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Khaligh A, Fazeli MS, Mahmoodzadeh H, Mehrtash A, Kompanian S, Zeinali S, Teimoori-Toolabi L. Improved microsatellite instability detection in colorectal cancer patients by a combination of fourteen markers especially DNMT3a, DCD, and MT1X. Cancer Biomark 2021; 31:385-397. [PMID: 34024817 DOI: 10.3233/cbm-203226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Microsatellite instability (MSI) results from genetic and epigenetic changes. Studying Microsatellite instability can help in treatment and categorization of colorectal cancer (CRC) patients. OBJECTIVES We aimed to investigate whether 14 genomic markers consisting of BAT-62, BAT-60, BAT-59a, BAT-56a, BAT-56b, DCD, RIOX, RNF, FOXP, ACVR, CASP2, HSP110, MT1X, and DNMT3a can increase the detection rate of MSI in CRC. METHODS Samples were stratified by pentaplex panel (Promega) and 14 markers using multiplex PCR and fragment analysis. In MSI+ samples, to identify the pattern of BRAF V600E mutation and MLH1 promoter methylation, ARMS-scorpion, and Methylation-Specific High-Resolution Melting Curve analysis, were applied respectively. RESULTS Totally, 35 MSI+ cases identified by 14 marker panel. Only 18 cases of them were detected by both panels which are pentaplex and 14 marker. On the other hand, 17 new MSI+ cases just were identified by 14 markers panel. The highest diagnostic value among 14 markers is related to three makers, namely DCD, MT1X, and DNMT3a. In MSI+ cases, the rate of MLH1 promoter methylation was insignificant, (P value = 0.3979) while the rate of observed BRAFV600E mutation was significantly higher (P value = 0.0002). CONCLUSION Fourteen marker panel showed higher sensitivity in comparison with the pentaplex panel increasing the detection rate of MSI+ cases up to 1.94 fold. Three markers namely DNMT3a, DCD, and MT1X of 14 marker panel were the best among them showing excellent diagnostic value. A combination of these markers showed 100% sensitivity and specificity in the studied group. In contrary to the markers in the pentaplex panel, these markers had the ability to detect MSI without any bias for the clinicopathological features. These markers will help to identify more end-stage MSI+ tumors which are located distal colon.
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Affiliation(s)
- Ali Khaligh
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sadegh Fazeli
- Department of Surgery, Division of Colo-Rectal Surgery, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Habibollah Mahmoodzadeh
- Cancer Institute of Iran, Imam Khomeini Medical Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Amirhosein Mehrtash
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Setareh Kompanian
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sirous Zeinali
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ladan Teimoori-Toolabi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Eftekhariyazdi M, Meshkani M, Moslem A, Hakimi P, Safari S, Khaligh A, Zare-Abdollahi D. Ellis-van Creveld syndrome: Report of a case and recurrent variant. J Gene Med 2020; 22:e3175. [PMID: 32072716 DOI: 10.1002/jgm.3175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 05/16/2019] [Revised: 01/06/2020] [Accepted: 01/28/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ellis-van Creveld syndrome (EvCS) is a rare autosomal recessive skeletal dysplasia that is characterized by short stature, short limbs, short ribs, polydactyly and structural heart defect. Despite locus heterogeneity, in the majority of the cases, the disorder segregates with mutations in the EVC and EVC2 genes, notably mutations with truncating protein as a final sequence. In the present study, we report the prenatal findings and genetic analysis of a terminated pregnancy affected by severe thoracic and skeletal dysplasia. METHODS After detailed physical and clinical examination, whole exome sequencing (WES) was performed and the variant was confirmed by Sanger sequencing. RESULTS One homozygote variant in EVC2 gene was identified in the fetus (NM_147127, c.942G>A, p.W314X). The EVC2 gene is strongly associated with EvCS, which is consistent with the sonographic findings of the fetus. CONCLUSIONS The homozygous p.W314X mutation found in this family was recently reported to be segregated in a consanguineous family originating from Pakistan. The occurrence of the p.W314X mutation in two unrelated families (Iranian and Pakistani) may be the result of an old founder effect or arose because of a mutational hotspot and is supporting evidence for the pathogenicity of this variant. Because skeletal dysplasia belongs to a broad spectrum of syndromes and therefore exhibits considerable background locus and allelic heterogeneity, our report highlights the need for appropriate genetic counseling and supports the feasibility of WES to determine an accurate diagnosis, as well as precise recurrence risk prediction.
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Affiliation(s)
- Mitra Eftekhariyazdi
- Department of Obstetrics and Gynecology, School of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Mahshid Meshkani
- Department of Genetics, Faculty of Biological sciences, Tarbiat Modares University, Tehran, Iran
| | | | - Pooria Hakimi
- Department of Biology, Faculty of science, Islamic azad University, Neyshabour, Iran
| | - Shamsi Safari
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Khaligh
- Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Davood Zare-Abdollahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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Eftekhariyazdi M, Khaligh A, Suizi B, Naghibi Nasab M, Zare-Abdollahi D. Triploidy and Routine Combined First Trimester Pregnancy Screening. Avicenna J Med Biotechnol 2019; 11:124-126. [PMID: 30800253 PMCID: PMC6359692] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND This report is about a pregnancy with a triploid fetus and underscores the potential of first trimester combined screening to detect this devastating chromosomal aberration earlier in pregnancy. This report is about a pregnancy with a triploid fetus identified from the first trimester combined screening and confirmed by amniocentesis. METHODS A 28 year old, G5P2AB2 woman was referred to our clinic at 15 weeks of gestation due to a remarkable decrease of her first trimester double biochemical markers and therefore in the high-risk range for trisomy 13 and 18. The woman underwent amniocentesis which revealed a karyotype of 69,XXX. The parents opted for termination and in post mortem physical examination, a hydrocephalus fetus with marked Intra-Uterine Growth Retardation (IUGR) in addition to syndactyly of third and fourth digits, low set malformed ears, micrognathia and club foot, was seen. RESULTS Our results and previous reports highlight the need to consider a somewhat consistent pattern of the first trimester combined screening in a pregnancy with triploidy and underscore the potential of this screening strategy to detect this chromosomal aberration earlier in pregnancy. CONCLUSION Early prenatal diagnosis of this syndrome would provide women an opportunity to terminate an affected pregnancy earlier. This is also important in preventing the risks of associated later induced abortion or obstetric complications.
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Affiliation(s)
- Mitra Eftekhariyazdi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Ali Khaligh
- Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Behnaz Suizi
- Department of Obstetrics and Gynecology, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Maryam Naghibi Nasab
- Department of Obstetrics and Gynecology, Faculty of Medicine, Sabzevar University of Medical Sciences, Sabzevar, Iran
| | - Davood Zare-Abdollahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran,Corresponding author: Davood Zare-Abdollahi, Ph.D., Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran, Tel: +98 9138502360, E-mail:,
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Khaligh A, Goudarzian M, Moslem A, Mehrtash A, Jamshidi J, Darvish H, Emamalizadeh B. RAB7L1 promoter polymorphism and risk of Parkinson's disease; a case-control study. Neurol Res 2017; 39:468-471. [PMID: 28245721 DOI: 10.1080/01616412.2017.1297558] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Recent genome-wide association studies have explored some new loci in association with Parkinson's disease (PD). RAB7L1 is an important gene involved in one of the important neurological pathways, located in PARK16 locus. We performed a case-control study to examine the association between rs823144 SNP located in the promoter region of the RAB7L1 gene and PD risk in Iranian population. METHODS A total of 960 samples including 480 PD patients and 480 healthy controls were collected for analysis of the RAB7L1 rs823144 polymorphism using polymerase chain reaction-restriction fragment length polymorphism (PCR - RFLP) method. RESULTS We found significant differences in genotypic and allelic frequencies between patients and controls. Significant association was found between presence of minor allele (C) and decreased risk of PD development (p = 0.008, OR = 0.74 (0.605-0.924)). Also another significant association was observed between the CC genotype and PD (p = 0.004, OR = 0.441 (0.252-0.772)). CONCLUSION Our data support the association between rs823144 and decreased risk of PD.
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Affiliation(s)
- Ali Khaligh
- a Iranian Research Center of Healthy Aging , Sabzevar University of Medical Sciences , Sabzevar , Iran
| | - Maryam Goudarzian
- a Iranian Research Center of Healthy Aging , Sabzevar University of Medical Sciences , Sabzevar , Iran
| | - Alireza Moslem
- b Sabzevar University of Medical Sciences , Sabzevar , Iran
| | - Amirhosein Mehrtash
- c Molecular Medicine Department, Biotechnology Research Center , Pasteur Institute of Iran , Tehran , Iran
| | - Javad Jamshidi
- d Noncommunicable Diseases Research Center , Fasa University of Medical Sciences , Fasa , Iran
| | - Hossein Darvish
- e Department of Medical Genetics, School of Medicine , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Babak Emamalizadeh
- f Faculty of Medicine, Department of Medical Genetics , Tabriz University of Medical Sciences , Tabriz , Iran
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Beiranvand E, Abediankenari S, Valiyari S, Rezaei MS, Rostamian M, Beiranvand B, Khaligh A, Khani S. Single nucleotide polymorphisms of IFNγ (+874 A/T) and IFNγR1 (-56 C/T) in Iranian patients with TB. Trans R Soc Trop Med Hyg 2016; 110:604-609. [PMID: 27941164 DOI: 10.1093/trstmh/trw074] [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: 08/26/2016] [Revised: 10/19/2016] [Accepted: 11/08/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Two important genes for controlling TB are IFNγ and IFNγR1. However, little information exists regarding genetic susceptibility of the Iranian TB population. METHODS We investigated the single nucleotide polymorphisms (SNPs) in genes of IFNγ (+874 A/T) and IFNγR1 (-56 C/T) and serum level of IFNγ and their influence on TB in patients; 300 patients with TB and 300 healthy controls were enrolled in this study. PCR-restriction fragment length polymorphism was used to identify SNPs and serum level of IFNγ was measured by ELISA. RESULTS The allelic and the genotypic form of IFNγ+874 A/T SNP of the studied population were not significant (p>0.05). Allele T frequencies of IFNγR1 -56 C/T promoter region in patients with pulmonary TB (PTB) or extrapulmonary TB (EPTB) were significantly greater than allele C. The -56 TT motif of IFNγR1 is associated with both forms of TB (p<0.05). The serum level of IFNγ was significantly higher in patients with TB than in controls, but there was no significant difference between serum level of IFNγ and the studied genotypes (p>0.05). CONCLUSIONS The cause of active TB in the patients seems to be due to the lack of effective IFNγ function or the lack of effective signaling connection between IFNγ and its receptor in presence of -56 C/T polymorphism in promoter region of IFNγR1 gene.
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Affiliation(s)
- Elham Beiranvand
- Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran, Biotechnology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Saeid Abediankenari
- Immunogenetics Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Samira Valiyari
- Department of Medical Biotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Sadegh Rezaei
- Booalisina Hospital, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | | | | | - Ali Khaligh
- Sabzevar University of Medical Science, Sabzevar, Iran
| | - Soghra Khani
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
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Emamalizadeh B, Jamshidi J, Movafagh A, Ohadi M, khaniani MS, Kazeminasab S, Biglarian A, Taghavi S, Motallebi M, Fazeli A, Ahmadifard A, Shahidi GA, Petramfar P, Shahmohammadibeni N, Dadkhah T, Khademi E, Tafakhori A, Khaligh A, Safaralizadeh T, Kowsari A, Mirabzadeh A, Zarneh AES, Khorrami M, Shokraeian P, Banavandi MJS, Lima BS, Andarva M, Alehabib E, Atakhorrami M, Darvish H. RIT2 Polymorphisms: Is There a Differential Association? Mol Neurobiol 2016; 54:2234-2240. [DOI: 10.1007/s12035-016-9815-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 02/23/2016] [Indexed: 10/22/2022]
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Goudarzian M, Khaligh A, Fourozan R, Jamal Mirmoosavi S, Darvish H, Safaralizadeh T, Emamalizadeh B. The rs1572931 polymorphism of the RAB7L1 gene promoter is associated with reduced risk of Parkinson's disease. Neurol Res 2015; 37:1029-31. [DOI: 10.1179/1743132815y.0000000085] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Darvish H, Movafagh A, Omrani MD, Firouzabadi SG, Azargashb E, Jamshidi J, Khaligh A, Haghnejad L, Naeini NS, Talebi A, Heidari-Rostami HR, Noorollahi-Moghaddam H, Karkheiran S, Shahidi GA, Paknejad SMH, Ashrafian H, Abdi S, Kayyal M, Akbari M, Pedram N, Emamalizadeh B. Detection of copy number changes in genes associated with Parkinson's disease in Iranian patients. Neurosci Lett 2013; 551:75-8. [PMID: 23880019 DOI: 10.1016/j.neulet.2013.07.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/27/2013] [Accepted: 07/05/2013] [Indexed: 01/23/2023]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disorder, after Alzheimer's disease. Genomic rearrangements are common mutations reported in PD patients. In this study, we investigated the prevalence of genomic rearrangements in a total of 232 Iranian PD patients, out of which 102 were sporadic early-onset (age-at-onset ≤ 45 years) and 51 had a family history. We used multiplex ligation-dependent probe amplification (MLPA) method to detect exon dosage changes. Two new improved probe kits, SALSA P051 and P052, were used and altogether α-synuclein, parkin, UCHL1, PINK1, DJ-1, LRRK2, GCH1, ATP13A2, CAV1, CAV2, LPA and TNFRSF9 genes were analyzed. Exon or whole-gene rearrangements were identified in 14 (13.7%) sporadic early-onset PD patients in parkin, α-synuclein and PINK1. Of familial PD patients 46 cases from 18 families (35.3%) showed exon or whole-gene rearrangements in parkin, α-synuclein, PINK1, DJ-1, and ATP13A2 genes. All changes were verified by quantitative PCR (qPCR). Novel mutations and unusual clinical features are reported in this study. Mutations in parkin were the predominant genetic cause in both early-onset and familial PD groups. Also the mutations observed in family PD group are more in number and diversity than the sporadic early-onset PD group.
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