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Schraders K, Coad J, Kruger M. Bone Health in Premenopausal Women with Coeliac Disease: An Observational Study. Nutrients 2024; 16:2178. [PMID: 39064621 PMCID: PMC11279892 DOI: 10.3390/nu16142178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 06/29/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Low bone mineral density (BMD) is common in adults with coeliac disease (CD), even in individuals adhering to a gluten-free diet (GFD). Women are more likely to have low BMD and have an increased risk of osteoporosis, so women with pre-existing low BMD related to CD are at an even higher risk. BMD assessed by dual X-ray absorptiometry (DXA) and bone quality assessed through quantitative ultrasound (QUS) were investigated in 31 premenopausal women with CD consuming a GFD, and 39 matched healthy controls from the Lower North Island, New Zealand. In addition, bone metabolism and nutrient status were assessed, and four-day diet diaries were used to estimate nutrient intake. No statistically significant differences were found in BMD assessed by DXA between the two groups at the hip, lumbar spine or forearm. However, the parameters measured by the QUS were significantly lower in CD participants. Dietary data indicated significantly lower intakes of energy, dietary fibre, magnesium and phosphorus in women with CD, likely as a result of a reduced intake of wholegrain foods, and suggested that both groups had inadequate intake of calcium. No significant differences were demonstrated in biochemical parameters. BMD and bone biomarkers indicated no differences between coeliac and healthy women in New Zealand. However, these findings suggest that QUS may be more sensitive for the coeliac population, due to the disease's affect on the trabecular bone, and warrant further research.
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Affiliation(s)
- Katie Schraders
- School of Food Technology and Natural Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand;
| | - Jane Coad
- School of Food Technology and Natural Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand;
| | - Marlena Kruger
- School of Health Sciences, College of Health, Massey University, Palmerston North 4442, New Zealand;
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Liem B, Anderson NE, Wright SL, Anderson SC, Donnelly J, Austin P, Steele R. Encephalitis in adults in the Auckland and Northland regions of New Zealand, 2009 to 2018. J Clin Neurosci 2023; 107:172-177. [PMID: 36494269 DOI: 10.1016/j.jocn.2022.10.024] [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: 04/27/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 12/13/2022]
Abstract
We conducted a retrospective study to determine the incidence and frequency of different subtypes of encephalitis in patients aged 15 and older in the Auckland and Northland regions of New Zealand between 2009 and 2018. Residents in Auckland and Northland presenting with encephalitis between 2009 and 2018 were identified from three overlapping databases: positive cerebrospinal fluid (CSF) viral polymerase chain reaction (PCR) tests, CSF neuronal antibody requests, and CSF neuronal antibody tests sent overseas. A diagnosis of autoimmune encephalitis required fulfilment of diagnostic criteria published by Graus and colleagues (2016). One hundred and thirty-six (69, 50.7% female) patients met study inclusion criteria. The median age was 59 (range 15-92). The annual incidence was 1.10 cases per 100,000 person-years. Of these 136 patients, 56 (41.2%) had an infectious aetiology, with varicella zoster (26, 46.4%) and herpes simplex (23, 41.1%) being the most common agents. Autoimmune encephalitis was diagnosed in 32 patients (23.5%). LGI-1 antibody was the most commonly identified neuronal autoantibody (10 patients, 13.2%). Forty-eight patients (35.3%) had encephalitis of unknown cause. In-hospital mortality for infectious encephalitis was 12.5%, autoimmune encephalitis 6.3%, and encephalitis of unknown cause 10.4%. Compared to a previous analysis of encephalitis in adults in Auckland, the incidence of encephalitis and autoimmune encephalitis had increased. The proportion of patients with an unknown cause for encephalitis had decreased.
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Affiliation(s)
- Bernard Liem
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand.
| | - Neil E Anderson
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Sarah L Wright
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Sarah C Anderson
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Joseph Donnelly
- Department of Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Paul Austin
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
| | - Richard Steele
- Department of Virology and Immunology, LabPLUS, Auckland City Hospital, Auckland, New Zealand
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Edinur HA, Mat-Ghani SNA, Chambers GK. Ethnicity-based classifications and medical genetics: One Health approaches from a Western Pacific perspective. Front Genet 2022; 13:970549. [PMID: 36147511 PMCID: PMC9485872 DOI: 10.3389/fgene.2022.970549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
A new era presently dawns for medical genetics featuring individualised whole genome sequencing and promising personalised medical genetics. Accordingly, we direct readers attention to the continuing value of allele frequency data from Genome-Wide Association Surveys (GWAS) and single gene surveys in well-defined ethnic populations as a guide for best practice in diagnosis, therapy, and prescription. Supporting evidence is drawn from our experiences working with Austronesian volunteer subjects across the Western Pacific. In general, these studies show that their gene pool has been shaped by natural selection and become highly diverged from those of Europeans and Asians. These uniquely evolved patterns of genetic variation underlie contrasting schedules of disease incidence and drug response. Thus, recognition of historical bonds of kinship among Austronesian population groups across the Asia Pacific has distinct public health advantages from a One Health perspective. Other than diseases that are common among them like gout and diabetes, Austronesian populations face a wide range of climate-dependent infectious diseases including vector-borne pathogens as they are now scattered across the Pacific and Indian Oceans. However, we caution that the value of genetic survey data in Austronesians (and other groups too) is critically dependent on the accuracy of attached descriptive information in associated metadata, including ethnicity and admixture.
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Affiliation(s)
- Hisham A. Edinur
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | - Geoffrey K. Chambers
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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Hajar CGN, Md Akhir S, Zefarina Z, Riffin NSM, Tuan Mohammad TH, Hassan MN, Aziz MY, Pati S, Chambers GK, Kari ZA, Edinur HA, Che Mat NF. Distribution of 22 Single Nucleotide Polymorphisms in 13 Cytokine Genes in Malays, Chinese, and Indians in Peninsular Malaysia. Genet Test Mol Biomarkers 2022; 26:449-456. [PMID: 36166739 DOI: 10.1089/gtmb.2022.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: Cytokines are cell signaling glycoproteins that are particularly important in immunity and inflammatory responses. Therefore, variations, such as single nucleotide polymorphisms (SNPs), in genes encoding for cytokines may have important consequences for their roles in health. Materials and Methods: A total of 222 unrelated, healthy, and un-admixed Malays (n = 97), Chinese (n = 77), and Indians (n = 48) with a median age of 30 years old (range 21-50) were typed for 22 cytokine gene SNPs: IL-1α -889 T/C, IL-1β (-511 T/C, +3962 T/C), IL-1R pst1 1970 T/C, IL-1RA mspa1 11100 T/C, IL-4Rα +1902 G/A, IL-12 - 1188 C/A, IFN-γ +874 A/T, TGF-β (cdn 10 C/T, cdn 25 G/C), TNF-α (-308 A/G, -238 A/G) IL-2 (+166 G/T, -330 T/G), IL-4 (-1098 T/G, -590 T/C, -33 T/C), IL-6 (-174 C/G, nt565 G/A), and IL-10 (-1082 G/A, -819 C/T, -592 A/C). This involved using well-established polymerase chain reaction procedures with sequence-specific primers and restriction fragment length polymorphism methods. Results: The majority of the screened cytokine gene SNPs are polymorphic in all three ethnicities. Exceptions include TGF-β cdn 25 (G/C), IL-1β +3962 (T/C), and TNF-α -238 (A/G), which were all observed to be monomorphic in Malays, Chinese and Indians. Many of the analyzed cytokine gene SNP genotypes deviated from Hardy-Weinberg equilibrium and the three ethnic study groups were all well-separated from reference Asian, African and European populations in a principal component analysis plot. Conclusion: We successfully typed 22 SNPs in 13 cytokine genes from genetic material collected from unrelated and un-admixed Malay, Chinese and Indian individuals in Peninsular Malaysia. These new cytokine gene population datasets reveal interesting contrasts with other populations.
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Affiliation(s)
- Che Ghazali Norul Hajar
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Suhaida Md Akhir
- Biomedicine Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Zulkafli Zefarina
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | | | - Mohd Nazri Hassan
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Mohd Yusmaidie Aziz
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | | | | | - Zulhisyam Abdul Kari
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Kelantan, Malaysia
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nor Fazila Che Mat
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Biomedicine Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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Tao S, Kichula KM, Harrison GF, Farias TDJ, Palmer WH, Leaton LA, Hajar CGN, Zefarina Z, Edinur HA, Zhu F, Norman PJ. The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia. Immunology 2021; 162:389-404. [PMID: 33283280 PMCID: PMC7968402 DOI: 10.1111/imm.13289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs) interact with polymorphic human leucocyte antigen (HLA) class I molecules, modulating natural killer (NK) cell functions and affecting both the susceptibility and outcome of immune-mediated diseases. The KIR locus is highly diverse in gene content, copy number and allelic polymorphism within individuals and across geographical populations. To analyse currently under-represented Asian and Pacific populations, we investigated the combinatorial diversity of KIR and HLA class I in 92 unrelated Malay and 75 Malaysian Chinese individuals from the Malay Peninsula. We identified substantial allelic and structural diversity of the KIR locus in both populations and characterized novel variations at each analysis level. The Malay population is more diverse than Malay Chinese, likely representing a unique history including admixture with immigrating populations spanning several thousand years. Characterizing the Malay population are KIR haplotypes with large structural variants present in 10% individuals, and KIR and HLA alleles previously identified in Austronesian populations. Despite the differences in ancestries, the proportion of HLA allotypes that serve as KIR ligands is similar in each population. The exception is a significantly reduced frequency of interactions of KIR2DL1 with C2+ HLA-C in the Malaysian Chinese group, caused by the low frequency of C2+ HLA. One likely implication is a greater protection from preeclampsia, a pregnancy disorder associated with KIR2DL1, which shows higher incidence in the Malay than in the Malaysian Chinese. This first complete, high-resolution, characterization of combinatorial diversity of KIR and HLA in Malaysians will form a valuable reference for future clinical and population studies.
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Affiliation(s)
- Sudan Tao
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Genelle F. Harrison
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Ticiana Della Justina Farias
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - William H. Palmer
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | | | - Zulkafli Zefarina
- School of Medical SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Hisham Atan Edinur
- School of Health SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Faming Zhu
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
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Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Abdullah MT, Chambers GK, Edinur HA. Forensic parameters and ancestral fractions in the Kedayan population inferred using 21 autosomal STR loci. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Gaunt MW, Gubler DJ, Pettersson JHO, Kuno G, Wilder-Smith A, de Lamballerie X, Gould EA, Falconar AK. Recombination of B- and T-cell epitope-rich loci from Aedes- and Culex-borne flaviviruses shapes Zika virus epidemiology. Antiviral Res 2019; 174:104676. [PMID: 31837392 DOI: 10.1016/j.antiviral.2019.104676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/06/2019] [Accepted: 12/08/2019] [Indexed: 02/07/2023]
Abstract
Sporadic human Zika virus (ZIKV) infections have been recorded in Africa and Asia since the 1950s. Major epidemics occurred only after ZIKV emerged in the Pacific islands and spread to the Americas. Specific biological determinants of the explosive epidemic nature of ZIKV have not been identified. Phylogenetic studies revealed incongruence in ZIKV placement in relation to Aedes-borne dengue viruses (DENV) and Culex-borne flaviviruses. We hypothesized that this incongruence reflects interspecies recombination resulting in ZIKV evasion of cross-protective T-cell immunity. We investigated ZIKV phylogenetic incongruence in relation to: DENV T-cell epitope maps experimentally identified ex vivo, published B-cell epitope loci, and CD8+ T-cell epitopes predicted in silico for mosquito-borne flaviviruses. Our findings demonstrate that the ZIKV proteome is a hybrid of Aedes-borne DENV proteins interspersed amongst Culex-borne flavivirus proteins derived through independent interspecies recombination events. These analyses infer that DENV-associated proteins in the ZIKV hybrid proteome generated immunodominant human B-cell responses, whereas ZIKV recombinant derived Culex-borne flavivirus-associated proteins generated immunodominant CD8+ and/or CD4+ T-cell responses. In silico CD8+ T-cell epitope ZIKV cross-reactive prediction analyses verified this observation. We propose that by acquiring cytotoxic T-cell epitope-rich regions from Culex-borne flaviviruses, ZIKV evaded DENV-generated T-cell immune cross-protection. Thus, Culex-borne flaviviruses, including West Nile virus and Japanese encephalitis virus, might induce cross-protective T-cell responses against ZIKV. This would explain why explosive ZIKV epidemics occurred in DENV-endemic regions of Micronesia, Polynesia and the Americas where Culex-borne flavivirus outbreaks are infrequent and why ZIKV did not cause major epidemics in Asia where Culex-borne flaviviruses are widespread.
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Affiliation(s)
- Michael W Gaunt
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Duane J Gubler
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Rd, 169857, Singapore
| | - John H-O Pettersson
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden; Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Goro Kuno
- 1648 Collindale Dr, Fort Collins, CO, 80525, USA
| | - Annelies Wilder-Smith
- London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK; Department of Public Health and Clinical Medicine, Epidemiology and Public Health, Umeå University, Umeå, Sweden; Heidelberg Institute of Global Health, University of Heidelberg, Germany
| | - Xavier de Lamballerie
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190, Inserm, 1207-IHU Méditerranée Infection, Marseille, France
| | - Ernest A Gould
- UMR "Unité des Virus Emergents", Aix-Marseille Université-IRD 190, Inserm, 1207-IHU Méditerranée Infection, Marseille, France
| | - Andrew K Falconar
- Departmento de Medicina, Universidad del Norte, Barranquilla, Colombia
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Dafalla AM, Edinur HA, Abdelwahed M, Elemam AA, Ibrahim AA, Mohamadani A, Magzoub M, ElGhazali G. Human Leukocyte Antigen (HLA) class I and II datasets for sudanese. Data Brief 2019; 24:104027. [PMID: 31193964 PMCID: PMC6545336 DOI: 10.1016/j.dib.2019.104027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 05/06/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
Sudan is located in the heart of Africa and surrounded by eight countries with people of different ethnic origins. Historical records show that the population of the Sudan is a mixture of Arabic, West Asian Arabic and sub-Saharan African elements. The present survey provides data on allele lineages, and haplotype frequencies of Human Leukocyte Antigen (HLA) class I (HLA-A and HLA-B) and class II (HLA-DR and –HLA-DQ) loci in 11 Sudanese populations. The sampled individuals are all local transplant donors who provided informed consent for HLA analyses on their blood samples and were registered at National Cancer Institute, University of Gezira, Wad Medani. The HLA class I and II data reported here can be subjected for future analyses of genetic structure and health in Sudan. These include as reference datasets for identifying the association between HLA and diseases and for designing donor recruitment strategies.
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Affiliation(s)
- Ameer Mohamed Dafalla
- HLA Laboratory, National Cancer Institute, University of Gezira, Wad Medani, P.O. Box 20, Sudan
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Mohammed Abdelwahed
- HLA Laboratory, National Cancer Institute, University of Gezira, Wad Medani, P.O. Box 20, Sudan
| | - Almutaz Abbas Elemam
- HLA Laboratory, National Cancer Institute, University of Gezira, Wad Medani, P.O. Box 20, Sudan
| | - Amel Abdeen Ibrahim
- HLA Laboratory, National Cancer Institute, University of Gezira, Wad Medani, P.O. Box 20, Sudan
| | - Ahmed Mohamadani
- Department of Pathology, Faculty of Medicine, University of Gezira, P.O. Box 20, Sudan
| | - Mubarak Magzoub
- HLA Laboratory, National Cancer Institute, University of Gezira, Wad Medani, P.O. Box 20, Sudan
| | - Gehad ElGhazali
- Department of Immunology, Pathology and Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, P.O Box 51900, United Arab Emirates
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Prospective Evaluation of the ESPGHAN Guidelines for Diagnosis of Celiac Disease in New Zealand Children. J Pediatr Gastroenterol Nutr 2018; 67:749-754. [PMID: 29916948 DOI: 10.1097/mpg.0000000000002065] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The 2012 European Society of Pediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) guideline for diagnosis of celiac disease (CD) questioned the requirement for intestinal biopsy to confirm the diagnosis. The guideline recommends that in symptomatic patients with consistent human leukocyte antigen (HLA) subtypes, the diagnostic accuracy of strongly positive serology is sufficient to confirm the diagnosis. We prospectively assessed these guidelines in a "real-life" clinical setting. METHODS One hundred and four children referred for evaluation of possible CD were prospectively recruited. Following informed consent, blood was drawn for serological testing and HLA analysis at upper gastrointestinal endoscopy. Histological findings according to Marsh criteria were correlated with blood results and the accuracy of the guideline analyzed.The study also examined the role of deamidated gliadin peptide (DGP) in the diagnosis of CD. RESULTS For symptomatic patients with consistent HLA subtypes, strongly positive serology (as described in the ESPGHAN guidelines) accurately predicted biopsy-proven CD in >95% of cases. DGP was positive in fewer patients than anti-TG2 or EMA. Incorporation of DGP as a second confirmatory serological test in place of EMA was associated with maintained predictive value of guideline, but fewer patients fulfilling criteria for biopsy-free diagnosis. CONCLUSIONS The ESPGHAN guideline performs well in our population. Adoption of the guideline would reduce the number of patients requiring endoscopy without compromise in diagnostic accuracy. The involvement of pediatric gastroenterological expertise, however, remains key to diagnosis of CD.
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An original Eurasian haplotype, HLA-DRB1*14:54-DQB1*05:03, influences the susceptibility to idiopathic achalasia. PLoS One 2018; 13:e0201676. [PMID: 30092016 PMCID: PMC6084941 DOI: 10.1371/journal.pone.0201676] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/19/2018] [Indexed: 01/04/2023] Open
Abstract
Idiopathic achalasia is a relatively infrequent esophageal motor disorder for which major histocompatibility complex (MHC) genes are well-identified risk factors. However, no information about HLA-achalasia susceptibility in Mexicans has previously been reported. We studied a group of 91 patients diagnosed with achalasia and 234 healthy controls with Mexican admixed ancestry. HLA alleles and conserved extended haplotypes were analyzed using high-resolution HLA typing based on Sanger and next-generation sequencing technologies. Admixture estimates were determined using HLA-B and short tandem repeats. Results were analyzed by non-parametric statistical analysis and Bonferroni correction. P-values < 0.05 were considered significant. Patients with achalasia had 56.7% Native American genes, 24.7% European genes, 16.5% African genes and 2.0% Asian genes, which was comparable with the estimates in the controls. Significant increases in the frequencies of alleles DRB1*14:54 and DQB1*05:03 and the extended haplotypes DRB1*14:54-DQB1*05:03 and DRB1*11:01-DQB1*03:01, even after Bonferroni correction (pC<0.05), were found in the achalasia group compared to those in the controls. Concluding, the HLA class II alleles HLA-DRB1*14:54:01 and DQB1*05:03:01 and the extended haplotype are risk factors for achalasia in mixed-ancestry Mexican individuals. These results also suggest that the HLA-DRB1*14:54-DQB1*05:03 haplotype was introduced by admixture with European and/or Asian populations.
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Ton KNT, Cree SL, Gronert-Sum SJ, Merriman TR, Stamp LK, Kennedy MA. Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. Front Genet 2018; 9:152. [PMID: 29760718 PMCID: PMC5936980 DOI: 10.3389/fgene.2018.00152] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles. Here, we describe an approach to HLA-B typing using next generation sequencing (NGS) on the MinION™ nanopore sequencer, combined with data analysis with the SeqNext-HLA software package. The nanopore sequencer offers the advantages of long-read capability and single molecule reads, which can facilitate effective haplotyping. We developed this method using reference samples as well as individuals of New Zealand Māori or Pacific Island descent, because HLA-B diversity in these populations is not well understood. We demonstrate here that nanopore sequencing of barcoded, pooled, 943 bp polymerase chain reaction (PCR) amplicons of 49 DNA samples generated ample read depth for all samples. HLA-B alleles were assigned to all samples at high-resolution with very little ambiguity. Our method is a scaleable and efficient approach for genotyping HLA-B and potentially any other HLA locus. Finally, we report our findings on HLA-B genotypes of this cohort, which adds to our understanding of HLA-B allele frequencies among Māori and Pacific Island people.
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Affiliation(s)
- Kim N T Ton
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Tony R Merriman
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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12
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Jones HF, Mohammad SS, Reed PW, Dunn PPJ, Steele RH, Dale RC, Sharpe C. Anti-N-methyl-d-aspartate receptor encephalitis in Māori and Pacific Island children in New Zealand. Dev Med Child Neurol 2017; 59:719-724. [PMID: 28328164 DOI: 10.1111/dmcn.13420] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2017] [Indexed: 12/19/2022]
Abstract
AIM To investigate the incidence and severity of anti-N-methyl-d-aspartate (anti-NMDA) receptor encephalitis in children from New Zealand. METHOD A retrospective case series was undertaken of all children (≤18y) diagnosed with anti-NMDA receptor encephalitis from January 2008 to October 2015. RESULTS Sixteen patients were identified with anti-NMDA receptor antibodies in the cerebrospinal fluid, three of whom had an associated teratoma. Fifteen children had Māori and/or Pacific Island ancestry. The incidence of anti-NMDA receptor encephalitis in Māori children was 3.4 per million children per year (95% confidence interval [CI] 1.4-7.0) and the incidence in Pacific children was 10.0 per million children per year (95% CI 4.3-19.8) compared with 0.2 per million children per year (95% CI 0.0-1.0) in children without Māori or Pacific Island ancestry. Sixty-seven per cent of children had a good outcome (modified Rankin Score ≤2) at 2 years' follow-up. This compares unfavourably with other cohorts despite a shorter median time to first-line immunotherapy (13d; range 4-89) and a higher proportion of children being treated with second-line therapy (50%). INTERPRETATION Māori and Pacific Island children have a higher incidence of anti-NMDA receptor encephalitis and possibly a more severe phenotype. These data suggest a genetic predisposition to anti-NMDA receptor encephalitis in these populations.
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Affiliation(s)
| | | | - Peter W Reed
- Starship Children's Hospital, Auckland, New Zealand
| | | | | | - Russell C Dale
- The Children's Hospital at Westmead, Westmead, NSW, Australia
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13
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Arnaiz-Villena A, Muñiz E, del Palacio-Gruber J, Campos C, Alonso-Rubio J, Gomez-Casado E, Lopez-Pacheco F, Martin-Villa M, Silvera C. Ancestry of Amerindians and its Impact in Anthropology, Transplantation, HLA Pharmacogenomics and Epidemiology by HLA Study in Wiwa Colombian Population. ACTA ACUST UNITED AC 2016. [DOI: 10.2174/1874220301603010269] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:HLA autosomic genes are unique because they conform the most polymorphic human system. Importance of this system is recognized in Medicine for Transplantation, Epidemiology (HLA and disease linkage), Pharmacogenomics (HLA linked to drug side effects) and for defining the origin of populations in both male and female lineages.Objectives:Studying HLA profile of a isolated Amerindian group from North Colombia (Wiwa) in order to draw conclusions about its Preventive Medicine, the genetic relationship with Worldwide populations and America peopling, since this last issue is hotly debated.Methodology:A total of 14,660 HLA chromosomes were included. Peripheral blood was obtained from volunteer blood donors belonging to Wiwa (also named Arsario) ethnic group. HLA-A, -B, -C, -DRB1 and -DQB1 genes were analyzed by standard methods. Wiwa Amerindians relationships with others were calculated by using Arlequin, Dispan and Vista software computer packages.Results:Extended HLA, -A, -B, -C, -DRB1 and -DQB1 haplotypes have been studied for the first time in this population. Classical Amerindian haplotypes have been found and also new Wiwa (Arsario) Amerindian haplotypes. New haplotypes are A*68:01 - B*15:01 - C*03:03 - DRB1*14:02 - DQB1*03:02, A*11:01 - B*07:02 - C*07:02 - DRB1*15:03 - DQB1*06:02 and A*68:01 - B*15:01 - C*03:04 - DRB1*14:02 - DQB1*03:01.Conclusion:They have been reached after exhaustive comparisons of Wiwa with other Amerindians and Worldwide populations by using genetic distances, Neighbor Joining trees, correspondence analysis and specific group of alleles which are common and frequent in both Amerindians and Pacific Islanders. They are: 1) The Americas First Inhabitants have been probably come through Bering Strait and also through Pacific (from Austronesia and Asia) and Atlantic (from Europe) routes. A bidirectional gene flow is not discarded. 2) Genetic HLA Amerindian profile is separated from that of other Worldwide populations. 3) Amerindians geographical proximity groups’ relatedness is not concordant with HLA genetic relatedness, neither with language. This may be explained by a substantial population decrease that occurred after Europeans invaded America in 1492 and carried new pathogens and epidemics. 4) Our results are also useful for Wiwa and other Amerindians future preventive medicine (HLA linked diseases), HLA pharmacogenomics and transplantation regional programs.
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14
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Norhalifah HK, Syaza FH, Chambers GK, Edinur HA. The genetic history of Peninsular Malaysia. Gene 2016; 586:129-35. [DOI: 10.1016/j.gene.2016.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 03/17/2016] [Accepted: 04/05/2016] [Indexed: 12/27/2022]
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15
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Buhler S, Nunes JM, Sanchez-Mazas A. HLA class I molecular variation and peptide-binding properties suggest a model of joint divergent asymmetric selection. Immunogenetics 2016; 68:401-416. [PMID: 27233953 PMCID: PMC4911380 DOI: 10.1007/s00251-016-0918-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/17/2016] [Indexed: 01/20/2023]
Abstract
The main function of HLA class I molecules is to present pathogen-derived peptides to cytotoxic T lymphocytes. This function is assumed to drive the maintenance of an extraordinary amount of polymorphism at each HLA locus, providing an immune advantage to heterozygote individuals capable to present larger repertories of peptides than homozygotes. This seems contradictory, however, with a reduced diversity at individual HLA loci exhibited by some isolated populations. This study shows that the level of functional diversity predicted for the two HLA-A and HLA-B genes considered simultaneously is similar (almost invariant) between 46 human populations, even when a reduced diversity exists at each locus. We thus propose that HLA-A and HLA-B evolved through a model of joint divergent asymmetric selection conferring all populations an equivalent immune potential. The distinct pattern observed for HLA-C is explained by its functional evolution towards killer cell immunoglobulin-like receptor (KIR) activity regulation rather than peptide presentation.
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Affiliation(s)
- Stéphane Buhler
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland. .,Transplantation Immunology Unit & National Reference Laboratory for Histocompatibility, Department of Genetic and Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland.
| | - José Manuel Nunes
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Alicia Sanchez-Mazas
- Laboratory of Anthropology, Genetics and Peopling History, Department of Genetics and Evolution, Anthropology Unit, University of Geneva, Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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16
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Diversity in exon 5 of HLA-C∗04:01:01G is significant in anthropological studies. Hum Immunol 2016; 77:426-8. [DOI: 10.1016/j.humimm.2016.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 03/15/2016] [Accepted: 03/23/2016] [Indexed: 11/21/2022]
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17
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Watrin L, Ghawché F, Larre P, Neau JP, Mathis S, Fournier E. Guillain-Barré Syndrome (42 Cases) Occurring During a Zika Virus Outbreak in French Polynesia. Medicine (Baltimore) 2016; 95:e3257. [PMID: 27057874 PMCID: PMC4998790 DOI: 10.1097/md.0000000000003257] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/08/2016] [Accepted: 03/10/2016] [Indexed: 12/14/2022] Open
Abstract
Zika virus (transmitted by mosquitoes) reached French Polynesia for the first time in 2013, leading to an epidemic affecting 10% of the total population. So far, it has not been known to induce any neurological complications, but, a few weeks after the outbreak, an unexpectedly high number of 42 patients presented with Guillain-Barré syndrome.We report the clinical and electrophysiological characteristics of this series. Males predominated with a sex ratio of 2.82 (mean age: 46). All patients (except 2) were native Polynesian. At admission, 55% were able to walk unaided against 38% at nadir, 24% had swallowing troubles (nadir: 45%), 74% had motor weakness of the limbs (nadir: 86%) and deep tendon reflexes were diminished or not found in the vast majority of patients. Mean duration of the progressive phase and of the plateau phase was respectively 7 and 9 days. Thirty-eight percent of the patients were admitted in intensive care unit and 10 patients underwent tracheotomy. Nerve electrophysiological studies at admission showed marked distal motor conduction alterations, which had almost completely disappeared at the 4th month; this pattern was more suggestive of acute motor axonal neuropathy (AMAN) than of acute inflammatory demyelinating polyneuropathy (AIDP). Lumbar puncture showed elevated proteins in 90% of the cases, with cell count always inferior to 50/μL.This epidemic raises several questions, such as the potential existence of interactions between Zika virus and Polynesian HLA system and/or the consequences of several recombination events of this virus. This situation should call for increased vigilance, especially in countries where Aedes mosquitoes are present.
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Affiliation(s)
- Louise Watrin
- From the Department of Neurology (LW, J-PN, SM), Poitiers University Hospital Center, Poitiers, France; Department of Neurology (FG, PL), French Polynesia Hospital Center, Papeete, Tahiti, French Polynesia; and Department of Clinical Neurophysiology (EF), La Pitié-Salpêtrière University Hospital Center, AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Bd de l'Hôpital, Paris cedex, France
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18
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Grace BS, Kara T, Kennedy SE, McDonald SP. Racial disparities in pediatric kidney transplantation in New Zealand. Pediatr Transplant 2014; 18:689-97. [PMID: 25039826 DOI: 10.1111/petr.12322] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/19/2014] [Indexed: 12/01/2022]
Abstract
Racial disparities in transplantation rates and outcomes have not been investigated in detail for NZ, a country with unique demographics. We studied a retrospective cohort of 215 patients <18 yr who started renal replacement therapy in NZ 1990-2012, using the Australia and New Zealand Dialysis and Transplant Registry (ANZDATA). Primary outcomes were time to first kidney transplant, death-censored graft survival, and retransplantation after loss of primary graft. Europeans and Asians were most likely to receive a transplant (92% and 91% transplanted within five yr, respectively), and Pacific and Māori patients were less likely to receive a transplant than Europeans (51% and 46%, respectively), reflecting disparities in live donor transplantation. Pacific patients were more likely to have glomerulonephritis and FSGS. Pacific patients had five-yr death-censored graft survival of 31%, lower than Māori (61%) and Europeans (88%). No Pacific patients who lost their grafts were re-transplanted within 72 patient-years of follow-up, whereas 14% of Māori patients and 36% of European and Asian patients were retransplanted within five yr. Current programs to improve live and deceased donation within Māori and Pacific people and management of recurrent kidney disease are likely to reduce these disparities.
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Affiliation(s)
- Blair S Grace
- Australia and New Zealand Dialysis and Transplant Registry (ANZDATA), Adelaide, SA, Australia; Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
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19
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Nemat-Gorgani N, Edinur HA, Hollenbach JA, Traherne JA, Dunn PPJ, Chambers GK, Parham P, Norman PJ. KIR diversity in Māori and Polynesians: populations in which HLA-B is not a significant KIR ligand. Immunogenetics 2014; 66:597-611. [PMID: 25139336 DOI: 10.1007/s00251-014-0794-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 08/04/2014] [Indexed: 12/25/2022]
Abstract
HLA class I molecules and killer cell immunoglobulin-like receptors (KIR) form a diverse system of ligands and receptors that individualize human immune systems in ways that improve the survival of individuals and populations. Human settlement of Oceania by island-hopping East and Southeast Asian migrants started ~3,500 years ago. Subsequently, New Zealand was reached ~750 years ago by ancestral Māori. To examine how this history impacted KIR and HLA diversity, and their functional interaction, we defined at high resolution the allelic and haplotype diversity of the 13 expressed KIR genes in 49 Māori and 34 Polynesians. Eighty KIR variants, including four 'new' alleles, were defined, as were 35 centromeric and 22 telomeric KIR region haplotypes, which combine to give >50 full-length KIR haplotypes. Two new and divergent variant KIR form part of a telomeric KIR haplotype, which appears derived from Papua New Guinea and was probably obtained by the Asian migrants en route to Polynesia. Māori and Polynesian KIR are very similar, but differ significantly from African, European, Japanese, and Amerindian KIR. Māori and Polynesians have high KIR haplotype diversity with corresponding allotype diversity being maintained throughout the KIR locus. Within the population, each individual has a unique combination of HLA class I and KIR. Characterizing Māori and Polynesians is a paucity of HLA-B allotypes recognized by KIR. Compensating for this deficiency are high frequencies (>50 %) of HLA-A allotypes recognized by KIR. These HLA-A allotypes are ones that modern humans likely acquired from archaic humans at a much earlier time.
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Affiliation(s)
- Neda Nemat-Gorgani
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
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20
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Purea T, McCready F, Dunn P, Cundy T. Late-onset type 1 diabetes in Pāsifika migrants living in Auckland. Intern Med J 2014; 44:104-5. [DOI: 10.1111/imj.12326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 08/21/2013] [Indexed: 11/27/2022]
Affiliation(s)
- T. Purea
- Auckland Diabetes Centre; Greenlane Clinical Centre; Auckland New Zealand
| | | | - P. Dunn
- NZ Blood; Auckland New Zealand
| | - T. Cundy
- Auckland Diabetes Centre; Greenlane Clinical Centre; Auckland New Zealand
- Langimalie Clinic; Auckland New Zealand
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