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4 results on '"Davison, Lucy"'

1. Mining the 99 Lives Cat Genome Sequencing Consortium database implicates genes and variants for the Ticked locus in domestic cats (Felis catus)

Author

Lyons, LA, Buckley, RM, Harvey, RJ, Abitbol, Marie, Aberdein, Danielle, Alves, Paulo C, Andersson, Asa Ohlsson, Bellone, Rebecca R, Bergström, Tomas F, Bilgen, Nuket, Boyko, Adam R, Brockman, Jeffrey A, Casal, Margret L, Castelhano, Marta G, Davis, Brian W, Davison, Lucy, Distl, Ottmar, Dodman, Nicholas H, Ellinwood, N Matthew, Fogle, Jonathan E, Forman, Oliver P, Garrick, Dorian J, Ginns, Edward I, Häggström, Jens, Hasegawa, Daisuke, Haase, Bianca, Jagannathan, Vidhya, Lait, Philippa, Hernandez, Isabel, Hytönen, Marjo K, Kaukonen, Maria, Kosho, Tomoki, Leclerc, Emilie, Lear, Teri L, Leeb, Tosso, Li, Ronald HL, Lohi, Hannes, Longeri, Maria, Magnuson, Mark A, Malik, Richard, Mane, Shrinivasrao P, Middleton, Rondo, Munday, John S, Murphy, William J, Myers, Alexandra N, Pedersen, Niels C, Peterson‐Jones, Simon M, Rothschild, Max F, Rusbridge, Clare, Schoenebeck, Jeffrey J, Shapiro, Beth, Stern, Joshua A, Swanson, William F, Terio, Karen A, Todhunter, Rory J, Warren, Wesley C, Wilcox, Elizabeth A, Wildschutte, Julia H, and Yu, Yoshihiko

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Alleles, Amino Acid Sequence, Animals, Breeding, Cats, Genome, Hair Color, Intercellular Signaling Peptides and Proteins, Phenotype, Abyssinian, coat pattern, Dickkopf&#160, Wnt&#160, Signaling&#160, Pathway Inhibitor 4, DKK4, Tabby, Lives Cat Genome Consortium, DKK4, Dickkopf Wnt Signaling Pathway Inhibitor 4, Tabby, Zoology, Veterinary Sciences, Dairy & Animal Science
Abstract

Tabby patterns of fur coats are defining characteristics in wild and domestic felids. Historically, three autosomal alleles at one locus (Tabby): Abyssinian (Ta ; a.k.a. ticked), mackerel (Tm ; a.k.a. striped) and blotched (tb ; a.k.a. classic, blotched) were thought to control these patterns in domestic cats and their breeds. Currently, at least three loci influence cat tabby markings, two of which are designated Tabby and Ticked. The Tabby locus is laeverin (LVRN) and affects the mackerel and blotched patterns. The unidentified gene for the Ticked locus on cat chromosome B1 was suggested to control the presence or absence of the ticked pattern (Tabby - Abyssinian (Ta ; a.k.a. ticked). The cat reference genome (Cinnamon, the Abyssinian) has the ticked phenotype and the variant dataset and coat phenotypes from the 99 Lives Cat Genome Consortium (195 cats) were used to identify candidate genes and variants associated with the Ticked locus. Two strategies were used to find the Ticked allele(s), one considered Cinnamon with the reference allele or heterozygous (Strategy A) and the other considered Cinnamon as having the variant allele or heterozygous (Strategy B). For Strategy A, two variants in Dickkopf Wnt Signaling Pathway Inhibitor 4 (DKK4), a p.Cys63Tyr (B1:41621481, c.188G>A) and a less common p.Ala18Val (B1:42620835, c.53C>T) variant are suggested as two alleles influencing the Ticked phenotype. Bioinformatic and molecular modeling analysis suggests that these changes disrupt a key disulfide bond in the Dkk4 cysteine-rich domain 1 or Dkk4 signal peptide cleavage respectively. All coding variants were excluded as Ticked alleles using Strategy B.

Published
2021

2. Proteome-Wide Analysis of Disease-Associated SNPs That Show Allele-Specific Transcription Factor Binding.

Author

Butter, Falk, Davison, Lucy, Viturawong, Tar, Scheibe, Marion, Vermeulen, Michiel, Todd, John A., and Mann, Matthias

Subjects
*SINGLE nucleotide polymorphisms, *TRANSCRIPTION factors, *GENETIC disorders, *MASS spectrometry, *ALLELES, *DIABETES
Abstract

A causative role for single nucleotide polymorphisms (SNPs) in many genetic disorders has become evident through numerous genome-wide association studies. However, identification of these common causal variants and the molecular mechanisms underlying these associations remains a major challenge. Differential transcription factor binding at a SNP resulting in altered gene expression is one possible mechanism. Here we apply PWAS ("proteome-wide analysis of SNPs"), a methodology based on quantitative mass spectrometry that enables rapid screening of SNPs for differential transcription factor binding, to 12 SNPs that are highly associated with type 1 diabetes at the IL2RA locus, encoding the interleukin-2 receptor CD25. We report differential, allele-specific binding of the transcription factors RUNX1, LEF1, CREB, and TFAP4 to IL2RA SNPs rs12722508*A, rs12722522*C, rs41295061*A, and rs2104286*A and demonstrate the functional influence of RUNX1 at rs12722508 by reporter gene assay. Thus, PWAS may be able to contribute to our understanding of the molecular consequences of human genetic variability underpinning susceptibility to multi-factorial disease. [ABSTRACT FROM AUTHOR]

Published
2012
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3. An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes

Author

Swafford, Austin D-E, Howson, Joanna MM, Davison, Lucy J, Wallace, Chris, Smyth, Deborah J, Schuilenburg, Helen, Maisuria-Armer, Meeta, Mistry, Trupti, Lenardo, Michael J, and Todd, John A

Subjects
Adult, Male, Genotype, Polymorphism, Single Nucleotide, White People, 3. Good health, Ikaros Transcription Factor, Diabetes Mellitus, Type 1, Logistic Models, Case-Control Studies, Odds Ratio, Humans, Female, Genetic Predisposition to Disease, Alleles
Abstract

OBJECTIVE: IKZF1 encoding Ikaros, an essential regulator of lymphopoiesis and immune homeostasis, has been implicated in the development of childhood acute lymphoblastic leukemia (C-ALL). Because recent genome-wide association (GWA) studies have linked a region of the 3'-UTR of IKZF1 with C-ALL susceptibility, we tested whether IKZF1 is associated with the autoimmune disease type 1 diabetes. RESEARCH DESIGN AND METHODS: rs10272724 (T>C) near IKZF1 at 7p12 was genotyped in 8,333 individuals with type 1 diabetes, 9,947 control subjects, and 3,997 families of European ancestry. Association was tested using logistic regression in the case-control data and by the transmission disequilibrium test in the families. Expression data for IKZF1 by rs10272724 genotype were obtained using quantitative PCR of mRNA/cDNA generated from peripheral blood mononuclear cells from 88 individuals, whereas expression data for five other neighboring genes were obtained from the online Genevar dataset. RESULTS: The minor allele of rs10272724 (C) was found to be protective from type 1 diabetes (odds ratio 0.87 [95% CI 0.83-0.91]; P = 1.1 × 10(-11)). rs10272724 was not correlated with levels of two transcripts of IKZF1 in peripheral blood mononuclear cells. CONCLUSIONS: The major susceptibility genotype for C-ALL confers protection from type 1 diabetes. Our finding strengthens the link between autoimmunity and lymphoid cancers. Further investigation is warranted for the genetic effect marked by rs10272724, its impact on IKZF1, and the role of Ikaros and other family members, Ailios (IKZF3) and Eos (IKZF4), in autoimmunity.

4. An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes

Author

Joanna M. M. Howson, Helen Schuilenburg, Michael J. Lenardo, L. J. Davison, Chris Wallace, Deborah J. Smyth, Austin D. Swafford, John A. Todd, Meeta Maisuria-Armer, Trupti Mistry, Howson, Joanna [0000-0001-7618-0050], Davison, Lucy [0000-0002-1920-0817], Wallace, Chris [0000-0001-9755-1703], and Apollo - University of Cambridge Repository

Subjects
Adult, Male, Genotype, Endocrinology, Diabetes and Metabolism, Biology, medicine.disease_cause, Polymorphism, Single Nucleotide, White People, Autoimmunity, Ikaros Transcription Factor, 03 medical and health sciences, 0302 clinical medicine, Genetics, Odds Ratio, Internal Medicine, medicine, Humans, Genetic Predisposition to Disease, Childhood Acute Lymphoblastic Leukemia, Alleles, 030304 developmental biology, 0303 health sciences, Type 1 diabetes, Transmission disequilibrium test, medicine.disease, IKZF3, 3. Good health, Minor allele frequency, Diabetes Mellitus, Type 1, Logistic Models, Case-Control Studies, Immunology, Female, 030215 immunology
Abstract

OBJECTIVE IKZF1 encoding Ikaros, an essential regulator of lymphopoiesis and immune homeostasis, has been implicated in the development of childhood acute lymphoblastic leukemia (C-ALL). Because recent genome-wide association (GWA) studies have linked a region of the 3′-UTR of IKZF1 with C-ALL susceptibility, we tested whether IKZF1 is associated with the autoimmune disease type 1 diabetes. RESEARCH DESIGN AND METHODS rs10272724 (T>C) near IKZF1 at 7p12 was genotyped in 8,333 individuals with type 1 diabetes, 9,947 control subjects, and 3,997 families of European ancestry. Association was tested using logistic regression in the case-control data and by the transmission disequilibrium test in the families. Expression data for IKZF1 by rs10272724 genotype were obtained using quantitative PCR of mRNA/cDNA generated from peripheral blood mononuclear cells from 88 individuals, whereas expression data for five other neighboring genes were obtained from the online Genevar dataset. RESULTS The minor allele of rs10272724 (C) was found to be protective from type 1 diabetes (odds ratio 0.87 [95% CI 0.83–0.91]; P = 1.1 × 10−11). rs10272724 was not correlated with levels of two transcripts of IKZF1 in peripheral blood mononuclear cells. CONCLUSIONS The major susceptibility genotype for C-ALL confers protection from type 1 diabetes. Our finding strengthens the link between autoimmunity and lymphoid cancers. Further investigation is warranted for the genetic effect marked by rs10272724, its impact on IKZF1, and the role of Ikaros and other family members, Ailios (IKZF3) and Eos (IKZF4), in autoimmunity.

Published
2011

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