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Ranjan B, Sun W, Park J, Mishra K, Schmidt F, Xie R, Alipour F, Singhal V, Joanito I, Honardoost MA, Yong JMY, Koh ET, Leong KP, Rayan NA, Lim MGL, Prabhakar S. DUBStepR is a scalable correlation-based feature selection method for accurately clustering single-cell data. Nat Commun 2021; 12:5849. [PMID: 34615861 PMCID: PMC8494900 DOI: 10.1038/s41467-021-26085-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 09/15/2021] [Indexed: 11/09/2022] Open
Abstract
Feature selection (marker gene selection) is widely believed to improve clustering accuracy, and is thus a key component of single cell clustering pipelines. Existing feature selection methods perform inconsistently across datasets, occasionally even resulting in poorer clustering accuracy than without feature selection. Moreover, existing methods ignore information contained in gene-gene correlations. Here, we introduce DUBStepR (Determining the Underlying Basis using Stepwise Regression), a feature selection algorithm that leverages gene-gene correlations with a novel measure of inhomogeneity in feature space, termed the Density Index (DI). Despite selecting a relatively small number of genes, DUBStepR substantially outperformed existing single-cell feature selection methods across diverse clustering benchmarks. Additionally, DUBStepR was the only method to robustly deconvolve T and NK heterogeneity by identifying disease-associated common and rare cell types and subtypes in PBMCs from rheumatoid arthritis patients. DUBStepR is scalable to over a million cells, and can be straightforwardly applied to other data types such as single-cell ATAC-seq. We propose DUBStepR as a general-purpose feature selection solution for accurately clustering single-cell data.
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Affiliation(s)
- Bobby Ranjan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Wenjie Sun
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Jinyu Park
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Kunal Mishra
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Florian Schmidt
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Ronald Xie
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Fatemeh Alipour
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Vipul Singhal
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Ignasius Joanito
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Mohammad Amin Honardoost
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
- Department of Medicine, School of Medicine, National University of Singapore, 21 Lower Kent Ridge Road, Singapore, 119077, Singapore
| | - Jacy Mei Yun Yong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Ee Tzun Koh
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore, 308433, Singapore
| | - Nirmala Arul Rayan
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Michelle Gek Liang Lim
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Shyam Prabhakar
- Laboratory of Systems Biology and Data Analytics, Genome Institute of Singapore, A*STAR, 60 Biopolis Street, Singapore, 138672, Singapore.
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Tang R, Han C, Yin R, Zhu P, Zhu L, Lu Y, Zheng C. Quality Control of DNA Extracted from All-Cell Pellets After Cryopreservation for More Than 10 Years. Biopreserv Biobank 2021; 20:211-216. [PMID: 34435893 DOI: 10.1089/bio.2021.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Cryopreserved whole blood, all-cell pellets (ACPs), and buffy coats in biobanks are widely used to obtain DNA for genetic testing. However, there are few studies concerning the quality control of DNA extracted from them. Our research aimed to perform quality control of DNA extracted from ACPs after cryopreservation for >10 years. Materials and Methods: A total of 1377 ACP samples (separated from 3 mL of whole blood) were retrieved from our biobank, where they had been cryopreserved for 10-15 years. Chemagic STAR was used to extract the DNA. Absorbance at A260, A280, and A230 were measured by spectrophotometry, and integrity was analyzed by agarose gel electrophoresis. The quality thresholds for an Illumina Asian Screening Array (ASA) were yields greater than 0.5 μg, concentration of 25-150 ng/μL, A260/280 ratio of 1.6-2.1, and no degradation fragments in the electrophoresis gel. Results: The median yield of genomic DNA was 54.30 μg (interquartile range [IQR] 35.55-74.64). The median A260/280 and A260/230 ratios were 1.90 (IQR 1.87-1.94) and 1.98 (IQR 1.64-2.41), respectively. In total, 1377 samples (100%) had qualified yields, and 1366 samples (99.20%) had qualified integrity results. Finally, 1328 (96.44%) samples were used for ASA. Of the remaining samples, 34 needed to be repurified, 4 were obtained at an insufficient concentration, and 11 were unqualified for integrity. In addition, we analyzed the influence of hemolysis (90 samples) and clots (102 samples) on the quality of DNA samples. Hemolysis and clotting did not influence yield or integrity, but a significant difference was found in A260/230 compared to normal samples (p < 0.05). Furthermore, the samples (14 samples) with both hemolysis and clots had higher A260/280 (p < 0.05). Conclusion: ACP samples stored for >10 years at -80°C produced DNA with high quality for use in genetic analysis. Hemolysis and clots in the ACPs led to lower purity, but did not significantly affect yield or integrity.
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Affiliation(s)
- Rong Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Cui Han
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ling Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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Auerbach A, Cohen A, Ofek Shlomai N, Weinberg-Shukron A, Gulsuner S, King MC, Hemi R, Levy-Lahad E, Abulibdeh A, Zangen D. NKX2-2 Mutation Causes Congenital Diabetes and Infantile Obesity With Paradoxical Glucose-Induced Ghrelin Secretion. J Clin Endocrinol Metab 2020; 105:5895035. [PMID: 32818257 DOI: 10.1210/clinem/dgaa563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/14/2020] [Indexed: 12/12/2022]
Abstract
CONTEXT NKX2-2 is a crucial transcription factor that enables specific β-cell gene expression. Nkx2-2(-/-) mice manifest with severe neonatal diabetes and changes in β-cell progenitor fate into ghrelin-producing cells. In humans, recessive NKX2-2 gene mutations have been recently reported as a novel etiology for neonatal diabetes, with only 3 cases known worldwide. This study describes the genetic analysis, distinctive clinical features, the therapeutic challenges, and the unique pathophysiology causing neonatal diabetes in human NKX2-2 dysfunction. CASE DESCRIPTION An infant with very low birth weight (VLBW) and severe neonatal diabetes (NDM) presented with severe obesity and developmental delay already at age 1 year. The challenge of achieving glycemic control in a VLBW infant was unexpectedly met by a regimen of 3 daily doses of long-acting insulin analogues. Sanger sequencing of known NDM genes (such as ABCC8 and EIF2AK3) was followed by whole-exome sequencing that revealed homozygosity of a pathogenic frameshift variant, c.356delG, p.P119fs64*, in the islet cells transcription factor, NKX2-2. To elucidate the cause for the severe obesity, an oral glucose tolerance test was conducted at age 3.5 years and revealed undetectable C-peptide levels with a paradoxically unexpected 30% increase in ghrelin levels. CONCLUSION Recessive NKX2-2 loss of function causes severe NDM associated with VLBW, childhood obesity, and developmental delay. The severe obesity phenotype is associated with postprandial paradoxical ghrelin secretion, which may be related to human β-cell fate change to ghrelin-secreting cells, recapitulating the finding in Nkx2-2(-/-) mice islet cells.
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Affiliation(s)
- Adi Auerbach
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Amitay Cohen
- Hadassah Mt. Scopus, Department of Pediatrics, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Noa Ofek Shlomai
- Department of Neonatology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Ariella Weinberg-Shukron
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Hadassah Medical School, Hebrew University, Jerusalem 9112102, Israel
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, DC
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, DC
| | - Rina Hemi
- Institute of Endocrinology, Chaim Sheba Medical Center, Ramat-Gan, Israel
| | - Ephrat Levy-Lahad
- Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel
- Hadassah Medical School, Hebrew University, Jerusalem 9112102, Israel
| | - Abdulsalam Abulibdeh
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - David Zangen
- Division of Pediatric Endocrinology, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- Hadassah Medical School, Hebrew University, Jerusalem 9112102, Israel
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Ferro P, Ortega-Pinazo J, Martínez B, Jiménez Á, Gómez-Zumaquero JM, Hortas ML, Díaz T. On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option? Biopreserv Biobank 2019; 17:577-582. [PMID: 31429592 DOI: 10.1089/bio.2019.0024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biobanks are collections of biological samples and health information that allow the organization of biomedical research for upgrading the knowledge of human disorders from different diseases (cancer, allergies, rare diseases, etc.), and reach real answers for diagnosis and treatment. A wide range of samples can be stored in these biorepositories such as hair, nails, urine, tissue, whole blood, red blood cells, buffy coat, plasma, serum, DNA, and RNA. Among these, buffy coat and whole blood are widely used by researchers because they can obtain DNA and RNA from these matrices. Some preliminary studies have been performed on animals to evaluate the quality and functionality of the nucleic acids obtained from some of these matrices, although more in-depth studies are needed in this area. In this study, blood samples extracted by venipuncture from 30 healthy volunteers were used to obtain DNA from buffy coat and whole blood. The purity and integrity of the nucleic acids obtained were assessed by spectrophotometry, fluorimetry, and agarose electrophoresis, and functionality was assessed by PCR and real-time PCR. Another aspect tested in this study was based on the comparison between short-term and long-term storage at -80°C and fresh samples from both matrices to evaluate the storage conditions at the biobank. Results showed differences in the yield obtained from both matrices as a function of the storage time, although the functionality of all the obtained DNA remained intact.
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Affiliation(s)
- Pedro Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Jesús Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - Beatriz Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Álvaro Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | | | | | - Tatiana Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
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Zhou G, Li Q, Huang L, Wu Y, Wu M, Wang WC. Quality Analysis of DNA from Cord Blood Buffy Coat: The Best Neonatal DNA Source for Epidemiological Studies? Biopreserv Biobank 2016; 14:165-71. [PMID: 26885947 DOI: 10.1089/bio.2015.0075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Guangdi Zhou
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qin Li
- Department of Obstetrics and Gynecology, Changhai Hospital Affiliated to the Second Military Medical University, Shanghai, China
| | - Lisu Huang
- Department of Pediatrics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhang Wu
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiqin Wu
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiye C. Wang
- MOE-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ram R, Mehta M, Nguyen QT, Larma I, Boehm BO, Pociot F, Concannon P, Morahan G. Systematic Evaluation of Genes and Genetic Variants Associated with Type 1 Diabetes Susceptibility. THE JOURNAL OF IMMUNOLOGY 2016; 196:3043-53. [PMID: 26912320 DOI: 10.4049/jimmunol.1502056] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/25/2016] [Indexed: 01/18/2023]
Abstract
Genome-wide association studies have found >60 loci that confer genetic susceptibility to type 1 diabetes (T1D). Many of these are defined only by anonymous single nucleotide polymorphisms: the underlying causative genes, as well as the molecular bases by which they mediate susceptibility, are not known. Identification of how these variants affect the complex mechanisms contributing to the loss of tolerance is a challenge. In this study, we performed systematic analyses to characterize these variants. First, all known genes in strong linkage disequilibrium (r(2) > 0.8) with the reported single nucleotide polymorphisms for each locus were tested for commonly occurring nonsynonymous variations. We found only a total of 22 candidate genes at 16 T1D loci with common nonsynonymous alleles. Next, we performed functional studies to examine the effect of non-HLA T1D risk alleles on regulating expression levels of genes in four different cell types: EBV-transformed B cell lines (resting and 6 h PMA stimulated) and purified CD4(+) and CD8(+) T cells. We mapped cis-acting expression quantitative trait loci and found 24 non-HLA loci that affected the expression of 31 transcripts significantly in at least one cell type. Additionally, we observed 25 loci that affected 38 transcripts in trans. In summary, our systems genetics analyses defined the effect of T1D risk alleles on levels of gene expression and provide novel insights into the complex genetics of T1D, suggesting that most of the T1D risk alleles mediate their effect by influencing expression of multiple nearby genes.
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Affiliation(s)
- Ramesh Ram
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia; Centre of Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Munish Mehta
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia; Centre of Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Quang T Nguyen
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia; Centre of Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Irma Larma
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia; Centre of Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia
| | - Bernhard O Boehm
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921; Ulm University Medical Centre, Department of Internal Medicine I, Ulm University, 89081 Ulm, Germany
| | - Flemming Pociot
- Department of Pediatrics, Herlev and Gentofte Hospital, 2730 Herlev, Denmark
| | - Patrick Concannon
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610; and Genetics Institute, University of Florida, Gainesville, FL 32610
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia; Centre of Medical Research, University of Western Australia, Nedlands, Western Australia 6009, Australia;
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Weinberg-Shukron A, Renbaum P, Kalifa R, Zeligson S, Ben-Neriah Z, Dreifuss A, Abu-Rayyan A, Maatuk N, Fardian N, Rekler D, Kanaan M, Samson AO, Levy-Lahad E, Gerlitz O, Zangen D. A mutation in the nucleoporin-107 gene causes XX gonadal dysgenesis. J Clin Invest 2015; 125:4295-304. [PMID: 26485283 DOI: 10.1172/jci83553] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/03/2015] [Indexed: 11/17/2022] Open
Abstract
Ovarian development and maintenance are poorly understood; however, diseases that affect these processes can offer insights into the underlying mechanisms. XX female gonadal dysgenesis (XX-GD) is a rare, genetically heterogeneous disorder that is characterized by underdeveloped, dysfunctional ovaries, with subsequent lack of spontaneous pubertal development, primary amenorrhea, uterine hypoplasia, and hypergonadotropic hypogonadism. Here, we report an extended consanguineous family of Palestinian origin, in which 4 females exhibited XX-GD. Using homozygosity mapping and whole-exome sequencing, we identified a recessive missense mutation in nucleoporin-107 (NUP107, c.1339G>A, p.D447N). This mutation segregated with the XX-GD phenotype and was not present in available databases or in 150 healthy ethnically matched controls. NUP107 is a component of the nuclear pore complex, and the NUP107-associated protein SEH1 is required for oogenesis in Drosophila. In Drosophila, Nup107 knockdown in somatic gonadal cells resulted in female sterility, whereas males were fully fertile. Transgenic rescue of Drosophila females bearing the Nup107D364N mutation, which corresponds to the human NUP107 (p.D447N), resulted in almost complete sterility, with a marked reduction in progeny, morphologically aberrant eggshells, and disintegrating egg chambers, indicating defective oogenesis. These results indicate a pivotal role for NUP107 in ovarian development and suggest that nucleoporin defects may play a role in milder and more common conditions such as premature ovarian failure.
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Akolkar B, Hilner J, Nierras CR. Design and Measurement of Nonislet-Specific Autoantibodies for the Type 1 Diabetes Genetics Consortium Autoantibody Workshop. Diabetes Care 2015; 38 Suppl 2:S4-7. [PMID: 26405071 PMCID: PMC4582913 DOI: 10.2337/dcs15-2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The Type 1 Diabetes Genetics Consortium (T1DGC) comprised groups of investigators from many countries throughout the world, with a common goal of identifying genes predisposing to type 1 diabetes. The T1DGC ascertained and collected samples from families with two or more affected siblings with type 1 diabetes and generated a broad array of clinical, genetic, and immunologic data. The T1DGC Autoantibody Workshop was designed to distribute data for analyses to discover genes associated with autoantibodies in those with type 1 diabetes. In the T1DGC-affected sibling pair families, three T1DGC Network laboratories measured antibodies to the islet autoantigens GAD65 and the intracellular portion of protein tyrosine phosphatase (IA-2A). The availability of extensive genetic data provided an opportunity to investigate the associations between type 1 diabetes and other autoimmune diseases for which autoantibodies could be measured. Measurements of additional nonislet autoantibodies, including thyroid peroxidase, tissue transglutaminase, 21-hydroxylase, and the potassium/hydrogen ion transporter H+/K+-ATPase, were performed by the T1DGC laboratory at the Barbara Davis Center for Childhood Diabetes, Aurora, CO. Measurements of all autoantibodies were transmitted to the T1DGC Coordinating Center, and the data were made available to members of the T1DGC Autoantibody Working Groups for analysis in conjunction with existing T1DGC genetic data. This article describes the design of the T1DGC Autoantibody Workshop and the quality-control procedures to maintain and monitor the performance of each laboratory and provides the quality-control results for the nonislet autoantibody measurements.
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Affiliation(s)
- Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Joan Hilner
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL
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Kiani AK, John P, Bhatti A, Zia A, Shahid G, Akhtar P, Wang X, Demirci FY, Kamboh MI. Association of 32 type 1 diabetes risk loci in Pakistani patients. Diabetes Res Clin Pract 2015; 108:137-42. [PMID: 25661663 DOI: 10.1016/j.diabres.2015.01.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 11/15/2014] [Accepted: 01/03/2015] [Indexed: 12/16/2022]
Abstract
AIM To identify risk alleles contributing towards type 1 diabetes in Pakistani patients. INTRODUCTION Type 1 diabetes (T1D) is an autoimmune disease which is caused by destruction of insulin producing β cells by immune system. Genetic predisposition as well as environmental factors contribute to its etiology. To date more than 40 risk loci have been identified for T1D. METHODOLOGY A total of 191 family-based and unrelated T1D cases and controls were recruited. DNA was extracted and 32 genome-wide significant single nucleotide polymorphisms (SNPs) previously reported in Europeans were genotyped. Genotyping was performed using TaqMan SNP genotyping assays and the data was analyzed using FamCC software. RESULTS Our results showed significant association of 10 single nucleotide polymorphisms (SNPs) with T1D at p<0.01, including HLA-DQA1/rs9272346, ERBB3/rs2292239, SIRPG/rs2281808, IL2-KIAA1109/rs4505848, GLIS3/rs7020673, CD226/rs763361, PTPN2/rs478582, IKZF1/rs10272724, BACH2/rs11755527, C6orf173/rs9388489, whereas 5 more SNPs showed their association at 0.01<p<0.05 in Pakistani population. CONCLUSION We have replicated many of the T1D loci established among Europeans in a Pakistani population.
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Affiliation(s)
- Aysha Karim Kiani
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Peter John
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.
| | - Attya Bhatti
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Asima Zia
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Gulbin Shahid
- Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | | | - Xingbin Wang
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - F Yesim Demirci
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - M Ilyas Kamboh
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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Zhou J, Wu J, Zhao X, Shen W, Liu X, Xu C, Jin H. Biostorage and Quality Control for Human Peripheral Blood Leukocytes. Biopreserv Biobank 2015; 13:13-9. [PMID: 25686042 DOI: 10.1089/bio.2014.0094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jiayi Zhou
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Jing Wu
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Xiaoyan Zhao
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
- Obstetrics and Gynecology, The First Hospital, Beijing University, Beijing, China
| | - Weihong Shen
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Xiaoyan Liu
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
| | - Congjian Xu
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
- Obstetrics and Gynecology, The First Hospital, Beijing University, Beijing, China
| | - Hongyan Jin
- Fudan University, Obstetrics and Gynecology Hospital, Shanghai, China
- Obstetrics and Gynecology, The First Hospital, Beijing University, Beijing, China
- Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
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CTSH regulates β-cell function and disease progression in newly diagnosed type 1 diabetes patients. Proc Natl Acad Sci U S A 2014; 111:10305-10. [PMID: 24982147 DOI: 10.1073/pnas.1402571111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Over 40 susceptibility loci have been identified for type 1 diabetes (T1D). Little is known about how these variants modify disease risk and progression. Here, we combined in vitro and in vivo experiments with clinical studies to determine how genetic variation of the candidate gene cathepsin H (CTSH) affects disease mechanisms and progression in T1D. The T allele of rs3825932 was associated with lower CTSH expression in human lymphoblastoid cell lines and pancreatic tissue. Proinflammatory cytokines decreased the expression of CTSH in human islets and primary rat β-cells, and overexpression of CTSH protected insulin-secreting cells against cytokine-induced apoptosis. Mechanistic studies indicated that CTSH exerts its antiapoptotic effects through decreased JNK and p38 signaling and reduced expression of the proapoptotic factors Bim, DP5, and c-Myc. CTSH overexpression also up-regulated Ins2 expression and increased insulin secretion. Additionally, islets from Ctsh(-/-) mice contained less insulin than islets from WT mice. Importantly, the TT genotype was associated with higher daily insulin dose and faster disease progression in newly diagnosed T1D patients, indicating agreement between the experimental and clinical data. In line with these observations, healthy human subjects carrying the T allele have lower β-cell function, which was evaluated by glucose tolerance testing. The data provide strong evidence that CTSH is an important regulator of β-cell function during progression of T1D and reinforce the concept that candidate genes for T1D may affect disease progression by modulating survival and function of pancreatic β-cells, the target cells of the autoimmune assault.
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Gail MH, Sheehy T, Cosentino M, Pee D, Diaz-Mayoral NA, Garcia-Closas M, Caporaso NE, Pitt K, Ziegler RG. Maximizing DNA yield for epidemiologic studies: no more buffy coats? Am J Epidemiol 2013; 178:1170-6. [PMID: 23857774 PMCID: PMC3783090 DOI: 10.1093/aje/kwt079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 03/29/2013] [Indexed: 11/13/2022] Open
Abstract
Some molecular analyses require microgram quantities of DNA, yet many epidemiologic studies preserve only the buffy coat. In Frederick, Maryland, in 2010, we estimated DNA yields from 5 mL of whole blood and from equivalent amounts of all-cell-pellet (ACP) fraction, buffy coat, and residual blood cells from fresh blood (n = 10 volunteers) and from both fresh and frozen blood (n = 10). We extracted DNA with the QIAamp DNA Blood Midi Kit (Qiagen Sciences, Germantown, Maryland) for silica spin column capture and measured double-stranded DNA. Yields from frozen blood fractions were not statistically significantly different from those obtained from fresh fractions. ACP fractions yielded 80.6% (95% confidence interval: 66, 97) of the yield of frozen whole blood and 99.3% (95% confidence interval: 86, 100) of the yield of fresh blood. Frozen buffy coat and residual blood cells each yielded only half as much DNA as frozen ACP, and the yields were more variable. Assuming that DNA yield and quality from frozen ACP are stable, we recommend freezing plasma and ACP. Not only does ACP yield twice as much DNA as buffy coat but it is easier to process, and its yield is less variable from person to person. Long-term stability studies are needed. If one wishes to separate buffy coat before freezing, one should also save the residual blood cell fraction, which contains just as much DNA.
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Affiliation(s)
- Mitchell H. Gail
- Correspondence to Dr. Mitchell H. Gail, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Room 7-E138, Bethesda, MD 20892-9780 (e-mail: )
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14
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Kobayashi DT, Decker D, Zaworski P, Klott K, McGonigal J, Ghazal N, Sly L, Chung B, Vanderlugt J, Chen KS. Evaluation of peripheral blood mononuclear cell processing and analysis for Survival Motor Neuron protein. PLoS One 2012; 7:e50763. [PMID: 23226377 PMCID: PMC3511312 DOI: 10.1371/journal.pone.0050763] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Accepted: 10/24/2012] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES Survival Motor Neuron (SMN) protein levels may become key pharmacodynamic (PD) markers in spinal muscular atrophy (SMA) clinical trials. SMN protein in peripheral blood mononuclear cells (PBMCs) can be quantified for trials using an enzyme-linked immunosorbent assay (ELISA). We developed protocols to collect, process, store and analyze these samples in a standardized manner for SMA clinical studies, and to understand the impact of age and intraindividual variability over time on PBMC SMN signal. METHODS Several variables affecting SMN protein signal were evaluated using an ELISA. Samples were from healthy adults, adult with respiratory infections, SMA patients, and adult SMA carriers. RESULTS Delaying PBMCs processing by 45 min, 2 hr or 24 hr after collection or isolation allows sensitive detection of SMN levels and high cell viability (>90%). SMN levels from PBMCs isolated by EDTA tubes/Lymphoprep gradient are stable with processing delays and have greater signal compared to CPT-collected samples. SMN signal in healthy individuals varies up to 8x when collected at intervals up to 1 month. SMN signals from individuals with respiratory infections show 3-5x changes, driven largely by the CD14 fraction. SMN signal in PBMC frozen lysates are relatively stable for up to 6 months. Cross-sectional analysis of PBMCs from SMA patients and carriers suggest SMN protein levels decline with age. CONCLUSIONS The sources of SMN signal variability in PBMCs need to be considered in the design and of SMA clinical trials, and interpreted in light of recent medical history. Improved normalization to DNA or PBMC subcellular fractions may mitigate signal variability and should be explored in SMA patients.
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Affiliation(s)
- Dione T Kobayashi
- Spinal Muscular Atrophy Foundation, New York, New York, United States of America.
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15
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Mychaleckyj JC, Farber EA, Chmielewski J, Artale J, Light LS, Bowden DW, Hou X, Marcovina SM. Buffy coat specimens remain viable as a DNA source for highly multiplexed genome-wide genetic tests after long term storage. J Transl Med 2011; 9:91. [PMID: 21663644 PMCID: PMC3128059 DOI: 10.1186/1479-5876-9-91] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/10/2011] [Indexed: 12/13/2022] Open
Abstract
Background Blood specimen collection at an early study visit is often included in observational studies or clinical trials for analysis of secondary outcome biomarkers. A common protocol is to store buffy coat specimens for future DNA isolation and these may remain in frozen storage for many years. It is uncertain if the DNA remains suitable for modern genome wide association (GWA) genotyping. Methods We isolated DNA from 120 Action to Control Cardiovascular Risk in Diabetes (ACCORD) clinical trial buffy coats sampling a range of storage times up to 9 years and other factors that could influence DNA yield. We performed TaqMan SNP and GWA genotyping to test whether the DNA retained integrity for high quality genetic analysis. Results We tested two QIAGEN automated protocols for DNA isolation, preferring the Compromised Blood Protocol despite similar yields. We isolated DNA from all 120 specimens (yield range 1.1-312 ug per 8.5 ml ACD tube of whole blood) with only 3/120 samples yielding < 10 ug DNA. Age of participant at blood draw was negatively associated with yield (mean change -2.1 ug/year). DNA quality was very good based on gel electrophoresis QC, TaqMan genotyping of 6 SNPs (genotyping no-call rate 1.1% in 702 genotypes), and excellent quality GWA genotyping data (maximum per sample genotype missing rate 0.64%). Conclusions When collected as a long term clinical trial or biobank specimen for DNA, buffy coats can be stored for up to 9 years in a -80degC frozen state and still produce high yields of DNA suitable for GWA analysis and other genetic testing. Trial Registration The Action to Control Cardiovascular Risk in Diabetes (ACCORD) trial is registered with ClinicalTrials.gov, number NCT00000620.
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Affiliation(s)
- Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
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16
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Hilner JE, Perdue LH, Sides EG, Pierce JJ, Wägner AM, Aldrich A, Loth A, Albret L, Wagenknecht LE, Nierras C, Akolkar B. Designing and implementing sample and data collection for an international genetics study: the Type 1 Diabetes Genetics Consortium (T1DGC). Clin Trials 2010; 7:S5-S32. [PMID: 20603248 PMCID: PMC2917852 DOI: 10.1177/1740774510373497] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
BACKGROUND AND PURPOSE The Type 1 Diabetes Genetics Consortium (T1DGC) is an international project whose primary aims are to: (a) discover genes that modify type 1 diabetes risk; and (b) expand upon the existing genetic resources for type 1 diabetes research. The initial goal was to collect 2500 affected sibling pair (ASP) families worldwide. METHODS T1DGC was organized into four regional networks (Asia-Pacific, Europe, North America, and the United Kingdom) and a Coordinating Center. A Steering Committee, with representatives from each network, the Coordinating Center, and the funding organizations, was responsible for T1DGC operations. The Coordinating Center, with regional network representatives, developed study documents and data systems. Each network established laboratories for: DNA extraction and cell line production; human leukocyte antigen genotyping; and autoantibody measurement. Samples were tracked from the point of collection, processed at network laboratories and stored for deposit at National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) Central Repositories. Phenotypic data were collected and entered into the study database maintained by the Coordinating Center. RESULTS T1DGC achieved its original ASP recruitment goal. In response to research design changes, the T1DGC infrastructure also recruited trios, cases, and controls. Results of genetic analyses have identified many novel regions that affect susceptibility to type 1 diabetes. T1DGC created a resource of data and samples that is accessible to the research community. LIMITATIONS Participation in T1DGC was declined by some countries due to study requirements for the processing of samples at network laboratories and/or final deposition of samples in NIDDK Central Repositories. Re-contact of participants was not included in informed consent templates, preventing collection of additional samples for functional studies. CONCLUSIONS T1DGC implemented a distributed, regional network structure to reach ASP recruitment targets. The infrastructure proved robust and flexible enough to accommodate additional recruitment. T1DGC has established significant resources that provide a basis for future discovery in the study of type 1 diabetes genetics.
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Affiliation(s)
- Joan E Hilner
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294-0022, USA.
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17
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Mychaleckyj JC, Noble JA, Moonsamy PV, Carlson JA, Varney MD, Post J, Helmberg W, Pierce JJ, Bonella P, Fear AL, Lavant E, Louey A, Boyle S, Lane JA, Sali P, Kim S, Rappner R, Williams DT, Perdue LH, Reboussin DM, Tait BD, Akolkar B, Hilner JE, Steffes MW, Erlich HA. HLA genotyping in the international Type 1 Diabetes Genetics Consortium. Clin Trials 2010; 7:S75-87. [PMID: 20595243 PMCID: PMC2917849 DOI: 10.1177/1740774510373494] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background Although human leukocyte antigen (HLA) DQ and
DR loci appear to confer the strongest genetic risk for
type 1 diabetes, more detailed information is required for other loci within the
HLA region to understand causality and stratify additional risk factors. The
Type 1 Diabetes Genetics Consortium (T1DGC) study design included
high-resolution genotyping of HLA-A, B,
C, DRB1, DQ, and
DP loci in all affected sibling pair and trio families, and
cases and controls, recruited from four networks worldwide, for analysis with
clinical phenotypes and immunological markers. Purpose In this article, we present the operational strategy of training,
classification, reporting, and quality control of HLA genotyping in four
laboratories on three continents over nearly 5 years. Methods Methods to standardize HLA genotyping at eight loci included: central
training and initial certification testing; the use of uniform reagents,
protocols, instrumentation, and software versions; an automated data transfer;
and the use of standardized nomenclature and allele databases. We implemented a
rigorous and consistent quality control process, reinforced by repeated
workshops, yearly meetings, and telephone conferences. Results A total of 15,246 samples have been HLA genotyped at eight loci to
four-digit resolution; an additional 6797 samples have been HLA genotyped at two
loci. The genotyping repeat rate decreased significantly over time, with an
estimated unresolved Mendelian inconsistency rate of 0.21%. Annual
quality control exercises tested 2192 genotypes (4384 alleles) and achieved
99.82% intra-laboratory and 99.68% inter-laboratory
concordances. Limitations The chosen genotyping platform was unable to distinguish many allele
combinations, which would require further multiple stepwise testing to resolve.
For these combinations, a standard allele assignment was agreed upon, allowing
further analysis if required. Conclusions High-resolution HLA genotyping can be performed in multiple laboratories
using standard equipment, reagents, protocols, software, and communication to
produce consistent and reproducible data with minimal systematic error. Many of
the strategies used in this study are generally applicable to other large
multi-center studies.
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Affiliation(s)
- Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
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