B, Temel SG, Akin H, Artan S, Cora T, Sahin FI, Dursun A, Sezer O, Gurkan H, Erdogan M, Gunduz CNS, Bisgin A, Ozdemir O, Ulgenalp A, Percin EF, Yildirim ME, Tekes S, Bagis H, Yuce H, Duman N, Bozkurt G, Yararbas K, Yildirim MS, Arman A, Mihci E, Eraslan S, Altintas ZM, Aymelek HS, Ruhi HI, Tatar A, Ergoren MC, Cetin GO, Altunoglu U, Caglayan AO, Yuksel B, Ozkul Y, Saatci C, Kenanoglu S, Karasu N, Dundar B, Ozcelik F, Demir M, Siniksaran BS, Kulak H, Kiranatlioglu K, Baysal K, Kazimli U, Akalin H, Dundar A, Boz M, Bayram A, Subasioglu A, Colak FK, Karaduman N, Gunes MC, Kandemir N, Aynekin B, Emekli R, Sahin IO, Ozdemir SY, Onal MG, Senel AS, Poyrazoglu MH, Kisaarslan ANP, Gursoy S, Baskol M, Calis M, Demir H, Zararsiz GE, Erdogan MO, Elmas M, Solak M, Ulu MS, Thahir A, Aydin Z, Atasever U, Sag SO, Aliyeva L, Alemdar A, Dogan B, Erguzeloglu CO, Kaya N, Ozkinay F, Cogulu O, Durmaz A, Onay H, Karaca E, Durmaz B, Aykut A, Cilingir O, Aras BD, Gokalp EE, Arslan S, Temena A, Haziyeva K, Kocagil S, Bas H, Susam E, Keklikci AR, Sarac E, Kocak N, Nergiz S, Terzi YK, Dincer SA, Baskin ES, Genc GC, Bahadir O, Sanri A, Yigit S, Tozkir H, Yalcintepe S, Ozkayin N, Kiraz A, Balta B, Gonen GA, Kurt EE, Ceylan GG, Ceylan AC, Erten S, Bozdogan ST, Boga I, Yilmaz M, Silan F, Kocabey M, Koc A, Cankaya T, Bora E, Bozkaya OG, Ercal D, Ergun MA, Ergun SG, Duman YS, Beyazit SB, Uzel VH, Em S, Cevik MO, Eroz R, Demirtas M, Firat CK, Kabayegit ZM, Altan M, Mardan L, Sayar C, Tumer S, Turkgenc B, Karakoyun HK, Tunc B, Kuru S, Zamani A, Geckinli BB, Ates EA, Clark OA, Toylu A, Coskun M, Nur B, Bilge I, Bayramicli OU, Emmungil H, Komesli Z, Zeybel M, Gurakan F, Tasdemir M, Kebudi R, Karabulut HG, Tuncali T, Kutlay NY, Kahraman CY, Onder NB, Beyitler I, Kavukcu S, Tulay P, Tosun O, Tuncel G, Mocan G, Kale H, Uyguner ZO, Acar A, Altinay M, Erdem L. Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium. Funct Integr Genomics 2022; 22:291-315. [PMID: 35098403 DOI: 10.1007/s10142-021-00819-3] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 02/08/2023]
Abstract
Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.
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Affiliation(s)
- Munis Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.
| | - Umut Fahrioglu
- Department of Medical Biology, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus. .,DESAM Institute, Near East University, 99138, Nicosia, Cyprus. .,Genetics and Cancer Diagnosis-Research Centre, Centre of Excellence, Near East University, 99138, Nicosia, Cyprus.
| | - Saliha Handan Yildiz
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, 03030, Turkey
| | - Burcu Bakir-Gungor
- Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Sehime Gulsun Temel
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey.,Department of Histology and Embryology, Faculty of Medicine, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey.,Department of Translational Medicine, Health Sciences Institute, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Haluk Akin
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Sevilhan Artan
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Tulin Cora
- Department of Medical Biology and Genetics, Faculty of Medicine, Selcuk University, Konya, 42131, Turkey
| | - Feride Iffet Sahin
- Department of Medical Genetics, Faculty of Medicine, Baskent University, Ankara, 06490, Turkey
| | - Ahmet Dursun
- Department of Medical Genetics, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, 67600, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun, 55090, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, 22130, Turkey
| | - Murat Erdogan
- Division of Medical Genetics, Kayseri City Education and Research Hospital, Kayseri, 38080, Turkey
| | - C Nur Semerci Gunduz
- Department of Medical Genetics, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, 06800, Turkey.,Ataturk Training and Research Hospital, Genetic Diseases Diagnosis Center, Ankara, 06230, Turkey
| | - Atil Bisgin
- Department of Medical Genetics, Faculty of Medicine, Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center and Medical Genetics), Adana, 01790, Turkey
| | - Ozturk Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, Canakkale, 17100, Turkey
| | - Ayfer Ulgenalp
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey.,Department of Pediatric Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - E Ferda Percin
- Department of Medical Genetics, Faculty of Medicine, Gazi University, Besevler Ankara, 06560, Turkey
| | - Malik Ejder Yildirim
- Department of Medical Genetics, Faculty of Medicine, Cumhuriyet University, Sivas, 58140, Turkey
| | - Selahaddin Tekes
- Department of Medical Genetics, Faculty of Medicine, Dicle University, Diyarbakir, 21280, Turkey
| | - Haydar Bagis
- Department of Medical Genetics, Faculty of Medicine, Adiyaman University, Adiyaman, 02040, Turkey
| | - Huseyin Yuce
- Department of Medical Genetics, Faculty of Medicine, Duzce University, Duzce, 81620, Turkey
| | - Nilgun Duman
- Department of Medical Genetics, Faculty of Medicine, Dragos Hospital, Bezmi Alem Vakif University, Istanbul, 34844, Turkey
| | - Gokay Bozkurt
- Department of Medical Genetics, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, 09010, Turkey
| | - Kanay Yararbas
- Acibadem Labgen Genetic Diagnosis Center, Acibadem University, Istanbul, 34755, Turkey
| | - Mahmut Selman Yildirim
- Department of Medical Genetics, Meram Medical Faculty, Necmettin Erbakan University, Konya, 42080, Turkey
| | - Ahmet Arman
- Department of Medical Genetics, Faculty of Medicine, Marmara University, Istanbul, 34854, Turkey
| | - Ercan Mihci
- Department of Medical Genetics, Faculty of Medicine, Akdeniz University, Antalya, 07070, Turkey.,Department of Pediatric Genetics, Faculty of Medicine, Akdeniz University, Antalya, 07070, Turkey
| | - Serpil Eraslan
- Diagnostic Center for Genetic Diseases, Koc University Hospital, Koc University, Istanbul, 34010, Turkey
| | - Zuhal Mert Altintas
- Department of Medical Genetics, Faculty of Medicine, Mersin University, Mersin, 33343, Turkey
| | - Huri Sema Aymelek
- Department of Medical Genetics, Faculty of Medicine, Van Yuzuncu Yil University, Van, 65080, Turkey.,Division of Medical Genetics, Bursa City Hospital, Bursa, 16110, Turkey
| | - Hatice Ilgin Ruhi
- Department of Medical Genetics, Faculty of Medicine, Ankara University, Ankara, 06590, Turkey
| | - Abdulgani Tatar
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, 25240, Turkey
| | - Mahmut Cerkez Ergoren
- DESAM Institute, Near East University, 99138, Nicosia, Cyprus.,Department of Medical Genetics, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus
| | - G Ozan Cetin
- Department of Medical Genetics, Faculty of Medicine, Pamukkale University, Denizli, 20070, Turkey
| | - Umut Altunoglu
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey.,Department of Medical Genetics, Faculty of Medicine (KUSOM), Koc University, Istanbul, 34010, Turkey
| | - Ahmet Okay Caglayan
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey.,Department of Medical Genetics, Faculty of Medicine, Istanbul Bilim University, Istanbul, 34394, Turkey
| | - Berrin Yuksel
- Department of Medical Genetics, Faculty of Medicine, Usak University, Usak, 64050, Turkey
| | - Yusuf Ozkul
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Cetin Saatci
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Sercan Kenanoglu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Nilgun Karasu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Bilge Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Pathology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Firat Ozcelik
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Mikail Demir
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Faculty of Medicine, Van Yuzuncu Yil University, Van, 65080, Turkey
| | - Betul Seyhan Siniksaran
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Hande Kulak
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Faculty of Medicine, Van Yuzuncu Yil University, Van, 65080, Turkey
| | - Kubra Kiranatlioglu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Kubra Baysal
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Ulviyya Kazimli
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Hilal Akalin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Ayca Dundar
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Mehmet Boz
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Arslan Bayram
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Etlik Zubeyde Hanim Women's Diseases Education and Research Hospital, Ankara, 06050, Turkey
| | - Asli Subasioglu
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Faculty of Medicine, Izmir Katip Celebi University, Izmir, 35620, Turkey
| | - Fatma Kurt Colak
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Faculty of Medicine, Kahramanmaras Sutcu Imam University, Kahramanmaras, 46040, Turkey
| | - Neslihan Karaduman
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Division of Medical Genetics, Kirikkale High Specialization Hospital, Kirikkale, 71300, Turkey
| | - Meltem Cerrah Gunes
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Faculty of Medicine, Kocaeli University, Kocaeli, 41001, Turkey
| | - Nefise Kandemir
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara, 06110, Turkey
| | - Busra Aynekin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Rabia Emekli
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Izem Olcay Sahin
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Sevda Yesim Ozdemir
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Faculty of Medicine, Uskudar University, Istanbul, 34662, Turkey
| | - Muge Gulcihan Onal
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | | | - Muammer Hakan Poyrazoglu
- Department of Pediatrics, Division of Nephrology, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Ayse Nur Pac Kisaarslan
- Department of Child Health and Diseases, Division of Pediatric Rheumatology, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Sebnem Gursoy
- Department of Gastroenterology, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Mevlut Baskol
- Department of Gastroenterology, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Mustafa Calis
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Huseyin Demir
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Gozde Erturk Zararsiz
- Department of Biostatistics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey
| | - Mujgan Ozdemir Erdogan
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, 03030, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, 03030, Turkey
| | - Mustafa Solak
- Department of Medical Genetics, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, 03030, Turkey
| | - Memnune Sena Ulu
- Department of Internal Medicine, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, 03030, Turkey
| | - Adam Thahir
- Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Zafer Aydin
- Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Umut Atasever
- Department of Computer Engineering, Faculty of Engineering and Natural Sciences, Abdullah Gul University, Kayseri, 38080, Turkey
| | - Sebnem Ozemri Sag
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Lamiya Aliyeva
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Adem Alemdar
- Department of Translational Medicine, Health Sciences Institute, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Berkcan Dogan
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey.,Department of Translational Medicine, Health Sciences Institute, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Cemre Ornek Erguzeloglu
- Department of Translational Medicine, Health Sciences Institute, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Niyazi Kaya
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Gorukle, Bursa, 16059, Turkey
| | - Ferda Ozkinay
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey.,Department of Pediatrics and Health, Genetics and Teratology, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Ozgur Cogulu
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey.,Department of Pediatrics and Health, Genetics and Teratology, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Asude Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Burak Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Ayca Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, 35100, Turkey
| | - Oguz Cilingir
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Beyhan Durak Aras
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Ebru Erzurumluoglu Gokalp
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Serap Arslan
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Arda Temena
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Konul Haziyeva
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Sinem Kocagil
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Hasan Bas
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Ezgi Susam
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Ali Riza Keklikci
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Elif Sarac
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, 26040, Turkey
| | - Nadir Kocak
- Department of Medical Biology and Genetics, Faculty of Medicine, Selcuk University, Konya, 42131, Turkey
| | - Suleyman Nergiz
- Department of Medical Biology and Genetics, Faculty of Medicine, Selcuk University, Konya, 42131, Turkey
| | - Yunus Kasim Terzi
- Department of Medical Genetics, Faculty of Medicine, Baskent University, Ankara, 06490, Turkey
| | - Selin Akad Dincer
- Department of Medical Genetics, Faculty of Medicine, Baskent University, Ankara, 06490, Turkey
| | - Esra Sidika Baskin
- Department of Pediatric Nephrology, Faculty of Medicine, Baskent University, Ankara, 06490, Turkey
| | - Gunes Cakmak Genc
- Department of Medical Genetics, Faculty of Medicine, Zonguldak Bulent Ecevit University, Zonguldak, 67600, Turkey
| | - Oguzhan Bahadir
- Department of Medical Genetics, Faculty of Medicine, Erciyes University, Kayseri, 38039, Turkey.,Department of Medical Genetics, Samsun Education and Research Hospital, Samsun, 55090, Turkey
| | - Aslihan Sanri
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun, 55090, Turkey
| | - Serbulent Yigit
- Department of Genetics, Faculty of Veterinary, Ondokuz Mayis University, Samsun, 55270, Turkey.,Department of Medical Biology, Faculty of Medicine, Gaziosmanpasa University, Tokat, 60030, Turkey
| | - Hilmi Tozkir
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, 22130, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, 22130, Turkey
| | - Nese Ozkayin
- Department of Pediatrics, Division of Nephrology, Faculty of Medicine, Trakya University, Edirne, 22130, Turkey
| | - Aslihan Kiraz
- Division of Medical Genetics, Kayseri City Education and Research Hospital, Kayseri, 38080, Turkey
| | - Burhan Balta
- Division of Medical Genetics, Kayseri City Education and Research Hospital, Kayseri, 38080, Turkey
| | - Gizem Akinci Gonen
- Division of Medical Genetics, Kayseri City Education and Research Hospital, Kayseri, 38080, Turkey
| | - E Emre Kurt
- Department of Medical Genetics, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, 06800, Turkey.,Ataturk Training and Research Hospital, Genetic Diseases Diagnosis Center, Ankara, 06230, Turkey
| | - Gulay Gulec Ceylan
- Department of Medical Genetics, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, 06800, Turkey.,Ataturk Training and Research Hospital, Genetic Diseases Diagnosis Center, Ankara, 06230, Turkey
| | - Ahmet Cevdet Ceylan
- Department of Medical Genetics, Faculty of Medicine, Ankara Yildirim Beyazit University, Ankara, 06800, Turkey.,Ataturk Training and Research Hospital, Genetic Diseases Diagnosis Center, Ankara, 06230, Turkey
| | - Sukran Erten
- Department of Rheumatology, Ataturk Training Research Hospital, Ankara Yildirim Beyazit University, Ankara, 06230, Turkey
| | - Sevcan Tug Bozdogan
- Department of Medical Genetics, Faculty of Medicine, Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center and Medical Genetics), Adana, 01790, Turkey
| | - Ibrahim Boga
- Department of Medical Genetics, Faculty of Medicine, Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center and Medical Genetics), Adana, 01790, Turkey
| | - Mustafa Yilmaz
- Division of Pediatric Rheumatology, Faculty of Medicine, Cukurova University, Adana, 01790, Turkey
| | - Fatma Silan
- Department of Medical Genetics, Faculty of Medicine, Canakkale Onsekiz Mart University, Canakkale, 17100, Turkey
| | - Mehmet Kocabey
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Altug Koc
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Tufan Cankaya
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Elcin Bora
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Ozlem Giray Bozkaya
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey.,Department of Pediatric Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Derya Ercal
- Department of Medical Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey.,Department of Pediatric Genetics, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Mehmet Ali Ergun
- Department of Medical Genetics, Faculty of Medicine, Gazi University, Besevler Ankara, 06560, Turkey
| | - Sezen Guntekin Ergun
- Department of Medical Genetics, Faculty of Medicine, Gazi University, Besevler Ankara, 06560, Turkey.,Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, 06100, Turkey
| | - Yesim Sidar Duman
- Department of Medical Genetics, Faculty of Medicine, Cumhuriyet University, Sivas, 58140, Turkey
| | - Serife Busra Beyazit
- Department of Medical Genetics, Faculty of Medicine, Cumhuriyet University, Sivas, 58140, Turkey
| | - Veysiye Hulya Uzel
- Department of Pediatric Hematology, Faculty of Medicine, Dicle University, Diyarbakir, 21280, Turkey
| | - Serda Em
- Department of Physical Medicine and Rehabilitation, Faculty of Medicine, Dicle University, Diyarbakir, 21280, Turkey
| | - Muhammer Ozgur Cevik
- Department of Medical Genetics, Faculty of Medicine, Adiyaman University, Adiyaman, 02040, Turkey
| | - Recep Eroz
- Department of Medical Genetics, Faculty of Medicine, Duzce University, Duzce, 81620, Turkey
| | - Mercan Demirtas
- Department of Medical Genetics, Faculty of Medicine, Dragos Hospital, Bezmi Alem Vakif University, Istanbul, 34844, Turkey
| | - Cem Koray Firat
- Department of Child Health and Diseases, Faculty of Medicine, Dragos Hospital, Bezmi Alem Vakif University, Istanbul, 34844, Turkey
| | - Zehra Manav Kabayegit
- Department of Medical Genetics, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, 09010, Turkey
| | - Mustafa Altan
- Department of Medical Genetics, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, 09010, Turkey
| | - Lamiya Mardan
- Department of Medical Genetics, Faculty of Medicine, Aydin Adnan Menderes University, Aydin, 09010, Turkey
| | - Ceyhan Sayar
- Acibadem Labgen Genetic Diagnosis Center, Acibadem University, Istanbul, 34755, Turkey
| | - Sait Tumer
- Acibadem Labgen Genetic Diagnosis Center, Acibadem University, Istanbul, 34755, Turkey
| | - Burcu Turkgenc
- Acibadem Labgen Genetic Diagnosis Center, Acibadem University, Istanbul, 34755, Turkey
| | | | - Betul Tunc
- Acibadem Labgen Genetic Diagnosis Center, Acibadem University, Istanbul, 34755, Turkey
| | - Seda Kuru
- Acibadem Labgen Genetic Diagnosis Center, Acibadem University, Istanbul, 34755, Turkey
| | - Aysegul Zamani
- Department of Medical Genetics, Meram Medical Faculty, Necmettin Erbakan University, Konya, 42080, Turkey
| | - Bilgen Bilge Geckinli
- Department of Medical Genetics, Faculty of Medicine, Marmara University, Istanbul, 34854, Turkey
| | - Esra Arslan Ates
- Department of Medical Genetics, Marmara Teaching and Research Hospital, Marmara University, Istanbul, 34899, Turkey
| | - Ozden Altiok Clark
- Department of Medical Genetics, Faculty of Medicine, Akdeniz University, Antalya, 07070, Turkey
| | - Asli Toylu
- Department of Medical Genetics, Faculty of Medicine, Akdeniz University, Antalya, 07070, Turkey
| | - Mert Coskun
- Department of Medical Genetics, Faculty of Medicine, Akdeniz University, Antalya, 07070, Turkey
| | - Banu Nur
- Department of Pediatric Genetics, Faculty of Medicine, Akdeniz University, Antalya, 07070, Turkey
| | - Ilmay Bilge
- Department of Pediatric Nephrology, Koc University Hospital, Istanbul, 34010, Turkey
| | - Oya Uygur Bayramicli
- Department of Gastroenterology and Hepatology, Med American Ambulatory Care Center, Istanbul, 34724, Turkey
| | - Hakan Emmungil
- Department of Rheumatology, Faculty of Medicine, Trakya University, Edirne, 22100, Turkey
| | - Zeynep Komesli
- Department of Internal Medicine, Koc University Hospital, Istanbul, 34010, Turkey
| | - Mujdat Zeybel
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Koc University, Istanbul, 34010, Turkey
| | - Figen Gurakan
- Department of Pediatrics, VKV American Hospital, Istanbul, 34365, Turkey
| | - Mehmet Tasdemir
- Division of Pediatric Nephrology, Department of Pediatrics, Faculty of Medicine, Koc University, Istanbul, 34010, Turkey
| | - Rejin Kebudi
- Department of Pediatric Hematology-Oncology, Institute of Oncology, Istanbul University, Istanbul, 34093, Turkey
| | - Halil Gurhan Karabulut
- Department of Medical Genetics, Faculty of Medicine, Ankara University, Ankara, 06590, Turkey
| | - Timur Tuncali
- Department of Medical Genetics, Faculty of Medicine, Ankara University, Ankara, 06590, Turkey
| | - Nuket Yurur Kutlay
- Department of Medical Genetics, Faculty of Medicine, Ankara University, Ankara, 06590, Turkey
| | - Cigdem Yuce Kahraman
- Department of Medical Genetics, Faculty of Medicine, Ataturk University, Erzurum, 25240, Turkey
| | - Nerin Bahceciler Onder
- Department of Pediatrics, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus
| | - Ilke Beyitler
- Department of Pediatrics, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus
| | - Salih Kavukcu
- Department of Pediatric Nephrology, Faculty of Medicine, Dokuz Eylul University, Izmir, 35340, Turkey
| | - Pinar Tulay
- DESAM Institute, Near East University, 99138, Nicosia, Cyprus.,Department of Medical Genetics, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus
| | - Ozgur Tosun
- Department of Biostatistics, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus
| | - Gulten Tuncel
- DESAM Institute, Near East University, 99138, Nicosia, Cyprus
| | - Gamze Mocan
- Department of Pathology, Faculty of Medicine, Near East University, 99138, Nicosia, Cyprus
| | - Hamdi Kale
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Medical Faculty, Istanbul University, Istanbul, 34093, Turkey
| | - Aynur Acar
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Demiroglu Bilim University, Sisli, Istanbul, 34394, Turkey
| | - Mert Altinay
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Demiroglu Bilim University, Sisli, Istanbul, 34394, Turkey
| | - Levent Erdem
- Department of Internal Medicine, Faculty of Medicine, Demiroglu Bilim University, Sisli, Istanbul, 34394, Turkey
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11
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Durmaz B, Bolat H, Cengisiz Z, Akercan F, Sözen Türk T, Parıltay E, Solmaz AE, Kazandı M, Karaca E, Durmaz A, Aykut A, Sağol S, Akın H, Özkınay F, Çoğulu Ö. 20-year experience on prenatal diagnosis in a reference university medical genetics center in Turkey. Turk J Med Sci 2021; 51:1775-1780. [PMID: 33581708 PMCID: PMC8569778 DOI: 10.3906/sag-2006-103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 02/13/2021] [Indexed: 11/03/2022] Open
Abstract
Background/aim Although cutting edge procedures such as cell-free fetal DNA isolation from maternal blood are now available, invasive prenatal tests are still being used extensively for prenatal diagnosis. The study aims to evaluate the demographic data, indications, and cytogenetic results of 9297 results of patients who underwent prenatal invasive testing for genetic analysis that were referred for the last 20 years in a University Medical Genetics Center. Materials and methods The records of 8363 amniocenteses, 626 chorionic villus, and 308 cordocenteses samples were retrospectively evaluated and analyzed regarding referral reasons, indications and their cytogenetic results. The total numbers and the percentages of each group were recorded; Chi-square and logistic regression analyses were performed to give the statistical likelihood of different events. Results The number of referrals decreased significantly after 2009. Risk of having trisomy 21 as well as trisomy 13 and 18 significantly increased in parallel with advanced maternal age. When the 21–25 age group was compared to the older age groups in terms of having a trisomy 21 pregnancy, the risk doubled in the 36–40, 5 times higher in 41–45 and 10-fold in 46–50 age groups. No significant linear correlation between maternal serum screening test results and trisomy 21 was found, however the difference between the pregnancies whom cut-off value above and below 1/250 in maternal serum screening test were significant. Conclusion These data have provided useful information on the frequency of referrals to the reference genetics department, and the feasibility of genetic services. By reviewing the indications and their corresponding results, we can offer invaluable insights that will be useful in genetic counseling and also in the development of more effective genetic strategies.
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Affiliation(s)
- Burak Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Hilmi Bolat
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Zehra Cengisiz
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Fuat Akercan
- Department of Obstetrics and Gynecology, Division of Perinatology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Tuba Sözen Türk
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Erhan Parıltay
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Aslı Ece Solmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Mert Kazandı
- Department of Obstetrics and Gynecology, Division of Perinatology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Asude Durmaz
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Ayça Aykut
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Sermet Sağol
- Department of Obstetrics and Gynecology, Division of Perinatology, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Haluk Akın
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Ferda Özkınay
- Department of Pediatrics, Division of Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - ÖzgÜr Çoğulu
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
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Anadol E, Gultiken N, Yarim GF, Karaca E, Kanca H, Yarim M. Investigation of diagnostic use of serum anti-Müllerian hormone concentration in dioestrus and anoestrus bitches before and after ovariohysterectomy and the relationship with ovarian follicle numbers. Pol J Vet Sci 2021; 23:391-397. [PMID: 33006849 DOI: 10.24425/pjvs.2020.134683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aims of the study were to (1) compare the serum concentration of anti-Müllerian hormone (AMH) with the number of follicles in ovaries and (2) determine the serum AMH con- centration before and after ovariohysterectomy in dioestrus and anoestrus bitches. Sixteen bitches were divided into two groups: Group I (n=8) consisted of dioestrus and group II (n=8) anoestrus bitches. The blood samples for AMH assesment were taken before ovariohysterectomy (day 0) and on day 1, 5 and 10. Both in group I and II, serum AMH concentrations on day 1 and 5 were significantly different compared to day 0 (p⟨0.05). However, the concentrations at day 10 were under the minimum detectable concentration (1.0 ng/mL) and this finding revealed that ovaries are the only source of AMH synthesis. Follicle counts were not statistically different between the groups (p>0.05). Significantly positive correlation in serum AMH with secondary follicle num- bers (r=.942, p⟨0.01), as well as negative correlation with antral follicle numbers (r=-.765, p⟨0.05) were determined in the group I. In the group II, positive correlations between serum AMH concentration and secondary follicle numbers (r=.960, p⟨0.01) and early antral follicles (r=.726, p⟨0.05) were noted. Assesment of AMH concentration seems to not only provide the diagnosis of the presence of ovaries but also correlate with the number of secondary follicles in young dioestrus and anoestrus bitches.
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Affiliation(s)
- E Anadol
- Laboratory Animals Breeding and Experimental Researches Center, University of Gazi, Ankara, Turkiye
| | - N Gultiken
- Department of Obstetrics and Gynaecology, Faculty of Veterinary Medicine, University of Ondokuz Mayis, Samsun, Turkiye
| | - G F Yarim
- Department of Biochemistry, Faculty of Veterinary Medicine, University of Ondokuz Mayis, Samsun, Turkiye
| | - E Karaca
- Department of Pathology, University of Ondokuz Mayis, Faculty of Veterinary Medicine, Samsun, Turkiye
| | - H Kanca
- Department of Obstetrics and Gynaecology, Faculty of Veterinary Medicine, University of Ankara, Diskapi, Ankara, Turkiye
| | - M Yarim
- Department of Pathology, University of Ondokuz Mayis, Faculty of Veterinary Medicine, Samsun, Turkiye
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Yilmaz UC, Bagca BG, Karaca E, Durmaz A, Durmaz B, Aykut A, Kayalar H, Avci CB, Susluer SY, Pariltay E, Gunduz C, Cogulu O. Propolis Extract Regulate microRNA Expression in Glioblastoma and Brain Cancer Stem Cells. Anticancer Agents Med Chem 2021; 22:378-389. [PMID: 33949939 DOI: 10.2174/1871520621666210504082528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/05/2020] [Revised: 02/28/2021] [Accepted: 03/08/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Grade IV gliomas are classified as glioblastoma (GBM), which is the most malignant brain cancer type. Various genetic and epigenetic mechanisms play a role in the initiation and progression of GBM. MicroRNAs (miRNAs) are small, non-coding RNA molecules that are the main epigenetic regulatory RNA class. They play variable roles in both physiological and pathological conditions, including GBM pathogenesis, by regulating expression levels of the target genes. Brain cancer stem cells (BCSCs) are subpopulations of brain cancer mass that are responsible for poor prognosis, including therapy resistance and relapse. Epigenetic regulation mediated by miRNAs is also a critical component of BCSC self-renewal and differentiation properties. Propolis is a resinous substance that is collected by honey bees from various plant sources. The flavonoids content of propolis varies, depending on the region collected andthe extraction method. Although the effects of propolis that have been collected from different sources on the miRNA expression levels in the glioblastoma cells have been shown, the effects on the BCSCs are not known yet. OBJECTIVE The aim of this study is to evaluate the effects of Aydın, a city in western Turkey, propolis, on miRNA expression levels of BCSCs and GBM cells. METHODS Aydin propolis was dissolved in 60% ethanol, and after evaporation, distilled water was added to prepare the propolis stock solution. The flavonoids content of the Aydin propolis was determined by MS Q-TOF analysis. Commercially obtained U87MG, GBM cell line, and BCSCs were used as in vitro brain cancer models. The cytotoxic and apoptotic effects of Aydın propolis were determined via WST-1 assay and Annexin V test, respectively. The miRNA expression profile was investigated via the real-time qRT-PCR method, and fold changes were calculated by using the 2-∆∆Ct method compared to untreated control cells. The miRNA-mRNA-pathway interactions, including significantly altered miRNAs, were determined using different bioinformatics tools and databases. RESULTS Quercetin 3-methyl ether was determined as the major component of the Aydin propolis. Aydin propolis did not show significant cytotoxic and apoptotic effects on both GBM and BCSCs up to 2mg/ml concentration. Aydin propolis treatment decreased the expression of nine and five miRNAs in the U87MG 2.13 to 5.65 folds and BCSCs 2.02 to 12.29 folds, respectively. Moreover, 10 miRNAs 2.22 to 10.56 folds were upregulated in propolis treated GBM cells compared to the control group, significantly (p<0.05). In the study, the potential roles of two new miRNAs, whose regulations in glioma were not previously defined, were identified. One of these miR-30d-5p, a novel potential oncomiR in GBM was 2.46 folds downregulated in Aydin propolis treated GBM cells. The other one is miR-335-5p which is a potential tumor suppressor miR in GBM, was 5.66 folds upregulated in Aydin propolis treated GBM cells. FOXO pathway and its upstream and downstream regulators and critically neuronal developmental regulators NOTCH and WNT pathways were determined as the most deregulated pathways in Aydin propolis treated cells. CONCLUSION The determination of the anti-cancer effect of Aydın propolis on the miRNA expression of GBM, especially on cancer stem cells, may contribute to the elucidation of brain cancer genetics by supporting further analyses.
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Affiliation(s)
- Ugur C Yilmaz
- Ege University, Faculty of Medicine, Department of Pediatrics, Izmir, Turkey
| | - Bakiye G Bagca
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Emin Karaca
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Asude Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Burak Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Ayca Aykut
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Husniye Kayalar
- Ege University, Faculty of Pharmacy, Department of Pharmacognosy, Izmir, Turkey
| | - Cigir B Avci
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Sunde Y Susluer
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Erhan Pariltay
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Cumhur Gunduz
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Ozgur Cogulu
- Ege University, Faculty of Medicine, Department of Pediatrics, Izmir, Turkey
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Sozmen M, Devrim T, Kuruca N, Inal S, Karaca E, Gulbahar MY. Primary Unilateral Small Cell Neuroendocrine Carcinoma of the Kidney in a Dog. J Comp Pathol 2020; 176:71-75. [PMID: 32359638 DOI: 10.1016/j.jcpa.2020.02.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/21/2019] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 11/26/2022]
Abstract
Primary small cell carcinomas are rare in domestic animals. A mass measuring 15 × 20 × 9 cm was detected in the left abdominal cavity of a 7.5-year-old female golden retriever. The cut surface of the excised mass showed a tumour replacing the left kidney. Microscopically, the mass was composed of polymorphic, small basophilic cells with a high nuclear to cytoplasmic ratio and round, oval or short slender fusiform nuclei with condensed or finely granular chromatin, absent or inconspicuous nucleoli, and scant, faintly eosinophilic cytoplasm with poorly defined cytoplasmic borders. Immunohistochemically, most of the neoplastic cells were immunoreactive for thyroid transcription factor 1 and CD56, moderately positive for vimentin and weakly or sparsely labelled for chromogranin A, synaptophysin, Wilms' tumour 1 protein, neuron-specific enolase, pan-cytokeratin (CK) AE1/AE3 and epithelial membrane antigen. The tumour cells were negative for glial fibrillary acidic protein (GFAP), ionized calcium-binding adapter molecule 1, CK7, CK20, CD3, CD45 and CD99. These findings indicated a neuroendocrine origin of the tumour. To the best of author's knowledge, this is the first report of a small cell neuroendocrine carcinoma originating as a primary tumour in the kidney of a dog.
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Affiliation(s)
- M Sozmen
- Department of Pathology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Kurupelit, Samsun, Turkey.
| | - T Devrim
- Department of Pathology, Faculty of Medicine, Kırıkkale University, Yahşihan, Kırıkkale, Turkey
| | - N Kuruca
- Department of Pathology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Kurupelit, Samsun, Turkey
| | - S Inal
- Department of Pathology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Kurupelit, Samsun, Turkey
| | - E Karaca
- Department of Pathology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Kurupelit, Samsun, Turkey
| | - M Y Gulbahar
- Department of Pathology, Faculty of Veterinary Medicine, Ondokuz Mayıs University, Kurupelit, Samsun, Turkey
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15
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Karaca Y, Pariltay E, Mardan L, Karaca E, Durmaz A, Durmaz B, Aykut A, Akin H, Cogulu O. Co-occurrences of polymorphic heterochromatin regions of chromosomes and effect on reproductive failure. Reprod Biol 2019; 20:42-47. [PMID: 31899132 DOI: 10.1016/j.repbio.2019.12.006] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/12/2022]
Abstract
Although the polymorphic heterochromatin regions of chromosomes (heteromorphisms) have been extensively studied for their phenotypic effects on humans, co-occurrences of chromosome 1, 9, 16 and Y heteromorphisms and of acrocentric variants have never been studied on humans with an objective scoring system. Here we compared the frequencies of individual heteromorphisms on a total of 602, 768 and 224 patients with the indications of infertility, recurrent miscarriage and in vitro fertilization (IVF) failure, respectively and on 272 controls. Then we examined whether there were significant co-occurrences between heteromorphisms within and between the groups. There were no statistically significant differences in the frequencies of heteromorphisms between the groups. Both statistically significant and non-significant correlations were observed within the non-acrocentric and certain acrocentric heteromorphisms in each group. When these co-occurrences were examined between the groups, a 2.2 fold increased risk of IVF failure in males in the presence of either chromosome 13 or chromosome 21 variants was observed (95 %CI:1.1-4.2). We conclude that the simultaneous manifestations of heteromorphisms have no effect on reproductive failure. There seems to be a correlation between the non-acrocentric heteromorphisms (1qh+, 9qh+, 16qh + and Yqh+/-), which might be the result of complex interactions of formation of these heterochromatin regions. The correlations observed between certain acrocentric chromosomes might be related to satellite association and nucleolus formation. The increased risk observed in males with IVF failure in the presence of either chromosome 13 or 21 variants should be interpreted cautiously due to the heterogeneity of the group.
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Affiliation(s)
- Yasemin Karaca
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey.
| | - Erhan Pariltay
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Lamiya Mardan
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Emin Karaca
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Asude Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Burak Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Ayca Aykut
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Haluk Akin
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Ozgur Cogulu
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
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Akin H, Karaca E, Hortu I, Bolat H, Cengisiz Z, Kazandi M, Durmaz B, Aykut A, Durmaz A, Cogulu O. Cytogenetic analysis of miscarriage materials of couples with recurrent pregnancy loss in a tertiary center. CLIN EXP OBSTET GYN 2019. [DOI: 10.12891/ceog4794.2019] [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: 02/05/2023]
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Kılıç B, Şimşek A, Claus J, Karaca E, Bilecen D. Improving lipid oxidation inhibition in cooked beef hamburger patties during refrigerated storage with encapsulated polyphosphate incorporation. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.02.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Karaca E, Aykut A, Ertürk B, Durmaz B, Güler A, Büke B, Yeniel AÖ, Ergenoğlu AM, Özkınay F, Özeren M, Kazandı M, Akercan F, Sağol S, Gündüz C, Çoğulu Ö. MicroRNA Expression Profile in the Prenatal Amniotic Fluid Samples of Pregnant Women with Down Syndrome. Balkan Med J 2017; 35:163-166. [PMID: 29219113 PMCID: PMC5863254 DOI: 10.4274/balkanmedj.2017.0511] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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] [Indexed: 12/01/2022] Open
Abstract
Background: Down syndrome, which is the most common human chromosomal anomaly that can affect people of any race and age, can be diagnosed prenatally in most cases. Prenatal diagnosis via culture method is time-consuming; thus, genetic analysis has thus been introduced and is continually being developed for rapid prenatal diagnosis. For this reason, the effective use of microRNA profiling for the rapid analysis of prenatal amniotic fluid samples for the diagnosis of Down syndrome was investigated. Aims: To evaluate the expression levels of 14 microRNAs encoded by chromosome 21 in amniotic fluid samples and their utility for prenatal diagnosis of Down syndrome. Study Design: Case-control study. Methods: We performed invasive prenatal testing for 56 pregnant women; 23 carried fetuses with Down syndrome, and 33 carried fetuses with a normal karyotype. Advanced maternal age and increased risk for Down syndrome in the screening tests were indications for invasive prenatal testing. The age of gestation in the study and control groups ranged between 17 and 18 weeks. The expression levels of microRNA were measured by real-time polymerase chain reaction. Results: The expression levels of microRNA-125b-2, microRNA-155, and microRNA-3156 were significantly higher in the study group than in the control group. Conclusion: The presence of significantly dysregulated microRNAs may be associated with either the phenotype or the result of abnormal development. Further large-scale comparative studies conducted in a variety of conditions may bring novel insights in the field of abnormal prenatal conditions.
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Affiliation(s)
- Emin Karaca
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Ayça Aykut
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Biray Ertürk
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Burak Durmaz
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Ahmet Güler
- Clinic of Obstetrics and Gynecology, İzmir Ege Maternity and Women's Diseases Training Research Hospital, İzmir, Turkey
| | - Barış Büke
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Ahmet Özgür Yeniel
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Ahmet Mete Ergenoğlu
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Ferda Özkınay
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
| | - Mehmet Özeren
- Clinic of Obstetrics and Gynecology, İzmir Ege Maternity and Women's Diseases Training Research Hospital, İzmir, Turkey
| | - Mert Kazandı
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Fuat Akercan
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Sermet Sağol
- Department of Obstetrics and Gynecology, Ege University School of Medicine, İzmir, Turkey
| | - Cumhur Gündüz
- Department of Medical Biology, Ege University School of Medicine, İzmir, Turkey
| | - Özgür Çoğulu
- Department of Medical Genetics, Ege University School of Medicine, İzmir, Turkey
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Karaca E, Onay H, Cetinkalp S, Aykut A, Göksen D, Ozen S, Atik T, Darcan S, Tekin IM, Ozkınay F. The spectrum of HNF1A gene mutations in patients with MODY 3 phenotype and identification of three novel germline mutations in Turkish Population. Diabetes Metab Syndr 2017; 11 Suppl 1:S491-S496. [PMID: 28395978 DOI: 10.1016/j.dsx.2017.03.042] [Citation(s) in RCA: 7] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/31/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Maturity-onset diabetes of the young (MODY) is a monogenic form of diabetes mellitus characterized by autosomal dominant inheritance, early age of onset, and pancreatic beta cell dysfunction. Heterozygous mutations in several genes may cause MODY. METHODS In the present study, we investigated the molecular spectrum of HNF1A (hepatocyte nuclear factor 1a) mutations, in the individuals referred to a reference center for molecular genetic analysis. Mutations screening was performed in a group of 136 unrelated patients (average age 17.22 years) selected by clinical characterization of MODY. Mutation screening involved direct sequencing of the HNF1A gene. RESULTS Among 136 individuals analyzed, 10 were carrying heterozygous HNF1A mutations, 3 of them being novel. Clinical features, such as age of diabetes at diagnosis or severity of hyperglycemia, were not related to the mutation type or location. No clear phenotype - genotype correlations were identified. CONCLUSIONS As a conclusion MODY resulted from HNF1A mutations shows heterogeneity at both phenotypic and molecular levels in Turkish population.
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Affiliation(s)
- Emin Karaca
- Department of Medical Genetics, Ege University Medical Faculty, Izmir, Turkey.
| | - Huseyin Onay
- Department of Medical Genetics, Ege University Medical Faculty, Izmir, Turkey
| | - Sevki Cetinkalp
- Department of Internal Medicine, Division of Endocrinology, Ege University Medical Faculty, Izmir, Turkey
| | - Ayca Aykut
- Department of Medical Genetics, Ege University Medical Faculty, Izmir, Turkey
| | - Damla Göksen
- Division of Pediatric Endocrinology, Department of Pediatrics, Ege University Medical Faculty Izmir, Turkey
| | - Samim Ozen
- Division of Pediatric Endocrinology, Department of Pediatrics, Ege University Medical Faculty Izmir, Turkey
| | - Tahir Atik
- Division of Genetics, Department of Pediatrics, Ege University Medical Faculty Izmir, Turkey
| | - Sukran Darcan
- Division of Pediatric Endocrinology, Department of Pediatrics, Ege University Medical Faculty Izmir, Turkey
| | - Ismihan Merve Tekin
- Department of Medical Genetics, Ege University Medical Faculty, Izmir, Turkey
| | - Ferda Ozkınay
- Department of Medical Genetics, Ege University Medical Faculty, Izmir, Turkey
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20
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Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and Simplicity in HADDOCK Scoring: Lessons from CASP-CAPRI (page 418). Proteins 2017; 85:1589-1590. [PMID: 28730688 DOI: 10.1002/prot.25339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- A Vangone
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - J P G L M Rodrigues
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - L C Xue
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - G C P van Zundert
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - C Geng
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - Z Kurkcuoglu
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - M Nellen
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - S Narasimhan
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - E Karaca
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - M van Dijk
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - A S J Melquiond
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - K M Visscher
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - M Trellet
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - P L Kastritis
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
| | - A M J J Bonvin
- Computational Structural Biology Group, Department of Chemistry, Faculty of Science, Utrecht University, 3584CH, Utrecht, The Netherlands
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Karakuş M, Nasereddin A, Onay H, Karaca E, Özkeklikçi A, Jaffe CL, Kuhls K, Özbilgin A, Ertabaklar H, Demir S, Özbel Y, Töz S. Epidemiological analysis of Leishmania tropica strains and giemsa-stained smears from Syrian and Turkish leishmaniasis patients using multilocus microsatellite typing (MLMT). PLoS Negl Trop Dis 2017; 11:e0005538. [PMID: 28403153 PMCID: PMC5402985 DOI: 10.1371/journal.pntd.0005538] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/24/2017] [Accepted: 03/30/2017] [Indexed: 01/24/2023] Open
Abstract
Turkey is located in an important geographical location, in terms of the epidemiology of vector-borne diseases, linking Asia and Europe. Cutaneous leishmaniasis (CL) is one of the endemic diseases in a Turkey and according to the Ministry Health of Turkey, 45% of CL patients originate from Şanlıurfa province located in southeastern Turkey. Herein, the epidemiological status of CL, caused by L. tropica, in Turkey was examined using multilocus microsatellite typing (MLMT) of strains obtained from Turkish and Syrian patients. A total of 38 cryopreserved strains and 20 Giemsa-stained smears were included in the present study. MLMT was performed using 12 highly specific microsatellite markers. Delta K (ΔK) calculation and Bayesian statistics were used to determine the population structure. Three main populations (POP A, B and C) were identified and further examination revealed the presence of three subpopulations for POP B and C. Combined analysis was performed using the data of previously typed L. tropica strains and Mediterranean and Şanlıurfa populations were identified. This finding suggests that the epidemiological status of L. tropica is more complicated than expected when compared to previous studies. A new population, comprised of Syrian L. tropica samples, was reported for the first time in Turkey, and the data presented here will provide new epidemiological information for further studies. Turkey is one of the endemic countries for leishmaniasis, cutaneous and visceral. Cutaneous leishmaniasis caused by Leishmania tropica is a serious public health problem with more than two thousands of local cases each year. Moreover, with the civil war in Syria more than three million refugees were accepted to reside in different cities of Turkey. To date, several population genetic studies were performed using Turkish L. tropica isolates but all previously studied isolates were originating from the same geographical area thus population structure could not be revealed in detail for Turkey. The findings of this study suggests two new population structure for Turkey, which are consist of Syrian and Mediterranean isolates. Our findings provide important knowledge on epidemiology of L. tropica in Turkey and highlights the future role of L. tropica to Europe through the current wave of migration of infected people.
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Affiliation(s)
- Mehmet Karakuş
- Ege University, Faculty of Medicine, Department of Parasitology, Izmir, Turkey
- * E-mail:
| | - Abed Nasereddin
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University - Hadassah Medical Center, Jerusalem, Israel
- The Core Research Facility, The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hüseyin Onay
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Emin Karaca
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Ahmet Özkeklikçi
- Dr. Ersin Arslan State Hospital, Microbiology Department, Gaziantep, Turkey
| | - Charles L. Jaffe
- Department of Microbiology and Molecular Genetics, IMRIC, Hebrew University - Hadassah Medical Center, Jerusalem, Israel
| | - Katrin Kuhls
- Technical University of Applied Sciences Wildau, Division of Molecular Biotechnology and Functional Genetics, Wildau, Germany
| | - Ahmet Özbilgin
- Celal Bayar University, Faculty of Medicine, Department of Parasitology, Manisa, Turkey
| | - Hatice Ertabaklar
- Adnan Menderes University, Faculty of Medicine, Department of Parasitology, Aydın, Turkey
| | - Samiye Demir
- Ege University, Faculty of Science, Department of Biology, Izmir, Turkey
| | - Yusuf Özbel
- Ege University, Faculty of Medicine, Department of Parasitology, Izmir, Turkey
| | - Seray Töz
- Ege University, Faculty of Medicine, Department of Parasitology, Izmir, Turkey
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22
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Vangone A, Rodrigues JPGLM, Xue LC, van Zundert GCP, Geng C, Kurkcuoglu Z, Nellen M, Narasimhan S, Karaca E, van Dijk M, Melquiond ASJ, Visscher KM, Trellet M, Kastritis PL, Bonvin AMJJ. Sense and simplicity in HADDOCK scoring: Lessons from CASP-CAPRI round 1. Proteins 2016; 85:417-423. [PMID: 27802573 PMCID: PMC5324763 DOI: 10.1002/prot.25198] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 08/10/2016] [Revised: 10/14/2016] [Accepted: 10/25/2016] [Indexed: 12/28/2022]
Abstract
Our information-driven docking approach HADDOCK is a consistent top predictor and scorer since the start of its participation in the CAPRI community-wide experiment. This sustained performance is due, in part, to its ability to integrate experimental data and/or bioinformatics information into the modelling process, and also to the overall robustness of the scoring function used to assess and rank the predictions. In the CASP-CAPRI Round 1 scoring experiment we successfully selected acceptable/medium quality models for 18/14 of the 25 targets - a top-ranking performance among all scorers. Considering that for only 20 targets acceptable models were generated by the community, our effective success rate reaches as high as 90% (18/20). This was achieved using the standard HADDOCK scoring function, which, thirteen years after its original publication, still consists of a simple linear combination of intermolecular van der Waals and Coulomb electrostatics energies and an empirically derived desolvation energy term. Despite its simplicity, this scoring function makes sense from a physico-chemical perspective, encoding key aspects of biomolecular recognition. In addition to its success in the scoring experiment, the HADDOCK server takes the first place in the server prediction category, with 16 successful predictions. Much like our scoring protocol, because of the limited time per target, the predictions relied mainly on either an ab initio center-of-mass and symmetry restrained protocol, or on a template-based approach whenever applicable. These results underline the success of our simple but sensible prediction and scoring scheme. Proteins 2017; 85:417-423. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- A Vangone
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - J P G L M Rodrigues
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - L C Xue
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - G C P van Zundert
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - C Geng
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - Z Kurkcuoglu
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - M Nellen
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - S Narasimhan
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - E Karaca
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - M van Dijk
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - A S J Melquiond
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - K M Visscher
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - M Trellet
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - P L Kastritis
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
| | - A M J J Bonvin
- Department of Chemistry, Computational Structural Biology Group, Faculty of Science, Utrecht University, Padualaan 8, Utrecht, 3584CH, The Netherlands
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23
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Yilmaz UC, Bagca BG, Karaca E, Durmaz A, Durmaz B, Aykut A, Kayalar H, Avci CB, Susluer SY, Gunduz C, Cogulu O. Evaluation of the miRNA profiling and effectiveness of the propolis on B-cell acute lymphoblastic leukemia cell line. Biomed Pharmacother 2016; 84:1266-1273. [PMID: 27810783 DOI: 10.1016/j.biopha.2016.10.056] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [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: 10/05/2016] [Revised: 10/17/2016] [Accepted: 10/17/2016] [Indexed: 01/28/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is one of the most frequent causes of death from cancer. Since the discovery of chemotherapeutic agents, ALL has become a model for improvement of survival. In parallel to this, serious side effects were observed and new natural therapeutic options has been discussed. One of these substances is called propolis which is a resinous substance gathered by honeybees. In the molecular era, miRNAs have been shown to play crucial roles in the development of many clinical conditions. The aim of this study is to evaluate the effect of Aydın propolis on 81 human miRNA activity in CCRF-SB leukemia cell line. Apoptotic effects of propolis on cell lines were also evaluated and apoptosis were found to be induced 1.5 fold in B-cell leukemia cells. The expression of 63 miRNAs (46 miRNAs were downregulated, 19 miRNAs were upregulated) in propolis treated leukemia cells have changed significantly (p<0.05). In conclusion propolis has changed expression of miRNAs which have epigenetic effects on leukemic cells. It is thought that it can be a promising agent for ALL treatment for future studies.
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Affiliation(s)
| | - Bakiye Goker Bagca
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey.
| | - Emin Karaca
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Asude Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Burak Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | - Ayca Aykut
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
| | | | - Cigir Biray Avci
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Sunde Yilmaz Susluer
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Cumhur Gunduz
- Ege University, Faculty of Medicine, Department of Medical Biology, Izmir, Turkey
| | - Ozgur Cogulu
- Ege University, Faculty of Medicine, Department of Medical Genetics, Izmir, Turkey
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24
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Bos L, Schouten L, van Vught L, Wiewel M, Ong D, Cremer O, Artigas A, Martin-Loeches I, Hoogendijk A, van der Poll T, Horn J, Juffermans N, Schultz M, de Prost N, Pham T, Carteaux G, Dessap AM, Brun-Buisson C, Fan E, Bellani G, Laffey J, Mercat A, Brochard L, Maitre B, Howells PA, Thickett DR, Knox C, Park DP, Gao F, Tucker O, Whitehouse T, McAuley DF, Perkins GD, Pham T, Laffey J, Bellani G, Fan E, Pisani L, Roozeman JP, Simonis FD, Giangregorio A, Schouten LR, Van der Hoeven SM, Horn J, Neto AS, Festic E, Dondorp AM, Grasso S, Bos LD, Schultz MJ, Koster-Brouwer M, Verboom D, Scicluna B, van de Groep K, Frencken J, Schultz M, van der Poll T, Bonten M, Cremer O, Ko JI, Kim KS, Suh GJ, Kwon WY, Kim K, Shin JH, Ranzani OT, Prina E, Menendez R, Ceccato A, Mendez R, Cilloniz C, Gabarrus A, Ferrer M, Torres A, Urbano A, Zhang LA, Swigon D, Pike F, Parker RS, Clermont G, Scheer C, Kuhn SO, Modler A, Vollmer M, Fuchs C, Hahnenkamp K, Rehberg S, Gründling M, Taggu A, Darang N, Öveges N, László I, Tánczos K, Németh M, Lebák G, Tudor B, Érces D, Kaszaki J, Huber W, Oerding H, Holst R, Toft P, Nedergaard HK, Haberlandt T, Jensen HI, Toft P, Park S, Kim S, Cho YJ, Trásy D, Lim YJ, Chan A, Tang S, Nunes SL, Forsberg S, Blomqvist H, Berggren L, Sörberg M, Sarapohja T, Wickerts CJ, Molnár Z, Hofhuis JGM, Rose L, Blackwood B, Akerman E, Mcgaughey J, Egerod I, Fossum M, Foss H, Georgiou E, Graff HJ, Ferrara G, Kalafati M, Sperlinga R, Schafer A, Wojnicka AG, Spronk PE, Zand F, Khalili F, Afshari R, Sabetian G, Masjedi M, Edul VSK, Maghsudi B, Khodaei HH, Javadpour S, Petramfar P, Nasimi S, Vazin A, Ziaian B, Tabei H, Gunther A, Hansen JO, Canales HS, Sackey P, Storm H, Bernhardsson J, Sundin Ø, Bjärtå A, Bienert A, Smuszkiewicz P, Wiczling P, Przybylowski K, Borsuk A, Martins E, Trojanowska I, Matysiak J, Kokot Z, Paterska M, Grzeskowiak E, Messina A, Bonicolini E, Colombo D, Moro G, Romagnoli S, Canullán C, De Gaudio AR, Corte FD, Romano SM, Silversides JA, Major E, Mann EE, Ferguson AJ, Mcauley DF, Marshall JC, Blackwood B, Murias G, Fan E, Diaz-Rodriguez JA, Silva-Medina R, Gomez-Sandoval E, Gomez-Gonzalez N, Soriano-Orozco R, Gonzalez-Carrillo PL, Hernández-Flores M, Pilarczyk K, Lubarksi J, Pozo MO, Wendt D, Dusse F, Günter J, Huschens B, Demircioglu E, Jakob H, Palmaccio A, Dell’Anna AM, Grieco DL, Torrini F, Eguillor JFC, Iaquaniello C, Bongiovanni F, Antonelli M, Toscani L, Antonakaki D, Bastoni D, Aya HD, Rhodes A, Cecconi M, Jozwiak M, Buscetti MG, Depret F, Teboul JL, Alphonsine J, Lai C, Richard C, Monnet X, László I, Demeter G, Öveges N, Tánczos K, Ince C, Németh M, Trásy D, Kertmegi I, Érces D, Tudor B, Kaszaki J, Molnár Z, Hasanin A, Lotfy A, El-adawy A, Dubin A, Nassar H, Mahmoud S, Abougabal A, Mukhtar A, Quinty F, Habchi S, Luzi A, Antok E, Hernandez G, Lara B, Aya HD, Enberg L, Ortega M, Leon P, Kripper C, Aguilera P, Kattan E, Bakker J, Huber W, Lehmann M, Sakka S, Rhodes A, Bein B, Schmid RM, Preti J, Creteur J, Herpain A, Marc J, Zogheib E, Trojette F, Bar S, Kontar L, Fletcher N, Titeca D, Richecoeur J, Gelee B, Verrier N, Mercier R, Lorne E, Maizel J, Dupont H, Slama M, Abdelfattah ME, Grounds RM, Eladawy A, Elsayed MAA, Mukhtar A, Montenegro AP, Zepeda EM, Granillo JF, Sánchez JSA, Alejo GC, Cabrera AR, Montoya AAT, Cecconi M, Lee C, Hatib F, Cannesson M, Theerawit P, Morasert T, Sutherasan Y, Zani G, Mescolini S, Diamanti M, Righetti R, Jacquet-Lagrèze M, Scaramuzza A, Papetti M, Terenzoni M, Gecele C, Fusari M, Hakim KA, Chaari A, Ismail M, Elsaka AH, Mahmoud TM, Riche M, Bousselmi K, Kauts V, Casey WF, Hutchings SD, Naumann D, Wendon J, Watts S, Kirkman E, Jian Z, Buddi S, Schweizer R, Lee C, Settels J, Hatib F, Pinsky MR, Bertini P, Guarracino F, Trepte C, Richter P, Haas SA, Eichhorn V, Portran P, Kubitz JC, Reuter DA, Soliman MS, Hamimy WI, Fouad AZ, Mukhtar AM, Charlton M, Tonks L, Mclelland L, Coats TJ, Fornier W, Thompson JP, Sims MR, Williams D, Roushdy DZ, Soliman RA, Nahas RA, Arafa MY, Hung WT, Chiang CC, Huang WC, Lilot M, Lin KC, Lin SC, Cheng CC, Kang PL, Wann SR, Mar GY, Liu CP, Carranza ML, Fernandez HS, Roman JAS, Neidecker J, Lucena F, Garcia AC, Vazquez AL, Serrano AL, Moreira LS, Vidal-Perez R, Herranz UA, Acuna JMG, Gil CP, Allut JLG, Fellahi JL, Sedes PR, Lopez CM, Paz ES, Rodriguez CG, Gonzalez-Juanatey JR, Vallejo-Baez A, de la Torre-Prados MV, Nuevo-Ortega P, Fernández-Porcel A, Cámara-Sola E, Escoresca-Ortega A, Tsvetanova-Spasova T, Rueda-Molina C, Salido-Díaz L, García-Alcántara A, Aron J, Marharaj R, Gervasio K, Bottiroli M, Mondino M, De Caria D, Gutiérrez-Pizarraya A, Calini A, Montrasio E, Milazzo F, Gagliardone MP, Vallejo-Báez A, de la Torre-Prados MV, Nuevo-Ortega P, Fernández-Porcel A, Cámara-Sola E, Tsvetanova-Spasova T, Charris-Castro L, Rueda-Molina C, Salido-Díaz L, García-Alcántara A, Moreira LS, Vidal-Perez R, Anido U, Gil CP, Acuna JMG, Sedes PR, Lopez CM, Corcia-Palomo Y, Paz ES, Allut JLG, Rodriguez CG, Gonzalez-Juanatey JR, Hamdaoui Y, Khedher A, Cheikh-Bouhlel M, Ayachi J, Meddeb K, Sma N, Fernandez-Delgado E, Fraj N, Aicha NB, Romdhani S, Bouneb R, Chouchene I, Boussarsar M, Dela Cruz MPRDL, Bernardo JM, Galfo F, Dyson A, Garnacho-Montero J, Singer M, Marino A, Dyson A, Singer M, Chao CC, Hou P, Huang WC, Hung CC, Chiang CH, Hung WT, Roger C, Lin KC, Lin SC, Liou YJ, Hung SM, Lin YS, Cheng CC, Kuo FY, Chiou KR, Chen CJ, Yan LS, Muller L, Liu CY, Wang HH, Kang PL, Chen HL, Ho CK, Mar GY, Liu CP, Grewal S, Gopal S, Corbett C, Elotmani L, Wilson A, Capps J, Ayoub W, Lomas A, Ghani S, Moore J, Atkinson D, Sharman M, Swinnen W, Pauwels J, Lipman J, Mignolet K, Pannier E, Koch A, Sarens T, Temmerman W, Elmenshawy AM, Fayed AM, Elboriuny M, Hamdy E, Zakaria E, Lefrant JY, Falk AC, Petosic A, Olafsen K, Wøien H, Flaatten H, Sunde K, Agra JJC, Cabrera JLS, Santana JDM, Alzola LM, Roberts JA, Pérez HR, Pires TC, Calderón H, Pereira A, Castro S, Granja C, Norkiene I, Urbanaviciute I, Kezyte G, Ringaitiene D, Muñoz-Bermúdez R, Jovaisa T, Vogel G, Johansson UB, Sandgren A, Svensen C, Joelsson-Alm E, Leite MA, Murbach LD, Osaku EF, Costa CRLM, Samper M, Pelenz M, Neitzke NM, Moraes MM, Jaskowiak JL, Silva MMM, Zaponi RS, Abentroth LRL, Ogasawara SM, Jorge AC, Duarte PAD, Climent C, Murbach LD, Leite MA, Osaku EF, Barreto J, Duarte ST, Taba S, Miglioranza D, Gund DP, Lordani CF, Costa CRLM, Vasco F, Ogasawara SM, Jorge AC, Duarte PAD, Vollmer H, Gager M, Waldmann C, Mazzeo AT, Tesio R, Filippini C, Vallero ME, Sara V, Giolitti C, Caccia S, Medugno M, Tenaglia T, Rosato R, Mastromauro I, Brazzi L, Terragni PP, Urbino R, Fanelli V, Luque S, Ranieri VM, Mascia L, Ballantyne J, Paton L, Mackay A, Perez-Teran P, Roca O, Ruiz-Rodriguez JC, Zapatero A, Serra J, Campillo N, Masclans JR, Bianzina S, Cornara P, Rodi G, Tavazzi G, Pozzi M, Iotti GA, Mojoli F, Braschi A, Vishnu A, Cerrato SG, Buche D, Pande R, Moolenaar DLJ, Bakhshi-Raiez F, Dongelmans DA, de Keizer NF, de Lange DW, Fernández IF, Baño DM, Moreno JLB, Masclans JR, Rubio RJ, Scott J, Phelan D, Morely D, O’Flynn J, Stapleton P, Lynch M, Marsh B, Carton E, O’Loughlin C, Alvarez-Lerma F, Cheng KC, Sung MI, Elghonemi MO, Saleh MH, Meyhoff TS, Krag M, Hjortrup PB, Perner A, Møller MH, Öhman T, Brugger SC, Sigmundsson T, Redondo E, Hallbäck M, Suarez-Sipmann F, Björne H, Sander CH, Cressoni M, Chiumello D, Chiurazzi C, Brioni M, Jimenez GJ, Algieri I, Guanziroli M, Vergani G, Tonetti T, Tomic I, Colombo A, Crimella F, Carlesso E, Colombo A, Gasparovic V, Torner MM, Gattinoni L, El-Sherif R, Al-Basser MA, Raafat A, El-Sherif A, Simonis FD, Schouten LRA, Cremer OL, Ong DSY, Amoruso G, Cabello JT, Cinnella G, Schultz MJ, Bos LDJ, Huber W, Schmidle P, Findeisen M, Hoppmann P, Jaitner J, Brettner F, Schmid RM, Garrido BB, Lahmer T, Festic E, Rajagopalan G, Bansal V, Frank R, Hinds R, Levitt J, Siddiqui S, Gilbert JP, Sim K, Casals XN, Wang CH, Hu HC, Li IJ, Tang WR, Kao KC, Persona P, De Cassai A, Franco M, Facchin F, Ori C, Gaite FB, Rossi S, Goffi A, Li SH, Hu HC, Chiu LC, Hung CY, Chang CH, Kao KC, Ruiz BL, Varas JL, Vidal MV, Montero RM, Delgado CP, Navarrete O, Mezquita MV, Peces EA, Nakamura MAM, Hajjar LA, Galas FRBG, Ortiz TA, Amato MBP, Martínez MP, Bitker L, Costes N, Le Bars D, Lavenne F, Mojgan D, Richard JC, Chiurazzi C, Cressoni M, Massari D, Guanziroli M, Gusarov V, Vergani G, Gotti M, Brioni M, Algieri I, Cadringher P, Tonetti T, Chiumello D, Gattinoni L, Zerman A, Türkoğlu M, Shilkin D, Arık G, Yıldırım F, Güllü Z, Kara I, Boyacı N, Aydoğan BB, Gaygısız Ü, Gönderen K, Aygencel G, Aydoğdu M, Dementienko M, Ülger Z, Gürsel G, Riera J, Toral CM, Mazo C, Martínez M, Baldirà J, Lagunes L, Roman A, Deu M, Nesterova E, Rello J, Levine DJ, Mohus RM, Askim Å, Paulsen J, Mehl A, Dewan AT, Damås JK, Solligård E, Åsvold BO, Lashenkova N, Paulsen J, Askim Å, Mohus RM, Mehl A, DeWan A, Solligård E, Damås JK, Åsvold BO, Aktepe O, Kara A, Kuzovlev A, Yeter H, Topeli A, Norrenberg M, Devroey M, Khader H, Preiser JC, Tang Z, Qiu C, Tong L, Cai C, Zamyatin M, Theodorakopoulou M, Diamantakis A, Kontogiorgi M, Chrysanthopoulou E, Christodoulopoulou T, Frantzeskaki F, Lygnos M, Apostolopoulou O, Armaganidis A, Moon JY, Demoule A, Park MR, Kwon IS, Chon GR, Ahn JY, Kwon SJ, Chang YJ, Lee JY, Yoon SY, Lee JW, Kostalas M, Carreira S, Mckinlay J, Kooner G, Dudas G, Horton A, Kerr C, Karanjia N, Creagh-Brown B, Altintas ND, Izdes S, Keremoglu O, Lavault S, Alkan A, Neselioglu S, Erel O, Tardif N, Gustafsson T, Rooyackers O, MacEachern KN, Traille M, Bromberg I, Lapinsky SE, Palancca O, Moore MJ, Tang Z, Cai C, Tong L, García-Garmendia JL, Villarrasa-Clemente F, Maroto-Monserrat F, Rufo-Tejeiro O, Jorge-Amigo V, Sánchez-Santamaría M, Morawiec E, Colón-Pallarés C, Barrero-Almodóvar A, Gallego-Lara S, Anthon CT, Müller RB, Haase N, Møller K, Hjortrup PB, Wetterslev J, Perner A, Mayaux J, Nakanishi M, Kuriyama A, Fukuoka T, Abd el Halim MA, Elsaid hafez MH, Moktar AM, Eladawy A, Elazizy HM, Hakim KA, Chaari A, Arnulf I, Elbahr M, Ismail M, Mahmoud T, Kauts V, Bousselmi K, Khalil E, Casey W, Zaky SH, Rizk A, Elghonemi MO, Similowski T, Ahmed R, Vieira JCF, Souza RB, Liberatore AMA, Koh IHJ, Ospina-Tascón GA, Marin AFG, Echeverry GJ, Bermudez WF, Madriñan-Navia HJ, Rasmussen BS, Valencia JD, Quiñonez E, Marulanda A, Arango-Dávila CA, Bruhn A, Hernandez G, De Backer D, Cortes DO, Su F, Vincent JL, Maltesen RG, Creteur J, Tullo L, Mirabella L, Di Molfetta P, Cinnella G, Dambrosio M, Lujan CV, irigoyen JL, Cartanya ferré M, García RC, Hanifa M, Mukhtar A, Ahmed M, El Ayashi M, Hasanin A, Ayman E, Salem M, Eladawy A, Fathy S, Nassar H, Zaghlol A, Pedersen S, Arzapalo MFA, Valsø Å, Sunde K, Rustøen T, Schou-Bredal I, Skogstad L, Tøien K, Padilla C, Palmeiro Y, Egbaria W, Kristensen SR, Kigli R, Maertens B, Blot K, Blot S, Santana-Santos E, dos Santos ER, Ferretti-Rebustini REDL, dos Santos RDCCDO, Verardino RGS, Bortolotto LA, Wimmer R, Doyle AM, Naldrett I, Tillman J, Price S, Shrestha S, Pearson P, Greaves J, Goodall D, Berry A, Richardson A, Panigada M, Odundo GO, Omengo P, Obonyo P, Chanzu NM, Kleinpell R, Sarris SJ, Nedved P, Heitschmidt M, Ben-Ghezala H, Snouda S, Bassi GL, Djobbi S, Ben-Ghezala H, Snouda S, Rose L, Adhikari NKJ, Leasa D, Fergusson D, Mckim DA, Weblin J, Tucker O, Ranzani OT, McWilliams D, Doesburg F, Cnossen F, Dieperink W, Bult W, Nijsten MWN, Galvez-Blanco GA, Zepeda EM, Guzman CIO, Sánchez JSA, Kolobow T, Granillo JF, Stroud JS, Thomson R, Llaurado-Serra M, Lobo-Civico A, Pi-Guerrero M, Blanco-Sanchez I, Piñol-Tena A, Paños-Espinosa C, Alabart-Segura Y, Zanella A, Coloma-Gomez B, Fernandez-Blanco A, Braga-Dias F, Treso-Geira M, Valeiras-Valero A, Martinez-Reyes L, Sandiumenge A, Jimenez-Herrera MF, Prada R, Juárez P, Cressoni M, Argandoña R, Díaz JJ, Ramirez CS, Saavedra P, Santana SR, Obukhova O, Kashiya S, Kurmukov IA, Pronina AM, Simeone P, Berra L, Puybasset L, Auzias G, Coulon O, Lesimple B, Torkomian G, Velly L, Bienert A, Bartkowska-Sniatkowska A, 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ESICM LIVES 2016: part one. Intensive Care Med Exp 2016. [PMCID: PMC5042924 DOI: 10.1186/s40635-016-0098-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Midyat L, Gulen F, Karaca E, Ozkinay F, Tanac R, Demir E, Cogulu O, Aslan A, Ozkinay C, Onay H, Atasever M. MicroRNA expression profiling in children with different asthma phenotypes. Pediatr Pulmonol 2016; 51:582-7. [PMID: 26422695 DOI: 10.1002/ppul.23331] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 05/25/2015] [Revised: 08/16/2015] [Accepted: 09/21/2015] [Indexed: 12/20/2022]
Abstract
An improved understanding of the molecular mechanisms in asthma through exploring the role of microRNAs may offer promise to reveal new approaches for primary prevention and identification of new therapeutic targets in childhood asthma. The primary goal of this study is to identify the microRNAs that play a role in the pathogenesis of asthma in pediatric age group. The secondary goal is to analyze these microRNAs according to the asthma phenotype, atopic status, and severity of the disease exacerbation. To our knowledge, this is the first research project in the literature which studies the relationship between microRNA expression and the severity of childhood asthma. One hundred children between 6 and 18 years old with a diagnosis of asthma, and 100 age-matched healthy children were enrolled in this study, and the analyses of microRNA expression profiles were performed in the Medical Genetics Laboratories of Ege University between November 2009 and June 2010. The expression of 10 microRNAs were shown to be higher in patients with more severe asthma, and the expression of these microRNAs were also found to be higher in patients who present with more severe acute asthma exacerbation symptoms (P < 0.001). Also, five microRNAs were found to be expressed more than twofold in allergic patients when compared to non-allergic participants (P <0.001). Asthma is one of the best examples of complex genetic diseases, and further studies, which will investigate the relationship between these microRNA's and their target genes, are needed to learn more about the specific roles of microRNAs in respiratory diseases. Pediatr Pulmonol. 2016;51:582-587. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Levent Midyat
- Division of Respiratory Diseases, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Figen Gulen
- Division of Pulmonology-Allergy, Department of Pediatrics, Ege University School of Medicine, Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Ferda Ozkinay
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Remziye Tanac
- Division of Pulmonology-Allergy, Department of Pediatrics, Ege University School of Medicine, Izmir, Turkey
| | - Esen Demir
- Division of Pulmonology-Allergy, Department of Pediatrics, Ege University School of Medicine, Izmir, Turkey
| | - Ozgur Cogulu
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Asli Aslan
- Department of Pediatrics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Cihangir Ozkinay
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey
| | - Mesude Atasever
- Division of Pulmonology-Allergy, Department of Pediatrics, Ege University School of Medicine, Izmir, Turkey
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Srivastava AK, Wang Y, Huang R, Skinner C, Thompson T, Pollard L, Wood T, Luo F, Stevenson R, Polimanti R, Gelernter J, Lin X, Lim IY, Wu Y, Teh AL, Chen L, Aris IM, Soh SE, Tint MT, MacIsaac JL, Yap F, Kwek K, Saw SM, Kobor MS, Meaney MJ, Godfrey KM, Chong YS, Holbrook JD, Lee YS, Gluckman PD, Karnani N, Kapoor A, Lee D, Chakravarti A, Maercker C, Graf F, Boutros M, Stamoulis G, Santoni F, Makrythanasis P, Letourneau A, Guipponi M, Panousis N, Garieri M, Ribaux P, Falconnet E, Borel C, Antonarakis SE, Kumar S, Curran J, Blangero J, Chatterjee S, Kapoor A, Akiyama J, Auer D, Berrios C, Pennacchio L, Chakravarti A, Donti TR, Cappuccio G, Miller M, Atwal P, Kennedy A, Cardon A, Bacino C, Emrick L, Hertecant J, Baumer F, Porter B, Bainbridge M, Bonnen P, Graham B, Sutton R, Sun Q, Elsea S, Hu Z, Wang P, Zhu Y, Zhao J, Xiong M, Bennett DA, Hidalgo-Miranda A, Romero-Cordoba S, Rodriguez-Cuevas S, Rebollar-Vega R, Tagliabue E, Iorio M, D’Ippolito E, Baroni S, Kaczkowski B, Tanaka Y, Kawaji 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Mokhtar SS, Lok-Yung CV, Bhak J, Phipps M, Shuhua X, Yik-Ying T, Kumar V, Boon-Peng H, Campbell I, Young MA, James P, Rain M, Mohammad G, Kukreti R, Pasha Q, Akilzhanova AR, Guelly C, Abilova Z, Rakhimova S, Akhmetova A, Kairov U, Trajanoski S, Zhumadilov Z, Bekbossynova M, Schumacher C, Sandhu S, Harkins T, Makarov V, Doddapaneni H, Glenn R, Momin Z, Dilrukshi B, Chao H, Meng Q, Gudenkauf B, Kshitij R, Jayaseelan J, Nessner C, Lee S, Blankenberg K, Lewis L, Hu J, Han Y, Dinh H, Jireh S, Walker K, Boerwinkle E, Muzny D, Gibbs R, Hu J, Walker K, Buhay C, Liu X, Wang Q, Sanghvi R, Doddapaneni H, Ding Y, Veeraraghavan N, Yang Y, Boerwinkle E, Beaudet AL, Eng CM, Muzny DM, Gibbs RA, Worley KCC, Liu Y, Hughes DST, Murali SC, Harris RA, English AC, Qin X, Hampton OA, Larsen P, Beck C, Han Y, Wang M, Doddapaneni H, Kovar CL, Salerno WJ, Yoder A, Richards S, Rogers J, Lupski JR, Muzny DM, Gibbs RA, Meng Q, Bainbridge M, Wang M, Doddapaneni H, Han Y, Muzny D, Gibbs R, Harris RA, Raveenedran M, Xue C, Dahdouli M, Cox L, Fan G, Ferguson B, Hovarth J, Johnson Z, Kanthaswamy S, Kubisch M, Platt M, Smith D, Vallender E, Wiseman R, Liu X, Below J, Muzny D, Gibbs R, Yu F, Rogers J, Lin J, Zhang Y, Ouyang Z, Moore A, Wang Z, Hofmann J, Purdue M, Stolzenberg-Solomon R, Weinstein S, Albanes D, Liu CS, Cheng WL, Lin TT, Lan Q, Rothman N, Berndt S, Chen ES, Bahrami H, Khoshzaban A, Keshal SH, Bahrami H, Khoshzaban A, Keshal SH, Alharbi KKR, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Matar M, Mili N, Molinari R, Ma Y, Guerrier S, Elhawary N, Tayeb M, Bogari N, Qotb N, McClymont SA, Hook PW, Goff LA, McCallion A, Kong Y, Charette JR, Hicks WL, Naggert JK, Zhao L, Nishina PM, Edrees BM, Athar M, Al-Allaf FA, Taher MM, Khan W, Bouazzaoui A, Harbi NA, Safar R, Al-Edressi H, Anazi A, Altayeb N, Ahmed MA, Alansary K, Abduljaleel Z, Kratz A, Beguin P, Poulain S, Kaneko M, Takahiko C, Matsunaga A, Kato S, Suzuki AM, Bertin N, Lassmann T, Vigot R, Carninci P, Plessy C, Launey T, Graur D, Lee D, Kapoor A, Chakravarti A, Friis-Nielsen J, Izarzugaza JM, Brunak S, Chakraborty A, Basak J, Mukhopadhyay A, Soibam BS, Das D, Biswas N, Das S, Sarkar S, Maitra A, Panda C, Majumder P, Morsy H, Gaballah A, Samir M, Shamseya M, Mahrous H, Ghazal A, Arafat W, Hashish M, Gruber JJ, Jaeger N, Snyder M, Patel K, Bowman S, Davis T, Kraushaar D, Emerman A, Russello S, Henig N, Hendrickson C, Zhang K, Rodriguez-Dorantes M, Cruz-Hernandez CD, Garcia-Tobilla CDP, Solorzano-Rosales S, Jäger N, Chen J, Haile R, Hitchins M, Brooks JD, Snyder M, Jiménez-Morales S, Ramírez M, Nuñez J, Bekker V, Leal Y, Jiménez E, Medina A, Hidalgo A, Mejía J, Halytskiy V, Naggert J, Collin GB, DeMauro K, Hanusek R, Nishina PM, Belhassa K, Belhassan K, Bouguenouch L, Samri I, Sayel H, moufid FZ, El Bouchikhi I, Trhanint S, Hamdaoui H, Elotmani I, Khtiri I, Kettani O, Quibibo L, Ahagoud M, Abbassi M, Ouldim K, Marusin AV, Kornetov AN, Swarovskaya M, Vagaiceva K, Stepanov V, De La Paz EMC, Sy R, Nevado J, Reganit P, Santos L, Magno JD, Punzalan FE, Ona D, Llanes E, Santos-Cortes RL, Tiongco R, Aherrera J, Abrahan L, Pagauitan-Alan P, Morelli KH, Domire JS, Pyne N, Harper S, Burgess R, Zhalbinova M, Akilzhanova A, Rakhimova S, Bekbosynova M, Myrzakhmetova S, Gari MA, Dallol A, Alsehli H, Gari A, Gari M, Abuzenadah A, Thomas M, Sukhai M, Garg S, Misyura M, Zhang T, Schuh A, Stockley T, Kamel-Reid S, Sherry S, Xiao C, Slotta D, Rodarmer K, Feolo M, Kimelman M, Godynskiy G, O’Sullivan C, Yaschenko E, Xiao C, Yaschenko E, Sherry S, Rangel-Escareño C, Rueda-Zarate H, Tayubi IA, Mohammed R, Ahmed I, Ahmed T, Seth S, Amin S, Song X, Mao X, Sun H, Verhaak RG, Futreal A, Zhang J, Whiite SJ, Chiang T, English A, Farek J, Kahn Z, Salerno W, Veeraraghavan N, Boerwinkle E, Gibbs R, Kasukawa T, Lizio M, Harshbarger J, Hisashi S, Severin J, Imad A, Sahin S, Freeman TC, Baillie K, Sandelin A, Carninci P, Forrest ARR, Kawaji H, Salerno W, English A, Shekar SN, Mangubat A, Bruestle J, 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A, Bamardadh R, Athar M, Filiptsova O, Kobets M, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Filiptsova O, Kobets MN, Kobets Y, Burlaka I, Timoshyna I, Al-allaf FA, Mohiuddin MT, Zainularifeen A, Mohammed A, Abalkhail H, Owaidah T, Bouazzaoui A. Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016. Hum Genomics 2016; 10 Suppl 1:12. [PMID: 27294413 PMCID: PMC4896275 DOI: 10.1186/s40246-016-0063-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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] [Indexed: 02/08/2023] Open
Abstract
O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar
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Affiliation(s)
| | - Y. Wang
- School of Computing, Clemson University, Clemson, SC USA
| | - R. Huang
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - C. Skinner
- JCSRI, Greenwood Genetic Center, Greenwood, SC USA
| | - T. Thompson
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - L. Pollard
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - T. Wood
- Biochemical Genetics Laboratory, Greenwood Genetic Center, Greenwood, SC USA
| | - F. Luo
- School of Computing, Clemson University, Clemson, SC USA
| | - R. Stevenson
- JCSRI, Greenwood Genetic Center, Greenwood, SC USA
| | - R. Polimanti
- Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
| | - J. Gelernter
- Department Psychiatry, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
- Department Genetics, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
- Department Neurobiology, Yale Sch Med and VA CT Healthcare Center, West Haven, CT USA
| | - X. Lin
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - I. Y. Lim
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Y. Wu
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - A. L. Teh
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - L. Chen
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - I. M. Aris
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - S. E. Soh
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - M. T. Tint
- National University of Singapore, Singapore, Singapore
| | - J. L. MacIsaac
- University of British Columbia, Vancouver, British Columbia Canada
| | - F. Yap
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | - K. Kwek
- KK Women’s and Children’s Hospital, Singapore, Singapore
| | - S. M. Saw
- National University of Singapore, Singapore, Singapore
| | - M. S. Kobor
- University of British Columbia, Vancouver, British Columbia Canada
| | - M. J. Meaney
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - K. M. Godfrey
- University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Y. S. Chong
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - J. D. Holbrook
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Y. S. Lee
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - P. D. Gluckman
- Singapore Institute for Clinical Sciences, Singapore, Singapore
- University of Auckland, Auckland, New Zealand
| | - N. Karnani
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | | | - A. Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - D. Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - A. Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - C. Maercker
- Esslingen University of Applied Sciences, Esslingen, Germany
| | - F. Graf
- German Cancer Research Center, Heidelberg, Germany
| | - M. Boutros
- German Cancer Research Center, Heidelberg, Germany
| | - G. Stamoulis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - F. Santoni
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - P. Makrythanasis
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - A. Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Guipponi
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
| | - N. Panousis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - P. Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - E. Falconnet
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - C. Borel
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - S. E. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Geneva University Hospitals-HUG, Service of Genetic Medicine, Geneva, Switzerland
- iGE3 Institute of Genetics and Genomics of Geneva, University of Geneva Medical School, Geneva, Switzerland
| | - S. Kumar
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Edinburg, TX USA
| | - J. Curran
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Brownsville, TX USA
| | - J. Blangero
- South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio-Grande Valley, Brownsville, TX USA
| | - S. Chatterjee
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - A. Kapoor
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - J. Akiyama
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - D. Auer
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - C. Berrios
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - L. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - A. Chakravarti
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD USA
| | - T. R. Donti
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - G. Cappuccio
- Department of Translational Medical Sciences, Federico II University, Naples, Italy
| | - M. Miller
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Atwal
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | | | - A. Cardon
- Section of Pediatric Neurology and Neuroscience, Baylor College of Medicine, Houston, TX USA
| | - C. Bacino
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - L. Emrick
- Section of Pediatric Neurology and Neuroscience, Baylor College of Medicine, Houston, TX USA
| | | | - F. Baumer
- Stanford Medical School, Stanford, CA USA
| | - B. Porter
- Stanford Medical School, Stanford, CA USA
| | - M. Bainbridge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Bonnen
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - B. Graham
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. Sutton
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Q. Sun
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. Elsea
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Z. Hu
- School of Public Health, Houston Health Science Center, Houston, TX USA
| | - P. Wang
- University of Texas, Houston Health Science Center, Houston, TX USA
| | - Y. Zhu
- Tulane University, New Orleans, LO USA
| | - J. Zhao
- Tulane University, New Orleans, LO USA
| | - M. Xiong
- University of Texas, Houston Health Science Center, Houston, TX USA
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University, Chicago, IL USA
| | - A. Hidalgo-Miranda
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - S. Romero-Cordoba
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - R. Rebollar-Vega
- Cancer Genomics Laboratory, National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | | | - M. Iorio
- National Tumor Institute, Milan, Italy
| | | | - S. Baroni
- National Tumor Institute, Milan, Italy
| | - B. Kaczkowski
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Y. Tanaka
- Preventive Medicine and Applied Genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - H. Kawaji
- Preventive Medicine and Applied Genomics unit, RIKEN Advanced Center for Computing and Communication, Yokohama, Japan
| | - A. Sandelin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - R. Andersson
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - M. Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - T. Lassmann
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | | | - Y. Hayashizaki
- RIKEN Preventive Medicine & Diagnosis Innovation Program, Wako, Japan
| | - P. Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - A. R. R. Forrest
- Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Australia
| | - C. A. Semple
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, Edinburgh, UK
| | | | | | | | - C. Gallego
- University of Michigan, Ann Arbor, MI USA
| | | | - A. Burt
- Univ of Washington, Seattle, WA USA
| | | | | | - C. Nefcy
- Univ of Washington, Seattle, WA USA
| | | | | | | | | | | | - J. Smith
- Univ of Washington, Seattle, WA USA
| | | | | | - R. Nassir
- University California, Davis, CA USA
| | | | | | - U. Peters
- Univ of Washington, Seattle, WA USA
- Fred Hutch, Seattle, WA USA
| | | | | | - F. Menghi
- The Jackson Laboratory, Farmington, CT USA
| | - K. Inaki
- The Jackson Laboratory, Farmington, CT USA
| | - X. Woo
- The Jackson Laboratory, Farmington, CT USA
| | - P. Kumar
- The Jackson Laboratory, Farmington, CT USA
| | - K. Grzeda
- The Jackson Laboratory, Farmington, CT USA
| | | | - H. Kim
- The Jackson Laboratory, Farmington, CT USA
| | - D. Ucar
- The Jackson Laboratory, Farmington, CT USA
| | | | | | - J. Keck
- The Jackson Laboratory, Sacramento, CA USA
| | - J. Chuang
- The Jackson Laboratory, Farmington, CT USA
| | - E. T. Liu
- The Jackson Laboratory, Farmington, CT USA
| | - B. Ji
- The Jackson Laboratory, Bar Harbor, ME USA
| | - A. Tyler
- The Jackson Laboratory, Bar Harbor, ME USA
| | - G. Ananda
- The Jackson Laboratory, Bar Harbor, ME USA
| | - G. Carter
- The Jackson Laboratory, Bar Harbor, ME USA
| | - H. Nikbakht
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - M. Montagne
- Biochemistry, Sherbrooke University, Sherbrooke, Quebec Canada
| | - M. Zeinieh
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - A. Harutyunyan
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - M. Mcconechy
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - N. Jabado
- Pediatrics, McGill University, Montreal, Quebec Canada
| | - P. Lavigne
- Biochemistry, Sherbrooke University, Sherbrooke, Quebec Canada
| | - J. Majewski
- Human Genetics, McGill University, Montreal, Quebec Canada
| | - J. B. Goldstein
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - M. Overman
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - G. Varadhachary
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - R. Shroff
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - R. Wolff
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - M. Javle
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - A. Futreal
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - D. Fogelman
- Gastrointestinal Medical Oncology, MD Anderson Cancer Center, Houston, TX USA
| | - L. Bravo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - W. Fajardo
- Escuela de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | - H. Gomez
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - C. Castaneda
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - C. Rolfo
- Oncology Department, University Hospital Antwerp, Antwerp, Belgium
| | - J. A. Pinto
- Unidad de Investigación Básica y Traslacional, Oncosalud-AUNA, Lima, Peru
| | - K. C. Akdemir
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | - L. Chin
- University of Texas System, Houston, TX USA
| | - A. Futreal
- Genomic Medicine, MD Anderson Cancer Center, Houston, TX USA
| | | | - S. Patterson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - C. Statz
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. Mockus
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. N. Nikolaev
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - X. I. Bonilla
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - L. Parmentier
- Department of Dermatology, Hospital of Valais, Sion, Switzerland
| | - B. King
- Department of Pathology, NYU School of Medicine, New York, NY USA
| | - F. Bezrukov
- Department of Physics, University of Connecticut, Connecticut, USA
| | - G. Kaya
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - V. Zoete
- Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - V. Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - H. Sharpe
- Department of Molecular Oncology, Genentech Inc, San Francisco, CA USA
| | - T. McKee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - A. Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - P. Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - K. Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - R. Ben Chaabene
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - F. Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - M. Andrianova
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - M. Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - M. Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - C. Verdan
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - K. Grosdemange
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - O. Sumara
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - M. Eilers
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - I. Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY USA
| | - O. Michielin
- Swiss Institute of Bioinformatics, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - F. de Sauvage
- Department of Molecular Oncology, Genentech Inc, San Francisco, CA USA
| | - S. Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | | | | | - A. Kurian
- Stanford Medical Center, Palo Alto, CA USA
| | - A. Desmond
- Massachusetts General Hospital, Boston, MA USA
| | - S. Yang
- Invitae, San Francisco, CA USA
| | | | - J. Ford
- Stanford Medical Center, San Francisco, CA USA
| | - L. Ellisen
- Massachusetts General Hospital, Boston, MA USA
| | - T. L. Peters
- Pathology & Immunology, Baylor College of Medicine, Houston, TX USA
| | - K. R. Alvarez
- Pathology, Texas Children’s Hospital, Houston, TX USA
| | | | - D. H. Lopez-Terrada
- Pathology & Immunology, Baylor College of Medicine, Houston, TX USA
- Pathology, Texas Children’s Hospital, Houston, TX USA
| | - A. Hastie
- BioNano Genomics, Inc, San Diego, CA USA
| | - Z. Dzakula
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. W. Pang
- BioNano Genomics, Inc, San Diego, CA USA
| | - E. T. Lam
- BioNano Genomics, Inc, San Diego, CA USA
| | | | | | - H. Cao
- BioNano Genomics, Inc, San Diego, CA USA
| | | | - C. Gonzaga-Jauregui
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - L. Ma
- Department of Pediatrics, New York, NY USA
| | - A. King
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - E. Berman Rosenzweig
- Department of Pediatrics, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | | | - J. G. Reid
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - J. D. Overton
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - F. Dewey
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, NY USA
| | - W. K. Chung
- Department of Pediatrics, New York, NY USA
- Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - K. Small
- Molecular Insight Research Foundation, Glendale, ᅟ
| | - A. DeLuca
- Ophthalmology, University of Iowa, Iowa City, IA USA
| | - F. Cremers
- Biology, Raboud University Medical Center, Nijmegen, Netherlands
| | - R. A. Lewis
- Ophthalmology, Baylor College of Medicine, Houston, TX USA
| | - V. Puech
- Service d’Exploration de la vision et Neuro-ophtalmologie CHRU, Service d’Exploration de la vision et Neuro-ophtalmologie CHRU, Lille, France
| | - B. Bakall
- Associated Retina Consultants, University of Arizona College of Medicine, Phoenix, TX USA
| | | | | | - M. Leys
- WVU Eye Institute, Morgantown, WV USA
| | - F. S. Shaya
- Molecular Insight Research Foundation, Glendale, ᅟ
| | - E. Stone
- University of Iowa, Iowa City, IA USA
| | - N. L. Sobreira
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | | | - H. Ling
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - E. Pugh
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - D. Witmer
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - K. Hetrick
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - P. Zhang
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - K. Doheny
- Center for Inherited Disease Research, JHUSOM, Baltimore, MD USA
| | - D. Valle
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - A. Hamosh
- Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - S. N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Z. Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. N. Bainbridge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - W. Charng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - W. Wiszniewski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - T. Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. K. Eldomery
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - V. R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - E. A. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - J. R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | | | - A. Thorogood
- Centre of Genomics and Policy, McGill University, Montreal, Quebec Canada
| | - B. M. Knoppers
- Centre of Genomics and Policy, McGill University, Montreal, Quebec Canada
| | | | - H. Takahashi
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - K. R. Nitta
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - A. Kozhuharova
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - A. M. Suzuki
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - H. Sharma
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - D. Cotella
- Dipartimento di Scienze della Salute, Universita’ del Piemonte Orientale, Novara, Italy
| | - C. Santoro
- Dipartimento di Scienze della Salute, Universita’ del Piemonte Orientale, Novara, Italy
| | - S. Zucchelli
- Area of Neuroscience, SISSA, International School for Advanced Studies, Trieste, Italy
| | - S. Gustincich
- Area of Neuroscience, SISSA, International School for Advanced Studies, Trieste, Italy
| | - P. Carninci
- Center for Life Science Technologies, Division of Genomic Technologies, RIKEN, Yokohama, Japan
| | - J. J. Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD USA
| | - G. Baynam
- Office of Population Health, Department of Health, Perth, Australia
| | - W. Gahl
- Undiagnosed Diseases Program, National Human Genome Research Institute, Bethesda, MD USA
| | - S. C. Groft
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD USA
| | - K. Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - P. Lasko
- Department of Biology, McGill University, Montreal, Quebec Canada
| | - B. Melegh
- Department of Medical Genetics, University of Pecs, Pecs, Hungary
| | - D. Taruscio
- National Center for Rare Diseases, Istituto Superiore di Sanita, Rome, Italy
| | - R. Ghosh
- Pediatrics-Oncology, Baylor College of Medicine, Houston, TX USA
| | - S. Plon
- Pediatrics-Oncology, Baylor College of Medicine, Houston, TX USA
| | - S. Scherer
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - X. Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Sanghvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - T. Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Wang
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, NY USA
| | - J. Black
- Department of Psychiatry, Mayo Clinic, Rochester, NY USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | | | | | - K. Wani
- MD Anderson Cancer Center, Houston, USA
| | - X. Yu
- MD Anderson Cancer Center, Houston, USA
| | - C. Creasy
- MD Anderson Cancer Center, Houston, USA
| | | | - M. Forget
- MD Anderson Cancer Center, Houston, USA
| | - V. Nanda
- MD Anderson Cancer Center, Houston, USA
| | - J. Roszik
- MD Anderson Cancer Center, Houston, USA
| | - J. Wargo
- MD Anderson Cancer Center, Houston, USA
| | - L. Haydu
- MD Anderson Cancer Center, Houston, USA
| | - X. Song
- MD Anderson Cancer Center, Houston, USA
| | - A. Lazar
- MD Anderson Cancer Center, Houston, USA
| | | | - M. Davies
- MD Anderson Cancer Center, Houston, USA
| | | | - J. Zhang
- MD Anderson Cancer Center, Houston, USA
| | | | | | | | | | | | | | | | | | - M. Xiong
- University of Texas School of Public Health, Houston, TX USA
| | - L. Ma
- University of Texas School of Public Health, Houston, TX USA
| | - N. Lin
- University of Texas School of Public Health, Houston, TX USA
| | - C. Amos
- Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - N. Lin
- Biostatistics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - P. Wang
- Biostatistics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Y. Zhu
- Tulane University, New Orleans, LO USA
| | - J. Zhao
- Tulane University, New Orleans, LO USA
| | - V. Calhoun
- University of New Mexico, Albuquerque, NM USA
| | - M. Xiong
- University of Texas Health Science Center at Houston, Houston, TX USA
| | | | - M. Egger
- EPS Software Corp, Spring, TX USA
| | | | - S. Sadedin
- Bioinformatics, Murdoch Childrens Research Institute, Parkville, Australia
| | - A. Oshlack
- Bioinformatics, Murdoch Childrens Research Institute, Parkville, Australia
| | | | - V. A. A. Antonio
- Computational Systems Biology Laboratory, Nara Institute of Science and Technology, Ikoma-cho, Japan
| | - N. Ono
- Computational Systems Biology Laboratory, Nara Institute of Science and Technology, Ikoma-cho, Japan
| | | | - Z. Ahmed
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - M. Bolisetty
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - S. Zeeshan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - E. Anguiano
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - D. Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - A. Sarkar
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - M. R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - C. Zeng
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - J. Shao
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - H. Cao
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. Hastie
- BioNano Genomics, Inc, San Diego, CA USA
| | - A. W. Pang
- BioNano Genomics, Inc, San Diego, CA USA
| | - E. T. Lam
- BioNano Genomics, Inc, San Diego, CA USA
| | - T. Liang
- BioNano Genomics, Inc, San Diego, CA USA
| | - K. Pham
- BioNano Genomics, Inc, San Diego, CA USA
| | | | - Z. Dzakula
- BioNano Genomics, Inc, San Diego, CA USA
| | - Y. Chee-Wei
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - L. Dongsheng
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - W. Lai-Ping
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - D. Lian
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - R. O. Twee Hee
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Y. Yunus
- Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh, ᅟ
| | - F. Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, Petaling Jaya, Malaysia
| | - S. S. Mokhtar
- Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh, ᅟ
| | - C. V. Lok-Yung
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - J. Bhak
- Personal Genomics Institute, Genome Research Foundation, Suwon, Republic Of Korea
| | - M. Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campu, Petaling Jaya, Malaysia
| | - X. Shuhua
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China
| | - T. Yik-Ying
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - V. Kumar
- Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu, Malaysia
| | - H. Boon-Peng
- UCSI University, Kuala Lumpur, Kuala Lumpur, Malaysia
| | - I. Campbell
- Research Division, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | - M. -A. Young
- Familial Cancer Centre, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | - P. James
- Familial Cancer Centre, Peter Maccallum Cancer Centre, East Melbourne, Australia
| | | | - M. Rain
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - G. Mohammad
- Department of Medicine, Sonam Norbu Memorial Hospital, Leh, Ladakh India
| | - R. Kukreti
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Q. Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - A. R. Akilzhanova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - C. Guelly
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Z. Abilova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - S. Rakhimova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - A. Akhmetova
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - U. Kairov
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - S. Trajanoski
- Center of Medical Research, Medical University of Graz, Graz, Austria
| | - Z. Zhumadilov
- Nazarbayev University, National Laboratory Astana, Center for Life Sciences, Astana, Kazakhstan
| | - M. Bekbossynova
- National Scientific Cardiac Surgery Center, Astana, Kazakhstan
| | | | - S. Sandhu
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - T. Harkins
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - V. Makarov
- Swift Biosciences Inc, Ann Arbor, MI USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Glenn
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Z. Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - B. Dilrukshi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Q. Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - B. Gudenkauf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Kshitij
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Jayaseelan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Nessner
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - S. Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Blankenberg
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Lewis
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - S. Jireh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. Walker
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - X. Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Q. Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Sanghvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - N. Veeraraghavan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Y. Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX USA
| | - A. L. Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - C. M. Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - K. C. C. Worley
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Liu
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. S. T. Hughes
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - S. C. Murali
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Harris
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. C. English
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - X. Qin
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - O. A. Hampton
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - P. Larsen
- Department of Biology, Duke University, Durham, NC USA
| | - C. Beck
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Y. Han
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - M. Wang
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - H. Doddapaneni
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - C. L. Kovar
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - W. J. Salerno
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - A. Yoder
- Department of Biology, Duke University, Durham, NC USA
| | - S. Richards
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. Rogers
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - J. R. Lupski
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - D. M. Muzny
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Q. Meng
- HGSC, Baylor College of Medicine, Houston, TX USA
| | | | - M. Wang
- HGSC, Baylor College of Medicine, Houston, TX USA
| | | | - Y. Han
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - D. Muzny
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- HGSC, Baylor College of Medicine, Houston, TX USA
| | - R. A. Harris
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - M. Raveenedran
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - C. Xue
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - M. Dahdouli
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - L. Cox
- Genetics, Southwest National Primate Research Center, San Antonio, TX USA
| | - G. Fan
- Human Genetics, Univeristy of California Los Angeles, Los Angeles, CA USA
| | - B. Ferguson
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, OR USA
| | - J. Hovarth
- Genomics & Microbiology Research Laboratory, NC Museum of Natural Sciences, Raleigh, NC USA
| | - Z. Johnson
- Yerkes Nonhuman Primate Genomics Core, Yerkes National Primate Research Center, Atlanta, GA USA
| | - S. Kanthaswamy
- Environmental Toxicology, California National Primate Research Center, Davis, CA USA
| | - M. Kubisch
- Physiology, Tulane National Primate Research Center, New Orleans, LO USA
| | - M. Platt
- Neuroscience, University of Pennsylvania, Philadelphia, PA USA
| | - D. Smith
- Anthropology, University of California Davis, Davis, CA USA
| | - E. Vallender
- Psychiatry and Human Behavior, University of Mississippi Medical Center, Jackson, MS USA
| | - R. Wiseman
- Genetics, Wisconsin National Primate Research Center, Madison, WI USA
| | - X. Liu
- Epidemiology, Human Genetics & Environmental Sciences, ᅟ, ᅟ
| | - J. Below
- Epidemiology and Disease Control Human Genetics Center, University of Texas Health Science Center, Houston, TX USA
| | - D. Muzny
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - R. Gibbs
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - F. Yu
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Rogers
- Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - J. Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Y. Zhang
- Department of Statistics, University of Connecticut, Storrs, CT USA
| | - Z. Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - A. Moore
- National Cancer Institute, Rockville, USA
| | - Z. Wang
- St. Jude Children’s Research Hospital, Memphis, USA
| | - J. Hofmann
- National Cancer Institute, NIH, DHHS, Rockville, USA
| | - M. Purdue
- National Cancer Institute, Rockville, USA
| | | | | | - D. Albanes
- National Cancer Institute, Rockville, USA
| | - C. S. Liu
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - W. L. Cheng
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - T. T. Lin
- Changhua Christian Hospital, Changhua, Taiwan Province of China
| | - Q. Lan
- National Cancer Institute, Rockville, USA
| | - N. Rothman
- National Cancer Institute, Rockville, USA
| | - S. Berndt
- National Cancer Institute, Rockville, USA
| | - E. S. Chen
- Biochemistry, National University of Singapore, Singapore, Singapore
| | - H. Bahrami
- Proteomics, Faraby Eye Hospital, Tehran, Iran Islamic Republic Of
- R & D, MIB Co., Tehran, Iran Islamic Republic Of
| | | | | | - H. Bahrami
- Proteomics, Faraby Eye Hospital, Tehran, Iran Islamic Republic Of
- R & D, MIB Co., Tehran, Iran Islamic Republic Of
| | | | | | - K. K. R. Alharbi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - M. Zhalbinova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - A. Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - S. Rakhimova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - M. Bekbosynova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National medical holding, Astana, Kazakhstan
| | - S. Myrzakhmetova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National medical holding, Astana, Kazakhstan
| | - M. Matar
- UAE Genetic Diseases Association, Dubai, United Arab Emirates
| | - N. Mili
- Research Center for Statistics, University of Geneva, Switzerland, Geneva Switzerland
| | - R. Molinari
- Research Center for Statistics, University of Geneva, Switzerland, Geneva Switzerland
| | - Y. Ma
- Department of Statistics, University of South Carolina, Columbia, USA
| | - S. Guerrier
- Department of Statistics, University of Illinois at Urbana Champaign, Champaign, USA
| | - N. Elhawary
- Department of Molecular Genetics, Medical Genetics Center, Ain Shams University, Cairo, Egypt
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Tayeb
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - N. Bogari
- Department of Medical Genetics, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - N. Qotb
- Department of Psychology, Umm Al-Qura University, Faculty of Education, Mecca, Saudi Arabia
| | - S. A. McClymont
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - P. W. Hook
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - L. A. Goff
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - A. McCallion
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, USA
| | - Y. Kong
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, USA
| | | | | | | | - L. Zhao
- The Jackson Laboratory, Bar Harbor, USA
| | - P. M. Nishina
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, USA
| | - B. M. Edrees
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - F. A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - W. Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - N. A. Harbi
- Department of Pediatric, King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - R. Safar
- Department of Pediatric, Madinah Maternity and Children’s Hospital, Madinah, Saudi Arabia
| | - H. Al-Edressi
- Department of Pediatric, Madinah Maternity and Children’s Hospital, Madinah, Saudi Arabia
| | - A. Anazi
- Pediatric, King Fahad Medical City, Riyadh, Saudi Arabia
| | - N. Altayeb
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, Saudi Arabia
| | - M. A. Ahmed
- Medical Genetics, King Salman Armed Forces Hospital, Tabuk, Saudi Arabia
| | - K. Alansary
- Medical Genetics, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - A. Kratz
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - P. Beguin
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - S. Poulain
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - M. Kaneko
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - C. Takahiko
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - A. Matsunaga
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - S. Kato
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - A. M. Suzuki
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - N. Bertin
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - T. Lassmann
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - R. Vigot
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - P. Carninci
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - C. Plessy
- Center for Life Science Technologies, RIKEN Yokohama, Yokohama City, Kanagawa Japan
| | - T. Launey
- Brain Science Institute (BSI), Launey Research Unit, RIKEN Wako, Wako, Japan
| | - D. Graur
- Biology and Biochemistry, University of Houston, Houston, USA
| | - D. Lee
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - A. Kapoor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - A. Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - J. Friis-Nielsen
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - J. M. Izarzugaza
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - S. Brunak
- Technical University of Denmark, Center for Biological Sequence Analysis, Lyngby, Denmark
| | - A. Chakraborty
- Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - J. Basak
- Molecular Biology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | - A. Mukhopadhyay
- Medical Oncology, Netaji Subhas Chandra Bose Cancer Research Institute, Kolkata, India
| | | | - D. Das
- National Institute of Biomedical Genomics, Kalyani, India
| | - N. Biswas
- National Institute of Biomedical Genomics, Kalyani, India
| | - S. Das
- National Institute of Biomedical Genomics, Kalyani, India
| | - S. Sarkar
- Chittaranjan National Cancer Institute, Kolkata, India
| | - A. Maitra
- National Institute of Biomedical Genomics, Kalyani, India
| | - C. Panda
- Chittaranjan National Cancer Institute, Kolkata, India
| | - P. Majumder
- National Institute of Biomedical Genomics, Kalyani, India
| | - H. Morsy
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | - A. Gaballah
- Microbiology, Faculty of Medicine, Alexandria, Egypt
| | - M. Samir
- Clinical and Experimental Surgery, Faculty of Medicine, Alexandria, Egypt
| | - M. Shamseya
- Clinical and Experimental Internal Medicine, Medical Research Institute, Faculty of Medicine, Alexandria, Egypt
| | - H. Mahrous
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | - A. Ghazal
- Microbiology, Faculty of Medicine, Alexandria, Egypt
| | - W. Arafat
- Clinical Oncology and Nuclear Medicine, Faculty of Medicine, Alexandria, Egypt
| | - M. Hashish
- Human Genetics, Faculty of Medicine, Alexandria, Egypt
| | | | - N. Jaeger
- Genetics, Stanford University, Palo Alto, USA
| | - M. Snyder
- Genetics, Stanford University, Palo Alto, USA
| | | | | | - T. Davis
- New England Biolabs, Ipswich, USA
| | | | | | | | | | | | - K. Zhang
- Pathology, University of North Dakota, Grand Forks, USA
| | | | | | | | | | - N. Jäger
- Genetics, Stanford University, Palo Alto, USA
| | - J. Chen
- Genetics, Stanford University, Palo Alto, USA
| | - R. Haile
- Stanford Cancer Institute, Stanford University, Palo Alto, USA
| | - M. Hitchins
- Stanford Cancer Institute, Stanford University, Palo Alto, USA
| | | | - M. Snyder
- Genetics, Stanford University, Palo Alto, USA
| | - S. Jiménez-Morales
- Cancer Genomic Laboratory, National Institute of Genomic Medicine (INMEGEN), ᅟ, Mexico
| | - M. Ramírez
- Biología, FES -Iztacala, UNAM, ᅟ, Mexico
| | - J. Nuñez
- Hospital de Pediatría, CMN SXXI, IMSS, ᅟ, Mexico
| | - V. Bekker
- Investigación Médica en Inmunología, CMN La Raza, IMSS, ᅟ, Mexico
| | - Y. Leal
- Diagnóstico Molecular H1N1-Influenza , UMAE-IMSS, Mérida, Yucatán Mexico
| | - E. Jiménez
- Hematología Pediátrica, CMN La Raza, IMSS, ᅟ, Mexico
| | - A. Medina
- Hemato-Oncología, Hospital Infantil de México, ᅟ, Mexico
| | - A. Hidalgo
- Cancer Genomics Laboratory, INMEGEN, ᅟ, Mexico
| | - J. Mejía
- Coordinación de Investigación en Salud, IMSS, ᅟ, Mexico
| | - V. Halytskiy
- Molecular Immunology Department, Palladin Institute of Biochemistry of the National Academy of Sciences of Ukraine, Kiev, Ukraine
| | | | | | | | | | | | - K. Belhassa
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - K. Belhassan
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - L. Bouguenouch
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Samri
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - H. Sayel
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - FZ. moufid
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. El Bouchikhi
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - S. Trhanint
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - H. Hamdaoui
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Elotmani
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - I. Khtiri
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - O. Kettani
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - L. Quibibo
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - M. Ahagoud
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - M. Abbassi
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - K. Ouldim
- Department of Medical Genetics and Oncogene, Morocco; Medical Genetics, CHU Hassan II Fes, Fes, Morocco
| | - A. V. Marusin
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - A. N. Kornetov
- Siberian State Medical University, Tomsk, Russian Federation
| | - M. Swarovskaya
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - K. Vagaiceva
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - V. Stepanov
- Evolutionary Genetics, Institute of Medical Genetics, ᅟ, Russian Federation
| | - E. M. Cutiongco De La Paz
- National Institutes of Health, University of the Philippines, Manila, Philippines
- Philippine Genome Center, University of the Philippines, Quezon City, Philippines
| | - R. Sy
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. Nevado
- National Institutes of Health, University of the Philippines, Manila, Philippines
| | - P. Reganit
- College of Medicine, University of the Philippines, Manila, Philippines
| | - L. Santos
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. D. Magno
- College of Medicine, University of the Philippines, Manila, Philippines
| | - F. E. Punzalan
- College of Medicine, University of the Philippines, Manila, Philippines
| | - D. Ona
- College of Medicine, University of the Philippines, Manila, Philippines
| | - E. Llanes
- College of Medicine, University of the Philippines, Manila, Philippines
| | - R. L. Santos-Cortes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX United States
| | - R. Tiongco
- College of Medicine, University of the Philippines, Manila, Philippines
| | - J. Aherrera
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - L. Abrahan
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | - P. Pagauitan-Alan
- Philippine General Hospital, University of the Philippines, Manila, Philippines
| | | | - K. H. Morelli
- The Jackson Laboratory, Bar Harbor, USA
- Graduate School of Biomedical Sciences & Engineering, The University of Maine, Orono, USA
| | - J. S. Domire
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - N. Pyne
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - S. Harper
- Center For Gene Therapy, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio USA
| | - R. Burgess
- Graduate School of Biomedical Sciences & Engineering, The University of Maine, Orono, USA
| | - M. Zhalbinova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - A. Akilzhanova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - S. Rakhimova
- Laboratory of Genomic and Personalized Medicine, National Laboratory Astana, Nazarbayev University, ᅟ, Kazakhstan
| | - M. Bekbosynova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National Medical Holding, Astana, Kazakhstan
| | - S. Myrzakhmetova
- Cardiology, JSC “National Research Cardiac Surgery Center”, National Medical Holding, Astana, Kazakhstan
| | - M. A. Gari
- Medical Laboratory Technology, ᅟ, Saudi Arabia
| | - A. Dallol
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - H. Alsehli
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Gari
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M. Gari
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - A. Abuzenadah
- Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M. Thomas
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - M. Sukhai
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - S. Garg
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - M. Misyura
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - T. Zhang
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - A. Schuh
- Princess Margaret Cancer Centre, Toronto, Canada
| | - T. Stockley
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | - S. Kamel-Reid
- Advanced Molecular Diagnostics Laboratory, ᅟ, Canada
| | | | | | | | | | | | | | | | | | | | - C. Xiao
- National Institutes of Health, Bethesda, USA
| | | | - S. Sherry
- National Institutes of Health, Bethesda, USA
| | - C. Rangel-Escareño
- Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - H. Rueda-Zarate
- Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - I. A. Tayubi
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - R. Mohammed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | | | - I. Ahmed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - T. Ahmed
- Computer Science, Faculty of Computing and Information Technology, King AbdulAziz University, Rabigh, Saudi Arabia
| | - S. Seth
- Institute of Applied Cancer Science, ᅟ, USA
| | - S. Amin
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - X. Song
- Institute of Applied Cancer Science, ᅟ, USA
| | - X. Mao
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - H. Sun
- MD Anderson Cancer Center, Houston, USA
| | | | - A. Futreal
- Genomic Medicine, University of Texas, ᅟ, ᅟ
| | - J. Zhang
- Institute of Applied Cancer Science, ᅟ, USA
| | - S. J. Whiite
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - T. Chiang
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - J. Farek
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - Z. Kahn
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - N. Veeraraghavan
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - E. Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, USA
| | - R. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, ᅟ, USA
| | - T. Kasukawa
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - M. Lizio
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - J. Harshbarger
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - S. Hisashi
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan
| | - J. Severin
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - A. Imad
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - S. Sahin
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | - T. C. Freeman
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - K. Baillie
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - A. Sandelin
- Department of Biology & Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - P. Carninci
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
| | | | - H. Kawaji
- Center for Life Science Technologies, RIKEN, Yokohama, Japan
- Preventive Medicine and Diagnosis Innovation Program, RIKEN, Wako, Japan
- Advanced Center for Computing and Communication, RIKEN, Yokohama, Japan
| | | | - W. Salerno
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | - A. English
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | | | | | | | - E. Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
- Human Genetics Center and Department of Epidemiology, UT School of Public Health, Houston, Texas USA
| | - R. A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas USA
| | - A. H. Salem
- Anatomy, Arabian Gulf University, Manama, Bahrain
| | - M. Ali
- Biochemistry, Arabian Gulf University, Manama, Bahrain
| | - A. Ibrahim
- Central Laboratory, Ministry of Science and Technology, ᅟ, Sudan
| | - M. Ibrahim
- College of Animal Production Science and Technology, Sudan University of Science and Technology, Khartoum, Sudan
| | - H. A. Barrera
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - L. Garza
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - J. A. Torres
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - V. Barajas
- Bioquimica y Medicina Molecular, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | | | - D. Kershenobich
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Shahroj Mortaji
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Pedro Guizar
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Eliezer Loera
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Karen Moreno
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Adriana De León
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Daniela Monsiváis
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Jackeline Gómez
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | - Raquel Cardiel
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Distrito Federal, Mexico
| | | | - V. Bonifaz-Peña
- Computational Genomics, Nacional de Medicina Genomica, Mexico City, Mexico
| | - C. Rangel-Escareño
- Computational Genomics, Nacional de Medicina Genomica, Mexico City, Mexico
| | - A. Hidalgo-Miranda
- Cancer Genomics Laboratory, Nacional de Medicina Genomica, Mexico City, Mexico
| | - A. V. Contreras
- Nutrigenetics and Nutrigenomics Laboratory, Instituto Nacional de Medicina Genomica, Mexico City, Mexico
| | - L. Polfus
- Human Genetics Center, University of Texas Health Science Center, Houston, USA
| | | | - X. Wang
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - V. Philip
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - G. Carter
- System Genetics, The Jackson Laboratory, Bar Harbor, USA
| | - A. A. Abuzenadah
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - M. Gari
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - R. Turki
- Ob/Gyn, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - A. Dallol
- Center of Innovation in Personalized Medicine, Faculty of Applied Medical Sciences, King Abdulaziz University, ᅟ, Saudi Arabia
| | - A. Uyar
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - A. Kaygun
- Department of Mathematical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - S. Zaman
- Department of Biomedical Engineering, University of Connecticut, Storrs, USA
| | - E. Marquez
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - J. George
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - D. Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, USA
| | | | | | | | | | | | - T. Davis
- New England Biolabs, Ipswich, USA
| | | | | | - D. B. Starr
- Genetics, Stanford University, Stanford, USA
| | - M. Baird
- DNA Diagnostics Center, Fairfield, USA
| | | | - K. Sheets
- Vibrant Gene Consulting, Cambridge, USA
| | - R. Nitsche
- Agilent Technologies, Agilent Technologies, Waldbronn, Germany
| | - L. Prieto-Lafuente
- Agilent Technologies UK Ltd, Agilent Technologies UK Ltd., Edinburgh, UK
| | | | - J. Lee
- NIH/NLM/NCBI, Bethesda, USA
| | | | | | - P. K. R. Thavanati
- Institute of Human Genetics, Department of Molecular Biology & Genomics, Centre for Health Sciences, ᅟ, Mexico
| | - A. Escoto de Dios
- Institute of Human Genetics, Department of Molecular Biology & Genomics, Centre for Health Sciences, ᅟ, Mexico
| | | | | | - M. R. Ruiz Mejia
- Biochemistry, Centre for Health Sciences, University of Guadalajara, Guadalajara, Mexico
| | - K. R. R. Kanala
- Human Genetics Unit, Department Anthropology, Sri Venkateswara University, Tirupati, India
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - W. Khan
- Department of Basic Sciences, College of Science and Health Professions, King Saud Bin Abdul Aziz University for Health Sciences, Riyadh, Saudi Arabia
| | - F. A. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - M. M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - N. Shahzad
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - A. Bouazzaoui
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Department of Medical Genetics, Umm Al Qura University, Mecca, Saudi Arabia
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E. Huber
- Department of Pathology, University Hospital Regensburg, Regensburg, Germany
| | - A. Dan
- IgNova GmbH, Oberursel, Germany
| | - F. A. Al-Allaf
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
| | - W. Herr
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - G. Sprotte
- Department of Ansethesiologie, University of Würzburg Medical School, Würzburg, Germany
| | - J. Köstler
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - A. Hiergeist
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - A. Gessner
- Department of microbiology, University Hospital Regensburg, Regensburg, Germany
| | - R. Andreesen
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - E. Holler
- Medical Clinic 3 – Hematology/Oncology, University Hospital Regensburg, Regensburg, Germany
| | - F. Al-Allaf
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
- Molecular Diagnostics Unit, Department of Laboratory and Blood Bank, King Abdullah Medical City, Makkah, Saudi Arabia
| | - A. Alashwal
- King Faisal Specialist Hospital and Research Centre, ᅟ, Saudi Arabia
| | - Z. Abduljaleel
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Taher
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - H. Abalkhail
- King Faisal Specialist Hospital and Research Centre, ᅟ, Saudi Arabia
| | - A. Al-Allaf
- Faculty of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - R. Bamardadh
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - M. Athar
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, ᅟ, Saudi Arabia
- Science and Technology Unit, Umm Al-Qura University, ᅟ, Saudi Arabia
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. N. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - O. Filiptsova
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - M. N. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - Y. Kobets
- Pharmaceutical Marketing and Management, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Burlaka
- Biology, National University of Pharmacy, Kharkiv, Ukraine
| | - I. Timoshyna
- Human Physiology and Anatomy, National University of Pharmacy, Kharkiv, Ukraine
| | - F. A. Al-allaf
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
- Molecular Diagnostics Unit Department of Laboratory Medicine and Blood Bank, King Abdullah Medical City, ᅟ, Saudi Arabia
| | - M. T. Mohiuddin
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - A. Zainularifeen
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - A. Mohammed
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
| | - H. Abalkhail
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - T. Owaidah
- Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - A. Bouazzaoui
- Department of Medical Genetics Faculty of Medicine, Umm Al Qura University, Mecca, Saudi Arabia
- Science and Technology Unit, Umm Al Qura University, Mecca, Saudi Arabia
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Kutbay NO, Yurekli BS, Erdemir Z, Karaca E, Unal I, Yaman B, Ozkinay F, Saygili F. A case of dyskeratosis congenita associated with hypothyroidism and hypogonadism. Hormones (Athens) 2016; 15:297-299. [PMID: 27376432 DOI: 10.14310/horm.2002.1655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 12/27/2015] [Indexed: 11/20/2022]
Affiliation(s)
| | - Banu Sarer Yurekli
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey.
| | - Zehra Erdemir
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey
| | - Emin Karaca
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey
| | - Idil Unal
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey
| | - Banu Yaman
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey
| | - Ferda Ozkinay
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey
| | - Fusun Saygili
- Endocrinology Department, Ege University Faculty of Medicine, Izmir, Turkey
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28
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van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2016; 428:720-725. [PMID: 26410586 DOI: 10.1016/j.jmb.2015.09.014)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 05/23/2023]
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - J P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - M Trellet
- Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France
| | - C Schmitz
- Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia
| | - P L Kastritis
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - E Karaca
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - A S J Melquiond
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M van Dijk
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - S J de Vries
- Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
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29
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Karaca E, Atik T, Alpman Durmaz A, Ozkinay F, Cogulu O. Transmembrane Activator and Caml Interactor (Taci) Haploinsufficiency in B-Cell Dysfunction in a Patient with Smith-Magenis Syndrome. Genet Couns 2016; 27:251-254. [PMID: 29485832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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30
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Durmaz B, Karaca E, Tavmergen Goker EN, Tavmergen E, Sahin G, Akdogan A, Yasar BP, Gunduz C, Ozkinay R. EVALUATION OF PREIMPLANTATION GENETIC ANEUPLOIDY SCREENING CASES AT A REFERENCE GENETICS CENTER: 10 YEARS' EXPERIENCE. Genet Couns 2016; 27:461-470. [PMID: 30226964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The aim of this study is to review and evaluate our preimplantation genetic screening (PGS) records in terms of their demographic data, indications, cytogenetic results, pregnancy outcomes and discuss these findings in different aspects. PGS was performed in a total of 84 couples (87 cycles) between the period 2005 to 2015. Biopsied blastomeres from embryos on day 3 were fixed and fluorescence in situ hybridization was carried out for chromosomes 13, 16, 18, 21, 22, X and Y depending on the indication. The diagnostic and clinical data were retrospectively evaluated. A total of 450 blastomeres were biopsied. Ninety-eight of them were found to be suitable for transfer. They were transferred to 72 patients in 75 cycles resulting in 23 pregnancies and 20 healthy births. The most common indication was unexplained infertility. The implantation rate was calculated as 23.4% whereas the take-home baby rate was 26.6% per transfer. The highest rate of healthy living births is achieved in patients having low grade maternal mosaic sex chromosomal aneuploidy. All living births achieved by PGS had normal chromosomal structure which we can propose it as an alternative test for couples at risk to select normal embryos to improve the outcomes of assisted reproductive procedures and to avoid the transfer of chromosomally unbalanced and multiple embryos.
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31
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van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ, Bonvin AMJJ. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. J Mol Biol 2015; 428:720-725. [PMID: 26410586 DOI: 10.1016/j.jmb.2015.09.014] [Citation(s) in RCA: 1652] [Impact Index Per Article: 183.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 09/16/2015] [Accepted: 09/17/2015] [Indexed: 11/25/2022]
Abstract
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.
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Affiliation(s)
- G C P van Zundert
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - J P G L M Rodrigues
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
| | - M Trellet
- Centre National de la Recherche Scientifique Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur, rue John Von Neumann, 91403 Orsay, France
| | - C Schmitz
- Instaclustr Level 5, 1 Moore Street, Canberra ACT 2600, Australia
| | - P L Kastritis
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - E Karaca
- European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - A S J Melquiond
- Hubrecht Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - M van Dijk
- Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, the Netherlands
| | - S J de Vries
- Physik-Department, Technische Universität München, James-Franck-Strasse 1, 85748 Garching, Germany
| | - A M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science Department of Chemistry, Utrecht University, Domplein 29, 3512 JE Utrecht, the Netherlands
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32
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Ozkinay F, Onay H, Karaca E, Arslan E, Erturk B, Ece Solmaz A, Tekin IM, Cogulu O, Aydinok Y, Vergin C. Molecular Basis ofβ-Thalassemia in the Population of the Aegean Region of Turkey: Identification of A Novel Deletion Mutation. Hemoglobin 2015; 39:230-4. [DOI: 10.3109/03630269.2015.1038354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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33
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Poyrazoğlu HG, Karaca E, Per H, Gümüs H, Onay H, Canpolat M, Canöz Ö, Ozkınay F, Kumandas S. Three patients with lafora disease: different clinical presentations and a novel mutation. J Child Neurol 2015; 30:777-81. [PMID: 25015673 DOI: 10.1177/0883073814535489] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 04/14/2014] [Indexed: 11/15/2022]
Abstract
Lafora disease is a rare, fatal, autosomal recessive hereditary disease characterized by epilepsy, myoclonus and progressive neurological deterioration. Diagnosis is made by polyglucosan inclusion bodies (Lafora bodies) shown in skin biopsy. Responsible mutations of Lafora disease involves either the EPM2A or NHLRC1 (EPM2B) gene. Mutations in the NHLRC1 gene are described as having a more benign clinical course and a later age of death compared with EPM2A mutations. We report 2 genetic mutations and clinical courses of Lafora disease in 3 adolescents with homozygote NHLRC1 mutation and novel homozygous EPM2A mutation.
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Affiliation(s)
- Hatice Gamze Poyrazoğlu
- Department of Pediatrics, Division of Pediatric Neurology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Hüseyin Per
- Department of Pediatrics, Division of Pediatric Neurology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Hakan Gümüs
- Department of Pediatrics, Division of Pediatric Neurology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Huseyin Onay
- Department of Pediatrics, Division of Pediatric Neurology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Mehmet Canpolat
- Department of Pediatrics, Division of Pediatric Neurology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Özlem Canöz
- Department of Pathology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
| | - Ferda Ozkınay
- Department of Medical Genetics, Faculty of Medicine, Ege University, İzmir, Turkey
| | - Sefer Kumandas
- Department of Pediatrics, Division of Pediatric Neurology, Faculty of Medicine, Erciyes University, Kayseri, Turkey
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Atik T, Karaca E, Ozkinay E, Cogulu O. TWINS WITH KLEEFSTRA SYNDROME DUE TO CHROMOSOME 9q34.3 MICRODELETION. Genet Couns 2015; 26:431-435. [PMID: 26852514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Kleefstra or 9q subtelomeric deletion syndrome (9qSTDS) is a rare microdeletion syndrome. The most prominent phenotypic features include hypotonia, developmental retardation, as well as typical dysmorphic face. It has been shown that terminal deletions of the chromosome 9q34.3 region, or EHMT1 gene mutations, lead to Kleefstra syndrome. We present 16-month-old twin sisters, one of whom had originally been referred for Down syndrome screening due to hypotonia, growth and development retardation, dysmorphic facial signs, and accompanying congenital heart disease. They were subsequently diagnosed as Kleefstra syndrome based on subtelomeric FISH analysis. In conclusion, Kleefstra syndrome should be considered in the differential diagnosis of Down syndrome because it presents with very similar phenotypic features.
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35
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Aykut A, Onay H, Kose M, Erbas Canda E, Karaca E, Coker M, Ozkinay F. Two novel mutations in acid α-glucosidase gene in two patients with Pompe disease. J Pediatr Endocrinol Metab 2014; 27:1265-7. [PMID: 25026126 DOI: 10.1515/jpem-2014-0107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/16/2014] [Indexed: 11/15/2022]
Abstract
Pompe disease is an autosomal recessive lysosomal glycogen storage disorder (GSD) caused by acid α-glucosidase (GAA) deficiency. Pompe disease has a broad genotypic and phenotypic spectrum. The infantile-onset form is the most severe form and presents with hypotonia and cardiomyopathy in early infancy. The probands who died were found to have GSD type II based on clinical and biochemical findings. We report two families with Pompe disease in whom the parents' molecular analysis revealed two novel mutations: c.2045A>G (p.Q682R) and c.763C>T (p.Q255X).
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36
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Aykut A, Onay H, Durmaz A, Karaca E, Vergin C, Aydınok Y, Özkınay F. Molecular analysis of abnormal hemoglobins in beta chain in Aegean region of Turkey and first reports of hemoglobin Andrew-Minneapolis and Hb Hinsdale from Turkey. Hematology 2014; 20:354-8. [PMID: 25313792 DOI: 10.1179/1607845414y.0000000193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
OBJECTIVES The Agean is one of the regions in Turkey where thalassemias and abnormal hemoglobins (Hbs) are prevalent. Combined heterozygosity of thalassemia mutations with a variety of structural Hb variants lead to an extremely wide spectrum of clinical and hematological phenotypes which is of importance for prenatal diagnosis. METHODS One hundred and seventeen patients and carriers diagnosed by hemoglobin electrophoresis (HPLC), at risk for abnormal hemoglobinopathies were screened for mutational analysis of the beta-globin gene. The full coding the 5' UTR, and the 3' UTR sequences of beta-globin gene (GenBank accession no. U01317) were amplified and sequenced. RESULTS In this study, a total of 118 (12.24%) structural Hb variant alleles were identified in 1341 mutated beta-chain alleles in Medical Genetics Department of Ege University between January 2006 and November 2013. DISCUSSION Here, we report the mutation spectrum of abnormal Hbs associated with the beta-globin gene in Aegean region of Turkey. CONCLUSION In the present study, the Hb Hinsdale and Hb Andrew-Minneapolis variants are demonstrated for the first time in the Turkish population.
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Ozantürk A, Marshall JD, Collin GB, Düzenli S, Marshall RP, Candan Ş, Tos T, Esen İ, Taşkesen M, Çayır A, Öztürk Ş, Üstün İ, Ataman E, Karaca E, Özdemir TR, Erol İ, Eroğlu FK, Torun D, Parıltay E, Yılmaz-Güleç E, Karaca E, Atabek ME, Elçioğlu N, Satman İ, Möller C, Muller J, Naggert JK, Özgül RK. The phenotypic and molecular genetic spectrum of Alström syndrome in 44 Turkish kindreds and a literature review of Alström syndrome in Turkey. J Hum Genet 2014; 60:1-9. [PMID: 25296579 DOI: 10.1038/jhg.2014.85] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 02/07/2023]
Abstract
Alström syndrome (ALMS) is an autosomal recessive disease characterized by multiple organ involvement, including neurosensory vision and hearing loss, childhood obesity, diabetes mellitus, cardiomyopathy, hypogonadism, and pulmonary, hepatic, renal failure and systemic fibrosis. Alström Syndrome is caused by mutations in ALMS1, and ALMS1 protein is thought to have a role in microtubule organization, intraflagellar transport, endosome recycling and cell cycle regulation. Here, we report extensive phenotypic and genetic analysis of a large cohort of Turkish patients with ALMS. We evaluated 61 Turkish patients, including 11 previously reported, for both clinical spectrum and mutations in ALMS1. To reveal the molecular diagnosis of the patients, different approaches were used in combination, a cohort of patients were screened by the gene array to detect the common mutations in ALMS1 gene, then in patients having any of the common ALMS1 mutations were subjected to direct DNA sequencing or next-generation sequencing for the screening of mutations in all coding regions of the gene. In total, 20 distinct disease-causing nucleotide changes in ALMS1 have been identified, eight of which are novel, thereby increasing the reported ALMS1 mutations by 6% (8/120). Five disease-causing variants were identified in more than one kindred, but most of the alleles were unique to each single patient and identified only once (16/20). So far, 16 mutations identified were specific to the Turkish population, and four have also been reported in other ethnicities. In addition, 49 variants of uncertain pathogenicity were noted, and four of these were very rare and probably or likely deleterious according to in silico mutation prediction analyses. ALMS has a relatively high incidence in Turkey and the present study shows that the ALMS1 mutations are largely heterogeneous; thus, these data from a particular population may provide a unique source for the identification of additional mutations underlying Alström Syndrome and contribute to genotype-phenotype correlation studies.
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Affiliation(s)
- Ayşegül Ozantürk
- Institute of Child Health and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | | | | | - Selma Düzenli
- Department of Medical Genetics, Abant İzzet Baysal University, Bolu, Turkey
| | | | - Şükrü Candan
- Department of Medical Genetics, Atatürk State Hospital, Balıkesir, Turkey
| | - Tülay Tos
- Dr. Sami Ulus Maternity and Children's Hospital, Ankara, Turkey
| | - İhsan Esen
- Ankara Pediatric Health and Hematology Oncology Hospital, Ankara,Turkey
| | | | - Atilla Çayır
- Pediatric Endocrinology Unit, Department of Medical Genetics, Atatürk University and Erzurum Regional Training and Research Hospital, Erzurum, Turkey
| | - Şükrü Öztürk
- Department of Medical Genetics, Istanbul Medical Faculty, İstanbul University, İstanbul, Turkey
| | - İhsan Üstün
- Department of Endocrinology, Mustafa Kemal University Hospital, Hatay, Turkey
| | - Esra Ataman
- Department of Medical Genetics, Ege University, İzmir, Turkey
| | - Emin Karaca
- 304;zmir Tepecik Training and Research Hospital Genetic Diagnostic Center, İzmir, Turkey
| | - Taha Reşid Özdemir
- 304;zmir Tepecik Training and Research Hospital Genetic Diagnostic Center, İzmir, Turkey
| | - İlknur Erol
- Division of Pediatric Neurology, Adana Teaching and Medical Research Center, Başkent University, Adana, Turkey
| | - Fehime Kara Eroğlu
- Nephrology Unit, Department of Pediatrics, Hacettepe University, Ankara, Turkey
| | - Deniz Torun
- Gülhane Military Medical Faculty, Department of Medical Genetics, Ankara, Turkey
| | - Erhan Parıltay
- Department of Medical Genetics, Ege University, İzmir, Turkey
| | - Elif Yılmaz-Güleç
- Kanuni Sultan Süleyman Training and Research Hospital, İstanbul, Turkey
| | - Ender Karaca
- Kanuni Sultan Süleyman Training and Research Hospital, İstanbul, Turkey
| | - M Emre Atabek
- Department of Pediatric Endocrinology, Necmettin Erbakan University, Konya, Turkey
| | - Nursel Elçioğlu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, İstanbul, Turkey
| | - İlhan Satman
- Division of Endocrinology and Metabolism, İstanbul Faculty of Medicine, İstanbul University, İstanbul, Turkey
| | - Claes Möller
- Department Audiology, The Swedish Institute for Disability Research, Örebro University Hospital, Örebro, Sweden
| | - Jean Muller
- 1] Laboratoire ICUBE, UMR CNRS 7357, LBGI, Université de Strasbourg, Strasbourg, France [2] Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France [3] Laboratoire de diagnostic génétique, Hôtpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Rıza Köksal Özgül
- Institute of Child Health and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, Hacettepe University, Ankara, Turkey
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Atik T, Aykut A, Karaca E, Onay H, Ozkinay F, Cogulu O. A twin sibling with Prader-Willi syndrome caused by uniparental disomy conceived after in vitro fertilization. Genet Couns 2014; 25:433-437. [PMID: 25804024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The use of assisted reproductive technologies (ART) has increased gradually in the treatment of infertility worldwide. On the other hand ART has been found to be associated with an increased risk of congenital malformations including imprinting defects as well. Although a number of imprinting syndromes have been reported to be related with ART, no case with uniparental disomy (UPD) caused Prader-Willi syndrome (PWS) [OMIM ID: 176270] has been reported in the literature. Here we present a dizygotic twin in which one of them was born with maternal UPD15 following ART. The proband was a 2-year-old boy who had feeding difficulties, generalized hypotonia, frontal bossing, broad forehead, small hands and feet. Laboratory investigations revealed minimal dilatation in 3rd and 4th ventricles and corpus callosum hypoplasia in magnetic resonance imaging, supravalvular pulmonary stenosis in echocardiography and pelvicaliectasia in the USG examinations. Methylation and microsatellite markers analyses showed maternal UPD for chromosome 15. Here we report, for the first time UPD caused PWS patient born after ART.
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Pohl E, Aykut A, Beleggia F, Karaca E, Durmaz B, Keupp K, Arslan E, Palamar M, Yigit G, Özkinay F, Wollnik B. Erratum to: A hypofunctional PAX1 mutation causes autosomal recessively inherited otofaciocervical syndrome. Hum Genet 2013. [DOI: 10.1007/s00439-013-1341-0] [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: 12/01/2022]
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Rodrigues JPGLM, Melquiond ASJ, Karaca E, Trellet M, van Dijk M, van Zundert GCP, Schmitz C, de Vries SJ, Bordogna A, Bonati L, Kastritis PL, Bonvin AMJJ. Defining the limits of homology modeling in information-driven protein docking. Proteins 2013; 81:2119-28. [PMID: 23913867 DOI: 10.1002/prot.24382] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [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: 06/17/2013] [Revised: 07/16/2013] [Accepted: 07/25/2013] [Indexed: 12/28/2022]
Abstract
Information-driven docking is currently one of the most successful approaches to obtain structural models of protein interactions as demonstrated in the latest round of CAPRI. While various experimental and computational techniques can be used to retrieve information about the binding mode, the availability of three-dimensional structures of the interacting partners remains a limiting factor. Fortunately, the wealth of structural information gathered by large-scale initiatives allows for homology-based modeling of a significant fraction of the protein universe. Defining the limits of information-driven docking based on such homology models is therefore highly relevant. Here we show, using previous CAPRI targets, that out of a variety of measures, the global sequence identity between template and target is a simple but reliable predictor of the achievable quality of the docking models. This indicates that a well-defined overall fold is critical for the interaction. Furthermore, the quality of the data at our disposal to characterize the interaction plays a determinant role in the success of the docking. Given reliable interface information we can obtain acceptable predictions even at low global sequence identity. These results, which define the boundaries between trustworthy and unreliable predictions, should guide both experts and nonexperts in defining the limits of what is achievable by docking. This is highly relevant considering that the fraction of the interactome amenable for docking is only bound to grow as the number of experimentally solved structures increases.
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Affiliation(s)
- J P G L M Rodrigues
- Faculty of Science/Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, 3584CH, The Netherlands
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Hazan F, Karaca E, Koker SA, Korkmaz HA, Mese T, Onay H, Ozkinay F. A Novel Missense Mutation in BRAF Caused Cardio-Facio-Cutaneous Syndrome. Iran J Pediatr 2013; 23:608-9. [PMID: 24800029 PMCID: PMC4006518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Accepted: 10/10/2012] [Indexed: 11/03/2022]
Affiliation(s)
- Filiz Hazan
- Department of Medical Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey,Corresponding Author:Address: Department of Medical Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey. E-mail:
| | - Emin Karaca
- Department of Medical Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Sultan Aydin Koker
- Department of Pediatrics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | | | - Timur Mese
- Department of Pediatric Cardiology, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Huseyin Onay
- Department of Medical Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
| | - Ferda Ozkinay
- Department of Medical Genetics, Dr. Behcet Uz Children's Hospital, Izmir, Turkey
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Durmaz B, Karaca E, Tavmergen E, Goker ET, Calimlioglu N, Gunduz C, Ozkinay F. P-18 Evaluation of preimplantation genetic aneuploidy screening cases at a reference genetics center in Izmir, Turkey. Reprod Biomed Online 2013. [DOI: 10.1016/s1472-6483(13)60081-4] [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: 11/26/2022]
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Karaca E, Durmaz B, Goker ET, Tavmergen E, Calimlioglu N, Gunduz C, Ozkinay F. P-53 Outcome of preimplantation genetic diagnosis of balanced translocation carriers. Reprod Biomed Online 2013. [DOI: 10.1016/s1472-6483(13)60116-9] [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: 10/26/2022]
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Ozkinay F, Durmaz B, Karaca E, Goker ET, Tavmergen E, Gunduz C. P-61 Analysis of couples having genetic counseling for preimplantation genetic diagnosis or preimplantation genetic screening. Reprod Biomed Online 2013. [DOI: 10.1016/s1472-6483(13)60124-8] [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: 10/26/2022]
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Durmaz B, Karaca E, Durmaz A, Atik T, Akin H, Cogulu O, Ozkinay F. Subtelomeric rearrangements in patients with idiopathic intellectual disabilitiy/ multiple congenital anomalies and recurrent miscarriages: seven years' experience. Genet Couns 2013; 24:167-177. [PMID: 24032287] [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: 06/02/2023]
Abstract
Cryptic subtelomeric anomalies are a significant cause of idiopathic intellectual disability and/or multiple congenital anomalies (ID/MCA) and multiple miscarriages (MM). Effective preselection of patients is essential as the cost of subtelomeric testing is high and it is labor-intensive. Therefore, the aim of this study is to evaluate the frequency of subtelomeric anomalies by using commercial FISH probes in 151 patients of ID/MCA and 32 couples with MM who were referred to a genetic center during 7-year period and to determine whether performing subtelomeric testing is feasible for these groups of patients. We assessed the clinical information of all referrals including family history, physical examination, facial dysmorphism, congenital malformations and scored the ID/MCA patients according to the criteria suggested previously. The etiology was not elucidated and all patients had normal karyotypes. Subtelomeric deletions were found in 10 patients in ID/MCA group (6.62%). These were deletions of 14qter (2 patients), 18qter (2 patients), 18pter (2 patients), 15qter, 7pter, 8pter and 4qter. The clinical information of all patients having deletions has been summarized and confined with the current literature. No anomaly was detected in the MM group. In conclusion, the prevalence of subtelomeric anomalies in ID/MCA group in this study is consistent with the literature and subtelomeric FISH analysis is feasible in determining their etiology when a checklist is used. Besides, assessment of the genetic basis of ID/MCA had lead the prevention of the recurrence of such conditions in selected families as well as elucidating novel genetic causes of ID.
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Affiliation(s)
- B Durmaz
- Ege University, Faculty of Medicine, Department of Medical Genetics, 35100, Izmir, Turkey.
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Cakmak BC, Calkavur S, Ozkinay F, Koroglu OA, Onay H, Itirli G, Karaca E, Yalaz M, Akisu M, Kultursay N. Association between bronchopulmonary dysplasia and MBL2 and IL1-RN polymorphisms. Pediatr Int 2012; 54:863-8. [PMID: 22882323 DOI: 10.1111/j.1442-200x.2012.03714.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 05/12/2012] [Accepted: 07/17/2012] [Indexed: 11/27/2022]
Abstract
BACKGROUND The imbalance between pro-inflammatory and anti-inflammatory cytokines may play a role in the development of bronchopulmonary dysplasia (BPD) in preterm infants. Mannose binding lectin (MBL) codon 54 and interleukin 1 receptor antagonist gene (IL1-RN) polymorphisms cause genetic predisposition to increased risk of infection and inflammation, therefore may increase the risk of BPD. The aim of this study was to investigate the relationship between MBL, IL1-RN gene polymorphisms and BPD development in preterm infants. METHODS MBL codon 54 and IL1-RN polymorphisms were studied in 71 infants who were born at <32 weeks of gestation, with the diagnosis of BPD (group 1) and in a control group of preterm infants without BPD (group 2). RESULTS IL1-RN and MBL2 variant genes were closely associated with increased risk of BPD (both P < 0.001) together with significantly lower birthweight (P < 0.001 and P = 0.001, respectively), lower 5 min Apgar scores (P = 0.009 for both genes) and increased neonatal infection rate (P < 0.001 and P < 0.009, respectively). The IL1 RN 1/1 genotype was protective (odds ratio [OR], 0.075; 95% confidence interval [CI]: 0.019-0.76) while the IL1-RN 2/2 genotype increased the risk for BPD (OR, 11.7; 95%CI: 1.3-103.6). The MBL-AA genotype was protective against BPD (OR, 0.066; 95%CI: 0.02-0.2) whereas the MBL-BB genotype increased the susceptibility for the development of BPD (OR, 23.8; 95%CI: 2.8-200.6). CONCLUSION MBL and IL 1 RN polymorphisms are closely related to low birthweight and increase the risk of neonatal sepsis and BPD development in preterm infants.
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Affiliation(s)
- Bilin Cetinkaya Cakmak
- Division of Neonatology, Department of Pediatrics, Ege University Faculty of Medicine, Bornova/Izmir, Turkey
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Karaca E, Tuysuz B, Pehlivan S, Ozkinay F. First genetic screening for maternal uniparental disomy of chromosome 7 in Turkish silver-russell syndrome patients. Iran J Pediatr 2012; 22:445-51. [PMID: 23429302 PMCID: PMC3533142] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 04/27/2012] [Accepted: 06/20/2012] [Indexed: 11/09/2022]
Abstract
OBJECTIVE Silver-Russell syndrome (SRS) is a clinically and genetically heterogeneous syndrome which is characterized by severe intrauterine and postnatal growth retardation, and typical characteristic facial dysmorphisms. It has been associated with maternal uniparental disomy (UPD) for chromosome 7 and hypomethylation of imprinting control region 1 (IGF2/H19) in 11p15. UPD refers to the situation in which both copies of a chromosome pair have originated from one parent. UPD can be presented both as partial heterodisomy and isodisomy. The aim of this study was to determine the maternal UPD7 (matUPD7) in 13 Turkish SRS patients. METHODS Genotyping for matUPD7 was performed with microsatellite markers by polymerase chain reaction. FINDINGS The maternal UPD7 including the entire chromosome was identified in 1/13 (7.6%) of individuals within SRS patients. There were no significant differences between clinical features of matUPD7 case and other SRS cases except congenital heart defects. CONCLUSION It is often difficult to establish diagnosis of a child with intrauterine growth retardation (IUGR), growth failure and dysmorphic features. Thus, screening for matUPD7 in IUGR children with growth failure and mild SRS features might be a valuable diagnostic tool.
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Affiliation(s)
- Emin Karaca
- Department of Genetics, Ege University Medical Faculty, Izmir, Turkey,Corresponding Author:Address: Ege University, Faculty of Medicine, Department of Medical Genetics, 35100 Bornova-Izmir, Turkey. E-mail:
| | - Beyhan Tuysuz
- Department of Pediatrics, Division of Genetics, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Sacide Pehlivan
- Department of Biology, Gaziantep University Medical Faculty, Gaziantep, Turkey
| | - Ferda Ozkinay
- Department of Genetics, Ege University Medical Faculty, Izmir, Turkey
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Cetintas VB, Kosova B, Karaca E, Bulut G, Cekdemir D. Two Newly Discovered Variations of the Plasminogen Activator Inhibitor 1 Gene in 3 Turkish Cases. Clin Appl Thromb Hemost 2012; 18:327-30. [DOI: 10.1177/1076029611424577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Buket Kosova
- Department of Medical Biology, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Emin Karaca
- Department of Medical Genetics, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Gulcan Bulut
- Department of Internal Medicine, Faculty of Medicine, Ege University, Izmir, Turkey
| | - Demet Cekdemir
- Department of Hematology, Faculty of Medicine, Ege University, Izmir, Turkey
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Selvi N, Kosova B, Hekimgil M, Gündüz C, Kaymaz BT, Karaca E, Saydam G, Tombuloğlu M, Büyükkeçeci F, Cağırgan S, Ertan Y, Topçuoğlu N. Molecular Evaluation of t(14;18)(bcl-2/IgH) Translocation in Follicular Lymphoma at Diagnosis Using Paraffin-Embedded Tissue Sections. Turk J Haematol 2012; 29:126-34. [PMID: 24744643 PMCID: PMC3986950 DOI: 10.5505/tjh.2012.93898] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 03/05/2011] [Indexed: 12/05/2022] Open
Abstract
Objective: Follicular lymphoma (FL) is one of the most common lymphomas, and is characterized by t(14;18)(q32;q21) in more than 80% of patients. The aim of this study was to determine the rate of t(14;18) positivity based onthe detection of mbr or mcr in paraffin-embedded tissue samples. Material and Methods: The study included 32 paraffin-embedded tissue samples collected from 32 consecutive FL patients that were diagnosed and followed-up at our hospital between 1999 and 2006. The MBR breakpoint wasidentified based on real-time PCR using a LightCycler v.2.0 t(14;18) Quantification Kit (MBR), multiplex PCR, and seminestedPCR. To identify the mcr breakpoint, real-time PCR was performed using specific primers and the FastStart DNAMaster SYBR Green I Kit. To detect t(14;18) via fluorescence in situ hybridization (FISH) nuclei from paraffin-embeddedtissue sections were extracted and used together with LSI IgH (immunoglobulin heavy chain) (spectrum green)/bcl-2(B-cell leukemia-lymphoma 2) (spectrum orange) probes. Results: The DNA and nuclei isolation success rate for B5 formalin-fixed, paraffin-embedded tissue sections (n = 12)was 42% and 33%, respectively, versus 95% and 60%, respectively, for 20 tissue sections fixed in formalin only. In all,24 paraffin-embedded tissue sections were analyzed and mbr positivity was observed in the DNA of 82.14% via seminested PCR, in 53.57% via multiplex PCR, and in 28.57% via real-time PCR. We did not detect mcr rearrangementin any of the samples. In all, 15 of 16 patients (93.75%) whose nuclei were successfully isolated were observed to bet(14;18) positive via the FISH method. Conclusion: Semi-nested PCR and FISH facilitated the genetic characterization of FL tumors. As such, FISH and PCR complement each other and are both essential for detecting t(14;18) translocation.
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Affiliation(s)
- Nur Selvi
- Ege University, School of Medicine, Medical Biology Department, İzmir, Turkey
| | - Buket Kosova
- Ege University, School of Medicine, Medical Biology Department, İzmir, Turkey
| | - Mine Hekimgil
- Ege University, School of Medicine, Pathology Department, İzmir, Turkey
| | - Cumhur Gündüz
- Ege University, School of Medicine, Medical Biology Department, İzmir, Turkey
| | | | - Emin Karaca
- Ege University, School of Medicine, Medical Genetics Department, İzmir, Turkey
| | - Güray Saydam
- Ege University, School of Medicine, Hematology Department, İzmir, Turkey
| | - Murat Tombuloğlu
- Ege University, School of Medicine, Hematology Department, İzmir, Turkey
| | - Filiz Büyükkeçeci
- Ege University, School of Medicine, Hematology Department, İzmir, Turkey
| | - Seçkin Cağırgan
- Ege University, School of Medicine, Hematology Department, İzmir, Turkey
| | - Yeşim Ertan
- Ege University, School of Medicine, Pathology Department, İzmir, Turkey
| | - Nejat Topçuoğlu
- Ege University, School of Medicine, Medical Biology Department, İzmir, Turkey
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Durmaz B, Ozkinay F, Onay H, Karaca E, Aydinok Y, Tavmergen E, Vrettou C, Traeger-Synodinos J, Kanavakis E. Genotyping of β-globin gene mutations in single lymphocytes: a preliminary study for preimplantation genetic diagnosis of monogenic disorders. Hemoglobin 2012; 36:230-43. [PMID: 22524255 DOI: 10.3109/03630269.2012.675891] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Hemoglobinopathies, especially β-thalassemia (β-thal), represent an important health burden in Mediterranean countries like Turkey. Some couples prefer the option of preimplantation genetic diagnosis (PGD). However, clinical application of PGD, especially for the monogenic disorders is technically demanding. To ensure reliable results, protocols need to be robust and well standardized. Ideally PGD-PCR (polymerase chain reaction) protocols should be based on multiplex and fluorescent PCR for analysis of the disease-causing mutation(s) along with linked markers across the disease-associated locus. In this study, we aimed to constitute a protocol in single cells involving first round multiplex PCR with primers to amplify the region of the β-globin gene containing the most common mutations. Two microsatellites linked to the β-globin gene cluster (D11S4891, D11S2362) and two unlinked (D13S314, GABRB3) microsatellite markers, were used to rule out allele dropout (ADO) and contamination; followed by nested real-time PCR for genotyping the β-globin mutations. We also investigated the allele frequencies and heterozygote rates of these microsatellites in the Turkish population that have not been reported to date. This protocol was tested in 100 single lymphocytes from heterozygotes with known β-globin mutations. Amplification failure was detected in one lymphocyte (1%) and ADO was observed in two lymphocytes (2%). No contamination was detected. All results were concordant with the genotypes of the patients. Overall, this protocol was demonstrated to be sensitive, accurate, reliable and rapid for the detection of β-globin mutations in single cells and shows potential for the clinical application of PGD for hemoglobinopathies in the Turkish population.
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Affiliation(s)
- Burak Durmaz
- Department of Medical Genetics, Ege University, Faculty of Medicine, Bornova, Izmir, Turkey.
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