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Chen S, Gao J, Wu Q, Li X, Lin S, Su J, Zheng K, Guo Z, Yao J, Duan S. Reduction of Missed Diagnosis of G6PD Deficiency in Heterozygous Females by G6PD/6PGD Ratio Assay Combined with Amplification Refractory Mutation System PCR. Hum Hered 2022; 88:1-7. [PMID: 36315991 PMCID: PMC9909718 DOI: 10.1159/000527806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/27/2022] [Indexed: 11/04/2022] Open
Abstract
OBJECTIVE Glucose-6-phosphate dehydrogenase (G6PD) deficiency is an X-linked genetic disorder that results in impaired enzyme activity. The G6PD/6PGD ratio assay was routinely used for G6PD deficiency screening in China, but there is an apparent defect of missed diagnosis in heterozygous females. The study aims to explore the means to improve its accuracy. METHODS A total of 4,161 Chinese females of childbearing age were collected in this retrospective study. All samples were first subjected to G6PD/6PGD ratio assay and then screened by amplification refractory mutation system PCR (ARMS-PCR) for six hotspot mutants in Chinese population (c.1376G>T, c.1388G>A, c.95A>G, c.1024C>T, c.392G>T, and c.871G>A). For the samples with G6PD/6PGD ratio<1.0 and no mutations were found by ARMS-PCR, next-generation sequencing (NGS) was performed. Sanger sequencing was finally used to verify all the variants. RESULTS The prevalence of G6PD deficiency in Shenzhen females of childbearing age was 7.31%. The proportion of the six hotspot mutations accounted for 98.03% of all 304 G6PD variants carriers. Taking the ARMS-PCR/NGS results as a reference, the missed diagnosis rate of the G6PD/6PGD ratio assay was 33.88%. Using ARMS-PCR to retest the samples with a G6PD/6PGD ratio between 1.00 and ∼1.10 or 1.00 and ∼1.15 could reduce the missed diagnosis rate from the original 33.88% to 18.09% or 12.05% separately. CONCLUSION ARMS-PCR is an appropriate supplementary method for discovering most carriers missed by the G6PD/6PGD ratio assay.
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Affiliation(s)
- Shiguo Chen
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
- Laboratory of Molecular Medicine, Shenzhen Health Development Research Center, Shenzhen, China
| | - Jian Gao
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Qunyan Wu
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Xi Li
- Laboratory of Molecular Medicine, Shenzhen Health Development Research Center, Shenzhen, China
| | - Sheng Lin
- Laboratory of Molecular Medicine, Shenzhen Health Development Research Center, Shenzhen, China
| | - Jindi Su
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Kaifeng Zheng
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Zhaopeng Guo
- Departments of Laboratory Medicine, Shenzhen Luohu Maternity and Child Healthcare Hospital, Shenzhen, China
| | - Jilong Yao
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Shan Duan
- Institute of Maternal and Child Medicine Research, Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
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Barrera-Reyes PK, Tejero ME. Genetic variation influencing hemoglobin levels and risk for anemia across populations. Ann N Y Acad Sci 2019; 1450:32-46. [PMID: 31385320 DOI: 10.1111/nyas.14200] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 06/30/2019] [Accepted: 07/05/2019] [Indexed: 01/19/2023]
Abstract
Hemoglobin (Hb) concentration is the outcome of the interaction between genetic variation and environmental factors, including nutritional status, sex, age, and altitude. Genetic diversity influencing this protein is complex and varies widely across populations. Variants related to abnormal Hb or altered characteristics of the erythrocytes increase the risk for anemia. The most prevalent are related to the inherited globin abnormalities affecting Hb production and structure. Malaria-endemic regions harbor the highest frequencies of variants associated with the most frequent monogenic diseases and the risk for nonnutritional anemia and are considered as public health problems. Variation in genes encoding for enzymes and membrane proteins in red blood cells also influence erythrocyte life span and risk for anemia. Most of these variants are rare. Interindividual variability of hematological parameters is also influenced by common genetic variation across the whole genome. Some of the identified variants are associated with Hb production, erythropoiesis, and iron metabolism. Specialized databases have been developed to organize and update the large body of available information on genetic variation related to Hb variation, their frequency, geographical distribution, and clinical significance. Our present review analyzed the underlying genetic factors that affect Hb concentrations, their clinical relevance, and geographical distribution across populations.
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Affiliation(s)
- Paloma K Barrera-Reyes
- Laboratorio de Nutrigenómica y Nutrigenética, Instituto Nacional de Medicina Genómica, Ciudad de, México, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de, México, Mexico
| | - M Elizabeth Tejero
- Laboratorio de Nutrigenómica y Nutrigenética, Instituto Nacional de Medicina Genómica, Ciudad de, México, Mexico
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Canu G, Mazzuccato G, Urbani A, Minucci A. Report of an Italian family carrying a typical Indian variant of the Nilgiris tribal groups resulting from a de novo occurrence. Hum Genome Var 2018; 5:17057. [PMID: 29333274 PMCID: PMC5752699 DOI: 10.1038/hgv.2017.57] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 12/03/2022] Open
Abstract
G6PD deficiency is quite common in Italy where it is characterized by extreme molecular and biochemical heterogeneity. We report a 15-year-old Italian boy with G6PD Nilgiri (c.593G>A, p.Arg198His), a typical Indian variant of the Nilgiris tribal groups. Further, this variant was biochemically characterized, and the molecular screening of the family highlighted a de novo mutational event. To date, this family is the first Caucasian family carrying the G6PD Nilgiri variant.
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Affiliation(s)
- Giulia Canu
- Department of Diagnostic and Laboratory Medicine, Institute of Biochemistry and Clinical Biochemistry, 'Agostino Gemelli' Foundation, Rome, Italy
| | - Giorgia Mazzuccato
- Department of Diagnostic and Laboratory Medicine, Institute of Biochemistry and Clinical Biochemistry, 'Agostino Gemelli' Foundation, Rome, Italy
| | - Andrea Urbani
- Department of Diagnostic and Laboratory Medicine, Institute of Biochemistry and Clinical Biochemistry, 'Agostino Gemelli' Foundation, Rome, Italy.,Proteomics and Metabolomics Unit, IRCCS- 'Santa Lucia' Foundation, Rome, Italy
| | - Angelo Minucci
- Department of Diagnostic and Laboratory Medicine, Institute of Biochemistry and Clinical Biochemistry, 'Agostino Gemelli' Foundation, Rome, Italy
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Point-of-Care Testing for G6PD Deficiency: Opportunities for Screening. Int J Neonatal Screen 2018; 4:34. [PMID: 31709308 PMCID: PMC6832607 DOI: 10.3390/ijns4040034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency, an X-linked genetic disorder, is associated with increased risk of jaundice and kernicterus at birth. G6PD deficiency can manifest later in life as severe hemolysis, when the individual is exposed to oxidative agents that range from foods such as fava beans, to diseases such as typhoid, to medications such as dapsone, to the curative drugs for Plasmodium (P.) vivax malaria, primaquine and tafenoquine. While routine testing at birth for G6PD deficiency is recommended by the World Health Organization for populations with greater than 5% prevalence of G6PD deficiency and to inform P. vivax case management using primaquine, testing coverage is extremely low. Test coverage is low due to the need to prioritize newborn interventions and the complexity of currently available G6PD tests, especially those used to inform malaria case management. More affordable, accurate, point-of-care (POC) tests for G6PD deficiency are emerging that create an opportunity to extend testing to populations that do not have access to high throughput screening services. Some of these tests are quantitative, which provides an opportunity to address the gender disparity created by the currently available POC qualitative tests that misclassify females with intermediate G6PD activity as normal. In populations where the epidemiology for G6PD deficiency and P. vivax overlap, screening for G6PD deficiency at birth to inform care of the newborn can also be used to inform malaria case management over their lifetime.
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Kim Y, Park J, Kim M. Diagnostic approaches for inherited hemolytic anemia in the genetic era. Blood Res 2017; 52:84-94. [PMID: 28698843 PMCID: PMC5503903 DOI: 10.5045/br.2017.52.2.84] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 02/06/2023] Open
Abstract
Inherited hemolytic anemias (IHAs) are genetic diseases that present with anemia due to the increased destruction of circulating abnormal RBCs. The RBC abnormalities are classified into the three major disorders of membranopathies, hemoglobinopathies, and enzymopathies. Traditional diagnosis of IHA has been performed via a step-wise process combining clinical and laboratory findings. Nowadays, the etiology of IHA accounts for germline mutations of the responsible genes coding for the structural components of RBCs. Recent advances in molecular technologies, including next-generation sequencing, inspire us to apply these technologies as a first-line approach for the identification of potential mutations and to determine the novel causative genes in patients with IHAs. We herein review the concept and strategy for the genetic diagnosis of IHAs and provide an overview of the preparations for clinical applications of the new molecular technologies.
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Affiliation(s)
- Yonggoo Kim
- Department of Laboratory Medicine, Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joonhong Park
- Department of Laboratory Medicine, Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Hargreaves KR, Thanki AM, Jose BR, Oggioni MR, Clokie MRJ. Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078. BMC Genomics 2016; 17:1020. [PMID: 27964731 PMCID: PMC5154133 DOI: 10.1186/s12864-016-3346-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/25/2016] [Indexed: 01/20/2023] Open
Abstract
Background How the pathogen Clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. Some ribotypes are found both in clinical and environmental settings. Whether these strains are distinct from each another and evolve in the specific environments is not established. The possession of a highly mobile genome has contributed to the genetic diversity and ongoing evolution of C. difficile. Interpretations of genetic diversity have been limited by fragmented assemblies resulting from short-read length sequencing approaches and by a limited understanding of epigenetic regulation of diversity. To address this, single molecule real time (SMRT) sequencing was used in this study as it produces high quality genome sequences, with resolution of repeat regions (including those found in mobile elements) and can generate data to determine methylation modifications across the sequence (the methylome). Results Chromosomal rearrangements and ribosomal operon duplications were observed in both genomes. The rearrangements occurred at insertion sites within two mobile genetic elements (MGEs), Tn6164 and Tn6293, present only in the M120 and CD105HS27 genomes, respectively. The gene content of these two transposons differ considerably which could impact upon horizontal gene transfer; differences include CDSs encoding methylases and a conjugative prophage only in Tn6164. To investigate mechanisms which could affect MGE transfer, the methylome, restriction modification (RM) and the CRISPR/Cas systems were characterised for each strain. Notably, the environmental isolate, CD105HS27, does not share a consensus motif for m4C methylation, but has one additional spacer when compared to the clinical isolate M120. Conclusions These findings show key differences between the two strains in terms of their genetic capacity for MGE transfer. The carriage of horizontally transferred genes appear to have genome wide effects based on two different methylation patterns. The CRISPR/Cas system appears active although perhaps slow to evolve. Data suggests that both mechanisms are functional and impact upon horizontal gene transfer and genome evolution within C. difficile. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3346-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine R Hargreaves
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK. .,Department Microbiology, The Ohio State University, Columbus, OH, USA.
| | - Anisha M Thanki
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Bethany R Jose
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | | | - Martha R J Clokie
- Department Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.
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