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Kannan B, Navamani HK, Jayaseelan VP, Arumugam P. A Rare Biotinidase Deficiency in the Pediatrics Population: Genotype-Phenotype Analysis. J Pediatr Genet 2023; 12:1-15. [PMID: 36684547 PMCID: PMC9848769 DOI: 10.1055/s-0042-1757887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/06/2022] [Indexed: 11/07/2022]
Abstract
Biotinidase (BTD) deficiency is a rare autosomal recessive metabolic disorder caused by insufficient biotin metabolism, where it cannot recycle the vitamin biotin. When this deficiency is not treated with supplements, it can lead to severe neurological conditions. Approximately 1 in 60,000 newborns are affected by BTD deficiency. The BTD deficiency causes late-onset biotin-responsive multiple carboxylase deficiency, which leads to acidosis or lactic acidosis, hypoglycemia, and abnormal catabolism. BTD deficiency is of two types based on the amount of BTD Enzyme present in the serum. A wide range of pathogenic mutations in the BTD gene are reported worldwide. Mutations in the BTD gene lead to profound and partial BTD deficiency. Profound BTD deficiency results in a severe pathogenic condition. A high frequency of newborns are affected with the partial deficiency worldwide. They are mostly asymptomatic, but symptoms may appear during stressful conditions such as fasting or viral infections. Several pathogenic mutations are significantly associated with neurological, ophthalmological, and skin problems along with several other clinical features. This review discusses the BTD gene mutation in multiple populations detected with phenotypic features. The molecular-based biomarker screening is necessary for the disease during pregnancy, as it could be helpful for the early identification of BTD deficiency, providing a better treatment strategy. Moreover, implementing newborn screening for the BTD deficiency helps patients prevent several diseases.
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Affiliation(s)
- Balachander Kannan
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Hepzibah Kirubamani Navamani
- Department of Obstetrics and Gynaecology, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Saveetha Medical College and Hospitals, Chennai, Tamil Nadu, India
| | - Vijayashree Priyadharsini Jayaseelan
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Paramasivam Arumugam
- Molecular Biology Lab, Centre for Cellular and Molecular Research, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
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Mukherjee P, Burgio G, Heitlinger E. Dual RNA Sequencing Meta-analysis in Plasmodium Infection Identifies Host-Parasite Interactions. mSystems 2021; 6:e00182-21. [PMID: 33879496 PMCID: PMC8546971 DOI: 10.1128/msystems.00182-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Dual RNA sequencing (RNA-Seq) is the simultaneous transcriptomic analysis of interacting symbionts, for example, in malaria. Potential cross-species interactions identified by correlated gene expression might highlight interlinked signaling, metabolic, or gene regulatory pathways in addition to physically interacting proteins. Often, malaria studies address one of the interacting organisms-host or parasite-rendering the other "contamination." Here we perform a meta-analysis using such studies for cross-species expression analysis. We screened experiments for gene expression from host and Plasmodium. Out of 171 studies in Homo sapiens, Macaca mulatta, and Mus musculus, we identified 63 potential studies containing host and parasite data. While 16 studies (1,950 samples) explicitly performed dual RNA-Seq, 47 (1,398 samples) originally focused on one organism. We found 915 experimental replicates from 20 blood studies to be suitable for coexpression analysis and used orthologs for meta-analysis across different host-parasite systems. Centrality metrics from the derived gene expression networks correlated with gene essentiality in the parasites. We found indications of host immune response to elements of the Plasmodium protein degradation system, an antimalarial drug target. We identified well-studied immune responses in the host with our coexpression networks, as our approach recovers known broad processes interlinked between hosts and parasites in addition to individual host and parasite protein associations. The set of core interactions represents commonalities between human malaria and its model systems for prioritization in laboratory experiments. Our approach might also allow insights into the transferability of model systems for different pathways in malaria studies.IMPORTANCE Malaria still causes about 400,000 deaths a year and is one of the most studied infectious diseases. The disease is studied in mice and monkeys as lab models to derive potential therapeutic intervention in human malaria. Interactions between Plasmodium spp. and its hosts are either conserved across different host-parasite systems or idiosyncratic to those systems. Here we use correlation of gene expression from different RNA-Seq studies to infer common host-parasite interactions across human, mouse, and monkey studies. First, we find a set of very conserved interactors, worth further scrutiny in focused laboratory experiments. Second, this work might help assess to which extent experiments and knowledge on different pathways can be transferred from models to humans for potential therapy.
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Affiliation(s)
- Parnika Mukherjee
- Department of Molecular Parasitology, Humboldt University, Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Gaétan Burgio
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Emanuel Heitlinger
- Department of Molecular Parasitology, Humboldt University, Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
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Salami B, Fernandez-Sanchez H, Fouche C, Evans C, Sibeko L, Tulli M, Bulaong A, Kwankye SO, Ani-Amponsah M, Okeke-Ihejirika P, Gommaa H, Agbemenu K, Ndikom CM, Richter S. A Scoping Review of the Health of African Immigrant and Refugee Children. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18073514. [PMID: 33800663 PMCID: PMC8038070 DOI: 10.3390/ijerph18073514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/02/2022]
Abstract
Migration is a growing phenomenon around the world, including within the African continent. Many migrants, especially African children, face challenges related to health and social inclusion and can face increased health risks. A systematic scoping review of available literature on the health of African migrant children across the globe was conducted to offer insight into these health risks. The review was conducted over a 15-month period from January 2019 to April 2020, yielding 6602 articles once duplicates were removed. This search included electronic databases, reference lists of articles reviewed, and searches of libraries of relevant organisations. A total of 187 studies met the inclusion criteria, of which 159 were quantitative, 22 were qualitative, and 6 used mixed methods. The findings reveal decreased health in this population in areas of nutrition, infectious diseases, mental health, birth outcomes, sexual and reproductive health, physical and developmental health, parasitic infections, oral health, respiratory health, preventative health, endocrine disorders, health care services, and haematological conditions. The findings offer insights into factors influencing the health of African immigrant and refugee children. Further studies, especially qualitative studies, are needed to determine barriers to service access after migration and to investigate other underexplored and overlooked health concerns of African migrant children, including pneumonia and child maltreatment.
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Affiliation(s)
- Bukola Salami
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
- Correspondence:
| | - Higinio Fernandez-Sanchez
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
| | - Christa Fouche
- Faculty of Education and Social Work, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Catrin Evans
- School of Health Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK;
| | - Lindiwe Sibeko
- Department of Nutrition, School of Public Health and Health Sciences, University of Massachusetts, 204 Chenoweth Laboratory, Amherst, MA 01003-9282, USA;
| | - Mia Tulli
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
| | - Ashley Bulaong
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
| | - Stephen Owusu Kwankye
- Regional Institute for Population Studies, University of Ghana, P.O. Box LG 96, Legon, Accra GA184, Ghana;
| | - Mary Ani-Amponsah
- School of Nursing, University of Ghana, P.O. Box LG 43, Legon, Accra GA184, Ghana;
| | | | - Hayat Gommaa
- Department of Nursing Science, Ahmadu Bello University, Sokoto Road, PMB 06, Zaria 810107, Nigeria;
| | - Kafuli Agbemenu
- School of Nursing, The State University of New York (SUNY), University at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA;
| | | | - Solina Richter
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
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Maguolo A, Rodella G, Dianin A, Monge I, Messina M, Rigotti E, Pellegrini F, Molinaro G, Lupi F, Pasini A, Campostrini N, Ion Popa F, Teofoli F, Vincenzi M, Camilot M, Piacentini G, Bordugo A. Newborn Screening for Biotinidase Deficiency. The Experience of a Regional Center in Italy. Front Pediatr 2021; 9:661416. [PMID: 34136440 PMCID: PMC8200396 DOI: 10.3389/fped.2021.661416] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction: Biotinidase deficiency (BD) is an autosomal recessive disease causing a defect in the biotin-releasing enzyme. Newborn screening (NBS) allows early diagnosis and treatment, ensuring excellent prognosis. The aim of this study was to describe our experience in the diagnosis, treatment, and follow-up showing key strategies and unsolved questions of the management of BD patients. Methods: We analyzed data of patients identified by the Regional Centre for Newborn Screening of Verona and followed by the Inherited Metabolic Disease Unit of Verona and Neonatal Intensive Care Unit of Bolzano, Italy, from 2014 to 2020. Results: Thirty-seven patients were diagnosed by NBS (five profound and 32 partial BD), with a total incidence of 1:5,996. All were started on biotin at diagnosis and presented no symptoms at follow-up. Analysis of parents and siblings led to identification of five asymptomatic patients with partial BD: one asymptomatic parent and four young siblings. Genetic analysis of the BTD gene identified 17 different genotypes and one mutation not previously known. Discussion: Our data confirm that NBS introduction had a dramatic impact on BD diagnosis, and the incidence has increased significantly compared to other areas. Partial defects are more common than profound and have a distinctive genotype. Partial BD treatment is still controversial even at what dose of biotin and for how long. At the end, BD treatment is very easy and inexpensive and prevents severe neurological damage. Sharing experiences is essential to achieving guidelines for treatment and follow-up and a better genotype-phenotype correlation.
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Affiliation(s)
- Alice Maguolo
- Department of Mother and Child, University of Verona, Verona, Italy
| | - Giulia Rodella
- Department of Mother and Child, University of Verona, Verona, Italy.,Inherited Metabolic Diseases Unit and Regional Centre for Newborn Screening, Diagnosis and Treatment of Inherited Metabolic Diseases and Congenital Endocrine Diseases, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Alice Dianin
- Inherited Metabolic Diseases Unit and Regional Centre for Newborn Screening, Diagnosis and Treatment of Inherited Metabolic Diseases and Congenital Endocrine Diseases, Azienda Ospedaliera Universitaria Integrata, Verona, Italy.,Pediatric Clinic Azienda Ospedaliera Universitaria Integrata (AOUI) of Verona, Verona, Italy
| | - Irene Monge
- Inherited Metabolic Diseases Unit and Regional Centre for Newborn Screening, Diagnosis and Treatment of Inherited Metabolic Diseases and Congenital Endocrine Diseases, Azienda Ospedaliera Universitaria Integrata, Verona, Italy
| | - Martina Messina
- Department of Mother and Child, University of Verona, Verona, Italy
| | - Erika Rigotti
- Pediatric Clinic Azienda Ospedaliera Universitaria Integrata (AOUI) of Verona, Verona, Italy
| | | | - Grazia Molinaro
- Neonatal Intensive Care Unit, Azienda Sanitaria Alto Adige, Bolzano, Italy
| | - Fiorenzo Lupi
- Neonatal Intensive Care Unit, Azienda Sanitaria Alto Adige, Bolzano, Italy
| | - Andrea Pasini
- Department of Pediatrics, The Regional Center for Neonatal Screening, Diagnosis and Treatment of Inherited Congenital Metabolic and Endocrinological Diseases, AOUI, Verona, Italy
| | - Natascia Campostrini
- Department of Pediatrics, The Regional Center for Neonatal Screening, Diagnosis and Treatment of Inherited Congenital Metabolic and Endocrinological Diseases, AOUI, Verona, Italy
| | - Florina Ion Popa
- Department of Pediatrics, The Regional Center for Neonatal Screening, Diagnosis and Treatment of Inherited Congenital Metabolic and Endocrinological Diseases, AOUI, Verona, Italy
| | - Francesca Teofoli
- Department of Mother and Child, University of Verona, Verona, Italy.,Department of Pediatrics, The Regional Center for Neonatal Screening, Diagnosis and Treatment of Inherited Congenital Metabolic and Endocrinological Diseases, AOUI, Verona, Italy
| | - Monica Vincenzi
- Department of Pediatrics, The Regional Center for Neonatal Screening, Diagnosis and Treatment of Inherited Congenital Metabolic and Endocrinological Diseases, AOUI, Verona, Italy
| | - Marta Camilot
- Department of Mother and Child, University of Verona, Verona, Italy.,Department of Pediatrics, The Regional Center for Neonatal Screening, Diagnosis and Treatment of Inherited Congenital Metabolic and Endocrinological Diseases, AOUI, Verona, Italy
| | - Giorgio Piacentini
- Department of Mother and Child, University of Verona, Verona, Italy.,Pediatric Clinic Azienda Ospedaliera Universitaria Integrata (AOUI) of Verona, Verona, Italy
| | - Andrea Bordugo
- Inherited Metabolic Diseases Unit and Regional Centre for Newborn Screening, Diagnosis and Treatment of Inherited Metabolic Diseases and Congenital Endocrine Diseases, Azienda Ospedaliera Universitaria Integrata, Verona, Italy.,Pediatric Clinic Azienda Ospedaliera Universitaria Integrata (AOUI) of Verona, Verona, Italy
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Canda E, Yazici H, Er E, Kose M, Basol G, Onay H, Ucar SK, Habif S, Ozkinay F, Coker M. Single center experience of biotinidase deficiency: 259 patients and six novel mutations. J Pediatr Endocrinol Metab 2018; 31:917-926. [PMID: 29995633 DOI: 10.1515/jpem-2018-0148] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/28/2018] [Indexed: 11/15/2022]
Abstract
Background Biotinidase deficiency (BD) is an autosomal recessively inherited disorder of biotin recycling. It is classified into two levels based on the biotinidase enzyme activity: partial deficiency (10%-30% enzyme activity) and profound deficiency (0%-10% enzyme activity). The aims of this study were to evaluate our patients with BD, identify the spectrum of biotinidase (BTD) gene mutations in Turkish patients and to determine the clinical and laboratory findings of our patients and their follow-up period. Methods A total of 259 patients who were diagnosed with BD were enrolled in the study. One hundred and forty-eight patients were male (57.1%), and 111 patients were female (42.9%). Results The number of patients detected by newborn screening was 221 (85.3%). By family screening, 31 (12%) patients were diagnosed with BD. Seven patients (2.7%) had different initial complaints and were diagnosed with BD. Partial BD was detected in 186 (71.8%) patients, and the profound deficiency was detected in 73 (28.2%) patients. Most of our patients were asymptomatic. The most commonly found variants were p.D444H, p.R157H, c.98_104delinsTCC. The novel mutations which were detected in this study are p.D401N(c.1201G>A), p.A82G (c.245C>G), p.F128S(c.383T>C), c617_619del/TTG (p.Val207del), p.A287T(c.859G>A), p.S491H(c.1471A>G). The most common mutation was p.R157H in profound BD and p.D444H in partial BD. All diagnosed patients were treated with biotin. Conclusions The diagnosis of BD should be based on plasma biotinidase activity and molecular analysis. We determined the clinical and genetic spectra of a large group of patients with BD from Western Turkey. The frequent mutations in our study were similar to the literature. In this study, six novel mutations were described.
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Affiliation(s)
- Ebru Canda
- Ege University Faculty of Medicine, Department of Pediatrics, Division of Metabolism and Nutrition, Bornova Izmir, 35100, Turkey, Phone: +90 232 3901293
| | - Havva Yazici
- Ege University Faculty of Medicine, Department of Pediatrics, Division of Metabolism and Nutrition, Bornova Izmir, Turkey
| | - Esra Er
- Ege University Faculty of Medicine, Department of Pediatrics, Division of Metabolism and Nutrition, Bornova Izmir, Turkey
| | - Melis Kose
- Ege University Faculty of Medicine, Department of Pediatrics, Division of Metabolism and Nutrition, Bornova Izmir, Turkey
| | - Gunes Basol
- Ege University Faculty of Medicine, Department of Biochemistry, Bornova Izmir, Turkey
| | - Huseyin Onay
- Ege University Faculty of Medicine, Department of Genetics, Bornova Izmir, Turkey
| | - Sema Kalkan Ucar
- Ege University Faculty of Medicine, Department of Pediatrics, Division of Metabolism and Nutrition, Bornova Izmir, Turkey
| | - Sara Habif
- Ege University Faculty of Medicine, Department of Biochemistry, Bornova Izmir, Turkey
| | - Ferda Ozkinay
- Ege University Faculty of Medicine, Department of Genetics, Bornova Izmir, Turkey
| | - Mahmut Coker
- Ege University Faculty of Medicine, Department of Pediatrics, Division of Metabolism and Nutrition, Bornova Izmir, Turkey
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Abstract
Malaria parasites require certain host nutrients for growth and survival. In this project, we examined the role of the human vitamin biotin in all stages of the malaria life cycle. We cultured blood- and liver-stage malaria parasites in the absence of biotin and found that, whereas blood-stage replication was unaffected, liver-stage parasites deprived of biotin were no longer capable of establishing a blood-stage infection. Interestingly, biotin depletion resulted in more severe developmental defects than the genetic disruption of parasite biotin metabolism. This finding suggests that host biotin metabolism also contributes to parasite development. Because neither the parasite nor the human host can synthesize biotin, parasite infectivity may be affected by the nutritional status of the host. Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme that is the target of several classes of herbicides. Malaria parasites contain a plant-like ACC, and this is the only protein predicted to be biotinylated in the parasite. We found that ACC is expressed in the apicoplast organelle in liver- and blood-stage malaria parasites; however, it is activated through biotinylation only in the liver stages. Consistent with this observation, deletion of the biotin ligase responsible for ACC biotinylation does not impede blood-stage growth, but results in late liver-stage developmental defects. Biotin depletion increases the severity of the developmental defects, demonstrating that parasite and host biotin metabolism are required for normal liver-stage progression. This finding may link the development of liver-stage malaria parasites to the nutritional status of the host, as neither the parasite nor the human host can synthesize biotin.
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7
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Liu Z, Zhao X, Sheng H, Cai Y, Yin X, Chen X, Su L, Lu Z, Zeng C, Li X, Liu L. Clinical features, BTD gene mutations, and their functional studies of eight symptomatic patients with biotinidase deficiency from Southern China. Am J Med Genet A 2018; 176:589-596. [PMID: 29359854 DOI: 10.1002/ajmg.a.38601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 11/12/2022]
Abstract
Biotinidase (BTD) deficiency is a rare autosomal recessive metabolic disease, which develops neurological and cutaneous symptoms because of the impaired biotin recycling. Pathogenic mutations on BTD gene cause BTD deficiency. Clinical features and mutation analysis of Chinese children with BTD deficiency were rarely described. Herein, for the first time, we reported the clinical features, BTD gene mutations and their functional studies of eight symptomatic children with BTD deficiency from southern China. Fatigue, hypotonia, proximal muscular weakness, hearing deficits, rash and respiratory problems are common clinical phenotype of our patients. Seizures are observed only in patients with profound BTD deficiency. Five novel mutations were detected, among which c.637delC (H213TfsTer51) was found in 50% of our patients and might be considered as a common mutation. In vitro studies confirmed three mild mutations c.1368A>C (Q456H), c.1613G>A (R538H), and c.644T>A (L215H) which retained 10-30% of wild type enzyme activity, and six severe mutations c.235C>T (R79C), c.1271G>C (C424S), c.1412G>A (C471Y), c.637delC (H213TfsTer51), c.395T>G (M132W), c.464T>C (L155P), and c.1493dupT (L498FfsTer13) which retained <10% of wild type enzyme activity. c.1330G>C (D444H) decreased the protein expression but not activity of BTD enzyme, and H213TfsTer51 was structurally damaging while L498FfsTer13 was functionally damaging. These results will be helpful in establishing the definitive diagnosis of BTD deficiency at the gene level, offering appropriate genetic counseling, and providing clues to structure/function relationships of the enzyme.
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Affiliation(s)
- Zongcai Liu
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiaoyuan Zhao
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Huiying Sheng
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Yanna Cai
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xi Yin
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiaodan Chen
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Ling Su
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Zhikun Lu
- The Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Chunhua Zeng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Xiuzhen Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P.R. China
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Broeckx BJG, Peelman L, Saunders JH, Deforce D, Clement L. Using variant databases for variant prioritization and to detect erroneous genotype-phenotype associations. BMC Bioinformatics 2017; 18:535. [PMID: 29191167 PMCID: PMC5710091 DOI: 10.1186/s12859-017-1951-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/22/2017] [Indexed: 01/08/2023] Open
Abstract
Background In the search for novel causal mutations, public and/or private variant databases are nearly always used to facilitate the search as they result in a massive reduction of putative variants in one step. Practically, variant filtering is often done by either using all variants from the variant database (called the absence-approach, i.e. it is assumed that disease-causing variants do not reside in variant databases) or by using the subset of variants with an allelic frequency > 1% (called the 1%-approach). We investigate the validity of these two approaches in terms of false negatives (the true disease-causing variant does not pass all filters) and false positives (a harmless mutation passes all filters and is erroneously retained in the list of putative disease-causing variants) and compare it with an novel approach which we named the quantile-based approach. This approach applies variable instead of static frequency thresholds and the calculation of these thresholds is based on prior knowledge of disease prevalence, inheritance models, database size and database characteristics. Results Based on real-life data, we demonstrate that the quantile-based approach outperforms the absence-approach in terms of false negatives. At the same time, this quantile-based approach deals more appropriately with the variable allele frequencies of disease-causing alleles in variant databases relative to the 1%-approach and as such allows a better control of the number of false positives. We also introduce an alternative application for variant database usage and the quantile-based approach. If disease-causing variants in variant databases deviate substantially from theoretical expectancies calculated with the quantile-based approach, their association between genotype and phenotype had to be reconsidered in 12 out of 13 cases. Conclusions We developed a novel method and demonstrated that this so-called quantile-based approach is a highly suitable method for variant filtering. In addition, the quantile-based approach can also be used for variant flagging. For user friendliness, lookup tables and easy-to-use R calculators are provided. Electronic supplementary material The online version of this article (doi: 10.1186/s12859-017-1951-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bart J G Broeckx
- Laboratory of Animal Genetics, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820, Merelbeke, Belgium.
| | - Luc Peelman
- Laboratory of Animal Genetics, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820, Merelbeke, Belgium
| | - Jimmy H Saunders
- Department of Medical Imaging and Orthopedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Faculty of Sciences, Ghent University, Ghent, Belgium
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Inborn Errors of Metabolism in the United Arab Emirates: Disorders Detected by Newborn Screening (2011-2014). JIMD Rep 2015; 28:127-135. [PMID: 26589311 DOI: 10.1007/8904_2015_512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/30/2015] [Accepted: 10/05/2015] [Indexed: 01/30/2023] Open
Abstract
This study reports on the inborn errors of metabolism (IEM) detected by our national newborn screening between 2011 and 2014. One hundred fourteen patients (55 UAE citizens and 59 residents) were diagnosed during this period. The program was most comprehensive (tested 29 IEM) and universally applied in 2013, giving an incidence of 1 in 1,787 citizens. This relatively high prevalence resulted from the frequent consanguineous marriages (81.5%) among affected families. The following eight disorders accounted for 80% of the entities: biotinidase deficiency (14 of 55), phenylketonuria (11 of 55), 3-methylcrotonyl glycinuria (9 of 55), medium-chain acyl-CoA dehydrogenase deficiency (4 of 55), argininosuccinic aciduria, glutaric aciduria type 1, glutaric aciduria type 2, and methylmalonyl-CoA mutase deficiency (2 of 55 each). Mutation analysis was performed in 48 (87%) of the 55 patients, and 33 distinct mutations were identified. Twenty-nine (88%) mutations were clinically significant and, thus, could be included in our premarital screening. Most mutations were homozygous, except for the biotinidase deficiency. The BTD mutations c.1207T>G (found in citizens) and c.424C>A (found in Somalians) were associated with undetectable biotinidase activity. Thus, the high prevalence of IEM in our region is amenable to newborn and premarital screening, which is expected to halt most of these diseases.
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Gannavarapu S, Prasad C, DiRaimo J, Napier M, Goobie S, Potter M, Chakraborty P, Karaceper M, Munoz T, Schulze A, MacKenzie J, Li L, Geraghty MT, Al-Dirbashi OY, Rupar CA. Biotinidase deficiency: Spectrum of molecular, enzymatic and clinical information from newborn screening Ontario, Canada (2007-2014). Mol Genet Metab 2015; 116:146-51. [PMID: 26361991 DOI: 10.1016/j.ymgme.2015.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 11/22/2022]
Abstract
Untreated profound biotinidase deficiency results in a wide range of clinical features, including optic atrophy, cutaneous abnormalities, hearing loss and developmental delay. Ontario, Canada incorporated this treatable deficiency in newborn screening over the past 8years. This study elucidates the molecular, biochemical, and clinical findings from the pilot project. Information from initial screens, serum biotinidase activity level assays, molecular testing, and family history for 246 positive newborns screens were analyzed. A mutation spectrum was created for the province of Ontario, including common mutations such as D444H, D444H/A171T, Q456H, C33fs, and R157H. Individuals with partial deficiency were separated into 3 groups: D444H homozygotes (Group 1); compound heterozygotes for D444H with another profound allele (Group 2); compound heterozygotes with two non-D444H alleles (Group 3). Biochemical phenotype-genotype associations in partial deficiency showed a significant difference in serum biotinidase activity in between any given two groups. Three children with partial deficiency discontinued biotin for varied lengths of time. Two of whom became symptomatic with abnormal gait, alopecia, skin rashes and developmental delay. A need for more congruency in diagnostic, treatment and educational practices was highlighted across the province. Heterogeneity and variation in clinical presentations and management was observed in patients with the partial deficiency.
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Affiliation(s)
- Srinitya Gannavarapu
- Department of Pediatrics London Health Sciences Centre and Western University, London ON, Canada
| | - Chitra Prasad
- Department of Pediatrics London Health Sciences Centre and Western University, London ON, Canada.
| | - Jennifer DiRaimo
- Department of Pediatrics London Health Sciences Centre and Western University, London ON, Canada
| | - Melanie Napier
- Department of Pediatrics London Health Sciences Centre and Western University, London ON, Canada
| | - Sharan Goobie
- Department of Pediatrics London Health Sciences Centre and Western University, London ON, Canada
| | - Murray Potter
- Department of Pathology and Molecular Medicine McMaster University, Hamilton ON, Canada
| | - Pranesh Chakraborty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa ON, Canada
| | - Maria Karaceper
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa ON, Canada
| | - Tatiana Munoz
- Divison of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children and University of Toronto, ON, Canada
| | - Andreas Schulze
- Divison of Clinical and Metabolic Genetics, Department of Pediatrics, the Hospital for Sick Children and University of Toronto, ON, Canada; Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, the Hospital for Sick Children, Toronto ON, Canada
| | | | - Lihua Li
- Division of Nephrology, Department of Medicine, Western University, London ON, Canada
| | - Michael T Geraghty
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa ON, Canada; Division of Metabolics, Department Pediatrics, University of Ottawa, ON, Canada
| | - Osama Y Al-Dirbashi
- Newborn Screening Ontario, Children's Hospital of Eastern Ontario, Ottawa ON, Canada; Division of Metabolics, Department Pediatrics, University of Ottawa, ON, Canada
| | - C Anthony Rupar
- Department of Pediatrics London Health Sciences Centre and Western University, London ON, Canada; Department of Pathology and Laboratory Medicine Western University, London, ON, Canada
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11
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Karaca M, Özgül RK, Ünal Ö, Yücel-Yılmaz D, Kılıç M, Hişmi B, Tokatlı A, Coşkun T, Dursun A, Sivri HS. Detection of biotinidase gene mutations in Turkish patients ascertained by newborn and family screening. Eur J Pediatr 2015; 174:1077-84. [PMID: 25754625 DOI: 10.1007/s00431-015-2509-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED The incidence of biotinidase deficiency in Turkey is currently one of the highest in the world. To expand upon the information about the biotinidase gene (BTD) variations in Turkish patients, we conducted a mutation screening in a large series (n = 210) of probands with biotinidase deficiency, using denaturing high-performance liquid chromatography and direct DNA sequencing. The putative effects of novel mutations were predicted by computational program. Twenty-six mutations, including six novels (p.C143F, p.T244I, c.1212-1222del11, c.1320delG, p.V457L, p.G480R) were identified. Nine of the patients were symptomatic at the initial clinical assessment with presentations of seizures, encephalopathy, and lactic acidemia. The most common mutation in this group of symptomatic patients was c.98-104 del7ins3. Among the screened patients, 72 have partial and 134 have profound biotinidase deficiency (BD) of which 106 are homozygous for BTD mutations. The common mutations (p.R157H, p.D444H, c.98-104del7ins3, p.T532M) cumulatively accounted for 72.3% of all the mutant alleles in the Turkish population. CONCLUSION The identification of common mutations and hot spot regions of the BTD gene in Turkish patients is important for mutation screening in the Turkish population and helps to ascertain carriers, may have impact on genetic counseling and implementing prevention programs.
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Affiliation(s)
- Mehmet Karaca
- Faculty of Science and Arts, Department of Biology, Aksaray University, Aksaray, Turkey,
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12
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Abstract
OBJECTIVE To assess the incidence of biotinidase deficiency among newborns and their clinical outcome up to one year of age in a large pilot screening study in Minas Gerais, Brazil. METHODS A prospective cohort study was conducted from September 2007 to June 2008 with heel-prick blood samples collected on filter paper for the purpose of newborn screening. A qualitative colorimetric test was used as the primary screening method. Colorimetric-positive cases were further tested with a serum confirmatory assay. Gene sequencing was performed for eight children suspected with biotinidase deficiency and for some of their parents. Positive cases were daily supplemented with oral biotin and were followed up for approximately six years. RESULTS Out of 182,891 newborns screened, 129 were suspected of having biotinidase deficiency. Partial deficiency was confirmed in seven children (one was homozygous for p.D543E) and profound deficiency in one child (homozygous p.H485Q). Thus the incidence was one in 22,861 live births (95% confidence interval 1:13,503 to 1:74,454) for profound and partial biotinidase deficiency combined. Two novel mutations were detected: p.A281V and p.E177K. In silico analysis and estimation of the enzyme activity in the children and their parents showed that p.A281V is pathogenic and p.E177K behaves like p.D444H. CONCLUSION The incidence of biotinidase deficiency in newborn screening in Minas Gerais was higher than several international studies. The sample size should be larger for final conclusions. Oral daily biotin apparently precluded clinical symptoms, but it may have been unnecessary in some newborns.
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Therrell BL, Padilla CD, Loeber JG, Kneisser I, Saadallah A, Borrajo GJC, Adams J. Current status of newborn screening worldwide: 2015. Semin Perinatol 2015; 39:171-87. [PMID: 25979780 DOI: 10.1053/j.semperi.2015.03.002] [Citation(s) in RCA: 347] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Newborn screening describes various tests that can occur during the first few hours or days of a newborn's life and have the potential for preventing severe health problems, including death. Newborn screening has evolved from a simple blood or urine screening test to a more comprehensive and complex screening system capable of detecting over 50 different conditions. While a number of papers have described various newborn screening activities around the world, including a series of papers in 2007, a comprehensive review of ongoing activities since that time has not been published. In this report, we divide the world into 5 regions (North America, Europe, Middle East and North Africa, Latin America, and Asia Pacific), assessing the current NBS situation in each region and reviewing activities that have taken place in recent years. We have also provided an extensive reference listing and summary of NBS and health data in tabular form.
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Affiliation(s)
- Bradford L Therrell
- National Newborn Screening and Genetics Resource Center (NNSGRC), Austin, TX; Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, TX.
| | - Carmencita David Padilla
- College of Medicine, University of the Philippines Manila, Manila, Philippines; Newborn Screening Reference Center, National Institutes of Health (Philippines), Manila, Ermita, Philippines
| | - J Gerard Loeber
- International Society for Neonatal Screening, Bilthoven, Netherlands
| | - Issam Kneisser
- Newborn Screening Unit, Medical Genetic Unit, Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
| | - Amal Saadallah
- Newborn Screening and Biochemical Genetics Laboratory, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Gustavo J C Borrajo
- Programa de Detección de Errores Congénitos, Fundación Bioquímica Argentina, La Plata, Argentina
| | - John Adams
- Canadian Organization for Rare Disorders, Toronto, Ontario, Canada
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Abstract
Biotinidase deficiency is an inherited disorder in which the vitamin, biotin, is not recycled. Individuals with biotinidase deficiency can develop neurological and cutaneous symptoms if they are not treated with biotin. Biotinidase deficiency screening has been incorporated into essentially all newborn screening programs in the United States and in many countries. We now report 140 known mutations in the biotinidase gene (BTD) that cause biotinidase deficiency. All types of mutations have been found to cause biotinidase deficiency. Variants have been identified throughout the coding sequence. Essentially all the variants result in enzymatic activities with less than 10% of mean normal enzyme activity (profound biotinidase deficiency) with the exception of the c.1330G>C (p.D444H) mutation, which results in an enzyme having 50% of mean normal serum activity. The putative three-dimensional structure of biotinidase has been predicted by homology to that of nitrilases/amidases. The effect of the various missense mutations can be predicted to affect various important sites within the structure of the enzyme. This compilation of variants causing biotinidase deficiency will be useful to clinical laboratories that are performing mutation analysis for confirmational testing when the enzymatic results are equivocal for children identified through newborn screening.
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Affiliation(s)
- Kirit Pindolia
- Department of Medical Genetics, Henry Ford Hospital, Detroit, Michigan 48202, USA
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Ohlsson A, Guthenberg C, Holme E, von Döbeln U. Profound biotinidase deficiency: a rare disease among native Swedes. J Inherit Metab Dis 2010; 33 Suppl 3:S175-80. [PMID: 20224900 DOI: 10.1007/s10545-010-9065-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/28/2010] [Accepted: 02/01/2010] [Indexed: 01/31/2023]
Abstract
Biotinidase deficiency is an autosomal recessive metabolic disorder included in many newborn screening programmes. Prior to the introduction of screening for biotinidase deficiency in Sweden in 2002, the disorder was almost unknown, with only one case diagnosed clinically. Biotinidase activity was measured in dried blood spots with a semiquantitative method using biotin-6-amidoquinoline as substrate. The cutoff value was set at 25% (later lowered to 20%) of the mean activity of all samples measured on that day. The disorder was confirmed by quantitative determination of biotinidase activity in plasma and DNA analyses. Over a period of 6 years, 13 patients were identified among 637,452 screened newborns and 5,068 adoptive/immigrant children. None of the patients had clinical symptoms at the time of diagnosis. Six patients had profound biotinidase deficiency, with an activity of 0-5% of normal in plasma. Four of these patients were born to parents who were first cousins of Middle Eastern or African origin. Eighteen gene alterations were identified, nine of which have not previously been described: seven mutations p.L83S (c.248T > C), p.R148H (c.443G > A), p.N202I (c.605A > T), p.I255T (c.764T > C), p.N402S (c.1205A > G), p.L405P (c.1214T > C), p.G445R (c.1333G > A) and two silent mutations p.L71L (c.211C > T) and p.L215L (c.645C > T). The predicted severity of the novel mutations was analyzed by sorting intolerant from tolerant (SIFT) and polymorphism phenotyping (PolyPhen), predicting p.L83S, p.L405P and p.G445R as severe mutations. Due to the high rate of immigrants since 1990 from non-Nordic countries, the incidence of biotinidase deficiency is similar to that found in many other Western countries.
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Affiliation(s)
- Annika Ohlsson
- Division of Metabolic Diseases, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, Stockholm SE-141 86, Sweden.
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