A GWAS including 192,986 European and 1636 Asian participants identifies 50 novel discrete associations with eye color.
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We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be... more
We carried out a trans-ancestry genome-wide association and replication study of blood pressure phenotypes among up to 320,251 individuals of East Asian, European and South Asian ancestry. We find genetic variants at 12 new loci to be associated with blood pressure (P = 3.9 × 10(-11) to 5.0 × 10(-21)). The sentinel blood pressure SNPs are enriched for association with DNA methylation at multiple nearby CpG sites, suggesting that, at some of the loci identified, DNA methylation may lie on the regulatory pathway linking sequence variation to blood pressure. The sentinel SNPs at the 12 new loci point to genes involved in vascular smooth muscle (IGFBP3, KCNK3, PDE3A and PRDM6) and renal (ARHGAP24, OSR1, SLC22A7 and TBX2) function. The new and known genetic variants predict increased left ventricular mass, circulating levels of NT-proBNP, and cardiovascular and all-cause mortality (P = 0.04 to 8.6 × 10(-6)). Our results provide new evidence for the role of DNA methylation in blood pressu...
Research Interests: Genetics, Developmental Biology, Biology, Cardiovascular disease, Biological Sciences, and 15 moreHumans, Kidney, Blood Pressure, Individuals, Female, Journal Article, DNA methylation, Aged, Genotype, Adult, Cardiovascular Diseases, European Continental Ancestry Group, Asian Continental Ancestry Group, Genetic variation, and Genetic Association
Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the... more
Normal thyroid function is essential for health, but its genetic architecture remains poorly understood. Here, for the heritable thyroid traits thyrotropin (TSH) and free thyroxine (FT4), we analyse whole-genome sequence data from the UK10K project (N=2,287). Using additional whole-genome sequence and deeply imputed data sets, we report meta-analysis results for common variants (MAF≥1%) associated with TSH and FT4 (N=16,335). For TSH, we identify a novel variant in SYN2 (MAF=23.5%, P=6.15 × 10(-9)) and a new independent variant in PDE8B (MAF=10.4%, P=5.94 × 10(-14)). For FT4, we report a low-frequency variant near B4GALT6/SLC25A52 (MAF=3.2%, P=1.27 × 10(-9)) tagging a rare TTR variant (MAF=0.4%, P=2.14 × 10(-11)). All common variants explain ≥20% of the variance in TSH and FT4. Analysis of rare variants…
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Variation in body iron is associated with or causes diseases, including anaemia and iron overload. Here, we analyse genetic association data on biochemical markers of iron status from 11 European-population studies, with replication in... more
Variation in body iron is associated with or causes diseases, including anaemia and iron overload. Here, we analyse genetic association data on biochemical markers of iron status from 11 European-population studies, with replication in eight additional cohorts (total up to 48,972 subjects). We find 11 genome-wide-significant…
Research Interests: Genetics, Biology, Multidisciplinary, Lipids, Humans, and 15 moreHepcidin, Genetic Association Studies, Transferrin, Iron, Risk factors, Phenotype, Ferroportin, Hemochromatosis, Homeostasis, Adult, Single Nucleotide Polymorphism, Reproducibility of Results, Risk Factors, Nature Communications, and Gene Expression Regulation
Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate... more
Reduced glomerular filtration rate defines chronic kidney disease and is associated with cardiovascular and all-cause mortality. We conducted a meta-analysis of genome-wide association studies for estimated glomerular filtration rate (eGFR), combining data across 133,413 individuals with replication in up to 42,166 individuals. We identify 24 new and confirm 29 previously identified loci. Of these 53 loci, 19 associate with eGFR among individuals with diabetes. Using bioinformatics, we show that identified genes at eGFR loci are enriched for expression in kidney tissues and in pathways relevant for kidney development and transmembrane transporter activity, kidney structure, and regulation of glucose metabolism. Chromatin state mapping and DNase I hypersensitivity analyses across adult tissues demonstrate preferential mapping of associated variants to regulatory regions in kidney but not extra-renal tissues. These findings suggest that genetic determinants of eGFR are mediated largel...
Research Interests: Nephrology, Biology, Chronic, Medicine, Multidisciplinary, and 14 moreHumans, Kidney, Genome Wide Association Studies, Clinical Genetics, Journal Article, Meta Analysis, Renal Function, Genotype, Kidney Disease, Genetic variation, Nature Communications, Uncategorized, Gene Expression Regulation, and renal insufficiency
Research Interests: Polymorphism, Biology, Risk, Menopause, Medicine, and 15 moreBiological Sciences, Humans, Female, Human Molecular Genetics, Etiology, Single Nucleotide Polymorphism, Quantitative Trait Loci, Premature, Genetic Association, Case Control Studies, Gene frequency, Medical and Health Sciences, early menopause, primary ovarian insufficiency, and Single nucleotide
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Research Interests: Geography and Population
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Glucose-6-phosphate dehydrogenase (G6PD) is a household enzyme that accounts, in many cells, for about 0.03% of cellular protein. We have developed an assay for G6PD-specific mRNA based on in vitro translation of RNA from human... more
Glucose-6-phosphate dehydrogenase (G6PD) is a household enzyme that accounts, in many cells, for about 0.03% of cellular protein. We have developed an assay for G6PD-specific mRNA based on in vitro translation of RNA from human fibroblasts and immunoprecipitation of the translation products with an anti-G6PD antiserum. By making use of this assay, G6PD mRNA has been purified 50 to 100-fold in three steps. We estimate that the mRNA encoding G6PD constitutes less than 0.02% of total poly(A)+ RNA in human fibroblasts. The size of the G6PD mRNA has been established in denaturing conditions as being in the range between 2800 and 3200 nucleotides. This has been confirmed by Northern blot analysis. Since the G6PD coding sequence is estimated to be about 1491 nucleotides, the G6PD mRNA has long untranslated sequences, most of which is at the 3' end and which may be heterogeneous in length. The sequence of the last 608 nucleotides of this mRNA has been determined.
The human X-linked gene encoding glucose 6-phosphate dehydrogenase (G6PD) is highly polymorphic; more than 300 G6PD variants have been identified. G6PD deficiency in different geographical areas appears to have arisen through independent... more
The human X-linked gene encoding glucose 6-phosphate dehydrogenase (G6PD) is highly polymorphic; more than 300 G6PD variants have been identified. G6PD deficiency in different geographical areas appears to have arisen through independent mutational events, but within the same population it may also be heterogeneous. One example is the island of Sardinia, where careful clinical and biochemical studies have identified four different G6PD variants. We cloned and sequenced the four G6PD variants from Sardinia and found that only two mutations are responsible for G6PD deficiency in this area: one mutation is the cause of the G6PD Seattle-like phenotype, a milder form of G6PD deficiency; the other mutation is responsible for all forms of very severe G6PD deficiency in Sardinia and, possibly, in the Mediterranean.
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The genetic polymorphism of an approximately 100-kb DNA region comprising and flanking the glucose-6-phosphate dehydrogenase (G6PD) gene on human chromosome Xq28 has been analyzed in detail. By using 14 unique sequence probes and 18... more
The genetic polymorphism of an approximately 100-kb DNA region comprising and flanking the glucose-6-phosphate dehydrogenase (G6PD) gene on human chromosome Xq28 has been analyzed in detail. By using 14 unique sequence probes and 18 restriction enzymes, we have characterized 257 restriction fragments or 370 restriction sites. On testing 12-57 individual X chromosomes, all sites but one were nonpolymorphic. However, a PstI site that maps to exon 10 of the G6PD gene, which is still monomorphic in all British and Italian subjects tested, is polymorphic in west-African people. Specifically, it is absent from 22% of Nigerian X chromosomes. By sequence analysis we have shown that the absence of this PstI site results from a G----A replacement at position 1116, corresponding to the third base of a glutamine codon; no amino acid change is produced in the protein. Thus, a polymorphic silent mutation is demonstrated in a human gene.
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We have investigated the process leading to differentiation of PC12 cells. This process is known to include extension of neurites and changes in the expression of subsets of proteins involved in cytoskeletal rearrangements or in... more
We have investigated the process leading to differentiation of PC12 cells. This process is known to include extension of neurites and changes in the expression of subsets of proteins involved in cytoskeletal rearrangements or in neurosecretion. To this aim, we have studied a PC12 clone (trk-PC12) stably transfected with the nerve growth factor receptor TrkA. These cells are able to undergo both spontaneous and neurotrophin-induced morphological differentiation. However, both undifferentiated and nerve growth factor-differentiated trk-PC12 cells appear to be completely defective in the expression of proteins of the secretory apparatus, including proteins of synaptic vesicles and large dense-core granules, neurotransmitter transporters, and neurotransmitter-synthesizing enzymes. These results indicate that neurite extension can occur independently of the presence of the neurosecretory machinery, including the proteins that constitute the fusion machine, suggesting the existence of dif...
Research Interests: Molecular Biology, Biology, Cell Biology, Flavonoids, Medicine, and 15 moreGene expression, Biological Sciences, Cell Differentiation, Humans, Protein Kinases, Animals, Neurite, Exocytosis, Nerve Growth Factor, Rab, Gtp Binding Proteins, Protein Kinase Inhibitors, Cell Size, Cell Membrane, and Medical and Health Sciences
Research Interests: Aging, Adolescent, Medicine, Humans, Female, and 14 moreContraceptives, Menstrual Cycle, Oral, Middle Aged, Adult, Hormone, European Continental Ancestry Group, Cross sectional Study, Reference Values, Cross Sectional Studies, Enzyme Linked Immunosorbent Assay, Ovarian Reserve, Oral Contraceptive, and Paediatrics and reproductive medicine
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19 probes for CpG islands, mapping to Xq28, have been used as probes to construct a physical map of genes of this band of the human X chromosome. A total of 22 CpG islands have been precisely mapped in respect to known loci along the 9-10... more
19 probes for CpG islands, mapping to Xq28, have been used as probes to construct a physical map of genes of this band of the human X chromosome. A total of 22 CpG islands have been precisely mapped in respect to known loci along the 9-10 Mb of Xq28. The fine mapping of such a large number of CpG islands has demonstrated that also in gene rich Giemsa light bands, like Xq28, gene distribution is non uniform: the CpG islands are clustered in the distal portion of the band in a 2 Mb region between the G6PD gene and the DXS15 locus. Moreover, 16 CpG islands were found between the G6PD and the RCP/GCP genes, a region of DNA of only about 300 kb. If this structural organization has a biological function it has yet to be determined. However, the isolation of large genomic regions enriched in gene sequences and the availability of cosmid or YAC contigs will provide the means to test the significance of such gene organization, as well as the material for large sequencing projects and gene search, for the identification of candidate genes for inherited disorders mapped to Xq28 and for comparative mapping.
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ABP-280 is a ubiquitous actin binding protein present in the cytoskeleton of many different cell types. ABP-280 was mapped to distal Xq28, 50-60 kb downstream of the Green Colour Pigment (GCP) genes. To establish if ABP-280 may be a... more
ABP-280 is a ubiquitous actin binding protein present in the cytoskeleton of many different cell types. ABP-280 was mapped to distal Xq28, 50-60 kb downstream of the Green Colour Pigment (GCP) genes. To establish if ABP-280 may be a candidate for one of the muscle disease localized by linkage analysis to distal Xq28 we looked for alternative forms of ABP-280 mRNA. Several different ABP-280 mRNAs were indeed identified: two are X-linked and are produced by alternative splicing of a small exon of 24 nucleotides. At least one additional gene encoding a RNA more than 70% identical to ABP-280 in the 1700 bp sequenced has also been found. It was mapped to chromosome 7. While both forms of the X-linked ABP-280 are ubiquitous, the gene on chromosome 7 is highly expressed only in skeletal muscle and heart. The two genes were therefore excellent candidates for the X-linked and for the autosomal dominant form of the Emery-Dreifuss Muscular Dystrophy (EDMD) both of which have been described. So far, however we were unable to demonstrate mutations in the coding region or affecting the alternative splicing of the X-linked form of ABP-280, in several patients studied, and we think that it is quite unlikely that this is the gene responsible for EDMD.
Research Interests: Genetics, Biology, Medicine, Biological Sciences, DNA, and 15 moreHumans, Male, Human Molecular Genetics, Alternative splicing, Gene, Genes, Molecular cloning, HeLa cells, Alternative Splicing, Amino Acid Sequence, Base Sequence, Dystrophin, Exon, Contractile Proteins, and Medical and Health Sciences
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We have isolated temperature-sensitive SV40-transformed 3T3 cells which are unable to grow in low or depleted serum at the nonpermissive temperature. At 39 degrees C, these cells do not grow in 1 percent serum, but they grow if the serum... more
We have isolated temperature-sensitive SV40-transformed 3T3 cells which are unable to grow in low or depleted serum at the nonpermissive temperature. At 39 degrees C, these cells do not grow in 1 percent serum, but they grow if the serum concentration is raised to 10 percent. At 32 degrees they grow in both serum concentrations. This phenotype seems to be due to a cellular mutation, as the virus rescued from these cells is wild-type. We tested whether other characteristics of transformed cells were expressed in a temperature sensitive way. While high saturation density is ts in these cells, other parameters of transformation are expressed at both temperatures. In addition, when these cells are incubated in low serum at 39 degrees C, they keep synthesizing DNA and lose viability very fast, while under the same conditions normal 3T3 cells remain viable for long times and are unable to initiate DNA synthesis. These cells therefore do not appear to revert to a normal phenotype at the high temperature, and they are more likely to represent transformed cell variants with a temperature-dependent serum requirement.
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White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the... more
White blood cell (WBC) count is a common clinical measure from complete blood count assays, and it varies widely among healthy individuals. Total WBC count and its constituent subtypes have been shown to be moderately heritable, with the heritability estimates varying across cell types. We studied 19,509 subjects from seven cohorts in a discovery analysis, and 11,823 subjects from ten cohorts for replication analyses, to determine genetic factors influencing variability within the normal hematological range for total WBC count and five WBC subtype measures. Cohort specific data was supplied by the CHARGE, HeamGen, and INGI consortia, as well as independent collaborative studies. We identified and replicated ten associations with total WBC count and five WBC subtypes at seven different genomic loci (total WBC count-6p21 in the HLA region, 17q21 near ORMDL3, and CSF3; neutrophil count-17q21; basophil count- 3p21 near RPN1 and C3orf27; lymphocyte count-6p21, 19p13 at EPS15L1; monocyte ...
Research Interests: Genetics, Developmental Biology, Molecular Biology, Polymorphism, Biology, and 15 moreCancer Research, Medicine, Gene expression, Molecular Epidemiology, Humans, Journal Article, Phenotype, PLoS Genetics, Leukocytes, Gene Expression Data, Genetic factors, Evaluation function, Complete Blood Count, leukocyte Count, and Single nucleotide
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High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million... more
High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.
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Research Interests: Genetics, Developmental Biology, Biology, Mortality, Medicine, and 15 moreBiological Sciences, Heart Failure, Humans, Hypertension, Mice, Blood Pressure, Gene, Metaanalysis, Linkage Disequilibrium, Pulse Pressure, Case Control Studies, Arteries, Diastolic Blood Pressure, Mean Arterial Pressure, and Medical and Health Sciences
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Research Interests: Biology, Intellectual Disability, Medicine, Episodic Memory, Molecular Mechanics, and 15 moreIn Situ Hybridization, Memory, Biological Sciences, Mental Retardation, Social behavior, Brain, Mice, Animals, Human Molecular Genetics, Central Nervous System, Associative Memory, Cognitive Function, Short Term Memory, Social Behavior, and Medical and Health Sciences
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Research Interests: Genetics, Human Genetics, Biology, Molecular Genetics, Adolescent, and 15 moreMedicine, Cytogenetics, Humans, Female, Clinical Genetics, Phenotype, European, Molecular Characterization, Adult, X chromosome, Turner Syndrome, Premature Ovarian Failure, Chromosome deletion, Environmental factor, and primary ovarian insufficiency
Research Interests: Caenorhabditis elegans, Biological Sciences, Saccharomyces cerevisiae, Humans, Sequence alignment, and 15 moreFemale, Animals, Male, Infant, Proteins, Pedigree, Dilated cardiomyopathy, Newborn Infant, Nuclear Family, Amino Acid Sequence, Base Sequence, Molecular Sequence Data, alleles, Cause of death, and Medical and Health Sciences
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To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci,... more
To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P…
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Research Interests: DNA, Methylation, Female, Animals, Male, and 3 moreGenetic linkage analysis, Genes, and X chromosome
Mental retardation (MR) is one of the most common human disorders. MR may be just one of the clinical signs of a complex syndrome or it may be associated with metabolic disorders or with disorders of brain development, but in many... more
Mental retardation (MR) is one of the most common human disorders. MR may be just one of the clinical signs of a complex syndrome or it may be associated with metabolic disorders or with disorders of brain development, but in many patients [nonspecific MR (NSMR)], it is the only consistent clinical manifestation. It is expected that NSMR is caused by alterations in molecular pathways important for cognitive functions. Insights into NSMR have recently come from the study of X-linked MR as eight genes were identified during the last few years. This development has represented a fundamental breakthrough in our understanding of NSMR and of cognitive functions and has opened new perspectives in the study of MR. The new genes identified are a heterogeneous group, but it is very intriguing that they are all directly or indirectly involved in signaling pathways and that the majority are proteins that regulate members of the Ras superfamily of small GTP binding proteins.
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Glucose-6-phosphate dehydrogenase (G6PD) is a ubiquitous enzyme that supplies the cell with NADPH required for a variety of reductive reactions and biosynthetic processes. Therefore, the gene G6PD, located in mammals on the X chromosome,... more
Glucose-6-phosphate dehydrogenase (G6PD) is a ubiquitous enzyme that supplies the cell with NADPH required for a variety of reductive reactions and biosynthetic processes. Therefore, the gene G6PD, located in mammals on the X chromosome, that specifies G6PD can be regarded as a typical housekeeping gene. We have investigated the expression of human G6PD in eight different fetal and adult tissues by determining the level of enzyme activity, the level of G6PD mRNA, and the methylation pattern of the 3' end of the gene, for which we have nucleic acid probes. By combining sequence information with results of Southern blot analysis of DNA samples digested with the methylation-sensitive restriction enzyme Hpa II, we have identified five specific sites that are unmethylated in all tissues examined, a number of sites that are uniformly methylated, and a number of sites that are sometimes methylated. A subset of Hpa II sites, designated on our restriction map as H37-H55, exhibit positive correlation between degree of methylation, level of mRNA, and level of G6PD activity. A comparison of these methylation patterns with those we previously have observed in the G6PD gene on the inactive X chromosome [Toniolo, D., D'Urso, M., Martini, G., Persico, M.G., Tufano, V., Battistuzzi, G. & Luzzatto, L. (1984) EMBO J. 3, 1987-1995] indicates that different sites are associated with X-inactivation and with the regulation of G6PD on the active X chromosome. We conclude that this housekeeping gene is subject to tissue-specific transcriptional regulation, which in turn correlates with methylation of specific sites located at and near the 3' end of the gene.