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450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy.

https://arctichealth.org/en/permalink/ahliterature122072
Source
Environ Health Perspect. 2012 Oct;120(10):1425-31
Publication Type
Article
Date
Oct-2012
Author
Bonnie R Joubert
Siri E Håberg
Roy M Nilsen
Xuting Wang
Stein E Vollset
Susan K Murphy
Zhiqing Huang
Cathrine Hoyo
Øivind Midttun
Lea A Cupul-Uicab
Per M Ueland
Michael C Wu
Wenche Nystad
Douglas A Bell
Shyamal D Peddada
Stephanie J London
Author Affiliation
Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.
Source
Environ Health Perspect. 2012 Oct;120(10):1425-31
Date
Oct-2012
Language
English
Publication Type
Article
Keywords
Adult
Basic Helix-Loop-Helix Transcription Factors - genetics - metabolism
Biological Markers - blood
Chromatography, Liquid
Cohort Studies
Cotinine - blood
Cytochrome P-450 CYP1A1 - genetics - metabolism
DNA Methylation
DNA-Binding Proteins - genetics - metabolism
Epigenesis, Genetic
Female
Fetal Blood
Genome-Wide Association Study
Humans
Infant, Newborn
Male
Maternal Exposure
Norway - epidemiology
Pregnancy
Prenatal Exposure Delayed Effects - chemically induced - epidemiology - genetics
Repressor Proteins - genetics - metabolism
Tandem Mass Spectrometry
Tobacco Smoke Pollution - adverse effects
Transcription Factors - genetics - metabolism
United States - epidemiology
Abstract
Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear.
We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy.
We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473,844 CpG sites (CpGs) in 1,062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K).
We found differential DNA methylation at epigenome-wide statistical significance (p-value
Notes
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Comment In: Environ Health Perspect. 2012 Oct;120(10):a40223026408
Erratum In: Environ Health Perspect. 2012 Dec;120(12):A455
PubMed ID
22851337 View in PubMed
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The accuracy of Genomic Selection in Norwegian red cattle assessed by cross-validation.

https://arctichealth.org/en/permalink/ahliterature98928
Source
Genetics. 2009 Nov;183(3):1119-26
Publication Type
Article
Date
Nov-2009
Author
Tu Luan
John A Woolliams
Sigbjørn Lien
Matthew Kent
Morten Svendsen
Theo H E Meuwissen
Author Affiliation
Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Box 5003, N-1432 As, Norway. tu.luan@umb.no
Source
Genetics. 2009 Nov;183(3):1119-26
Date
Nov-2009
Language
English
Publication Type
Article
Keywords
Algorithms
Animal Husbandry - methods
Animals
Bayes Theorem
Breeding - methods
Cattle - genetics - metabolism
Female
Genome - genetics
Genome-Wide Association Study
Genotype
Male
Milk - metabolism - standards
Norway
Polymorphism, Single Nucleotide - genetics
Quantitative Trait Loci - genetics
Reproducibility of Results
Selection, Genetic
Abstract
Genomic Selection (GS) is a newly developed tool for the estimation of breeding values for quantitative traits through the use of dense markers covering the whole genome. For a successful application of GS, accuracy of the prediction of genomewide breeding value (GW-EBV) is a key issue to consider. Here we investigated the accuracy and possible bias of GW-EBV prediction, using real bovine SNP genotyping (18,991 SNPs) and phenotypic data of 500 Norwegian Red bulls. The study was performed on milk yield, fat yield, protein yield, first lactation mastitis traits, and calving ease. Three methods, best linear unbiased prediction (G-BLUP), Bayesian statistics (BayesB), and a mixture model approach (MIXTURE), were used to estimate marker effects, and their accuracy and bias were estimated by using cross-validation. The accuracies of the GW-EBV prediction were found to vary widely between 0.12 and 0.62. G-BLUP gave overall the highest accuracy. We observed a strong relationship between the accuracy of the prediction and the heritability of the trait. GW-EBV prediction for production traits with high heritability achieved higher accuracy and also lower bias than health traits with low heritability. To achieve a similar accuracy for the health traits probably more records will be needed.
PubMed ID
19704013 View in PubMed
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Adipose co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes.

https://arctichealth.org/en/permalink/ahliterature118360
Source
BMC Med Genomics. 2012;5:61
Publication Type
Article
Date
2012
Author
Blake E Haas
Steve Horvath
Kirsi H Pietiläinen
Rita M Cantor
Elina Nikkola
Daphna Weissglas-Volkov
Aila Rissanen
Mete Civelek
Ivette Cruz-Bautista
Laura Riba
Johanna Kuusisto
Jaakko Kaprio
Teresa Tusie-Luna
Markku Laakso
Carlos A Aguilar-Salinas
Päivi Pajukanta
Author Affiliation
Department of Human Genetics, Gonda Center, Los Angeles, California, 90095-7088, USA.
Source
BMC Med Genomics. 2012;5:61
Date
2012
Language
English
Publication Type
Article
Keywords
Adipose Tissue - metabolism
Case-Control Studies
Finland
Gene Expression Profiling
Gene Expression Regulation
Gene Regulatory Networks - genetics
Genetic Loci - genetics
Genome-Wide Association Study
Humans
Immunity - genetics
Inflammation - blood - genetics
Mexico
Polymorphism, Single Nucleotide - genetics
Triglycerides - blood - genetics
Twins - genetics
Abstract
High serum triglyceride (TG) levels is an established risk factor for coronary heart disease (CHD). Fat is stored in the form of TGs in human adipose tissue. We hypothesized that gene co-expression networks in human adipose tissue may be correlated with serum TG levels and help reveal novel genes involved in TG regulation.
Gene co-expression networks were constructed from two Finnish and one Mexican study sample using the blockwiseModules R function in Weighted Gene Co-expression Network Analysis (WGCNA). Overlap between TG-associated networks from each of the three study samples were calculated using a Fisher's Exact test. Gene ontology was used to determine known pathways enriched in each TG-associated network.
We measured gene expression in adipose samples from two Finnish and one Mexican study sample. In each study sample, we observed a gene co-expression network that was significantly associated with serum TG levels. The TG modules observed in Finns and Mexicans significantly overlapped and shared 34 genes. Seven of the 34 genes (ARHGAP30, CCR1, CXCL16, FERMT3, HCST, RNASET2, SELPG) were identified as the key hub genes of all three TG modules. Furthermore, two of the 34 genes (ARHGAP9, LST1) reside in previous TG GWAS regions, suggesting them as the regional candidates underlying the GWAS signals.
This study presents a novel adipose gene co-expression network with 34 genes significantly correlated with serum TG across populations.
Notes
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PubMed ID
23217153 View in PubMed
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Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas.

https://arctichealth.org/en/permalink/ahliterature128155
Source
Hum Mol Genet. 2012 Apr 15;21(8):1907-17
Publication Type
Article
Date
Apr-15-2012
Author
Laura Fejerman
Gary K Chen
Celeste Eng
Scott Huntsman
Donglei Hu
Amy Williams
Bogdan Pasaniuc
Esther M John
Marc Via
Christopher Gignoux
Sue Ingles
Kristine R Monroe
Laurence N Kolonel
Gabriela Torres-Mejía
Eliseo J Pérez-Stable
Esteban González Burchard
Brian E Henderson
Christopher A Haiman
Elad Ziv
Author Affiliation
Department of Medicine, Division of General Internal Medicine, Institute for Human Genetics and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA.
Source
Hum Mol Genet. 2012 Apr 15;21(8):1907-17
Date
Apr-15-2012
Language
English
Publication Type
Article
Keywords
Breast Neoplasms - classification - genetics
Case-Control Studies
Chromosome Mapping
Chromosomes, Human, Pair 11 - genetics
Chromosomes, Human, Pair 6 - genetics
Estrogen Receptor alpha - genetics
European Continental Ancestry Group - genetics
Female
Gene Frequency
Genetic Loci
Genetic Predisposition to Disease
Genome-Wide Association Study
Genotype
Hispanic Americans - genetics
Humans
Microfilament Proteins - genetics
Polymorphism, Single Nucleotide
Risk factors
Abstract
Among US Latinas and Mexican women, those with higher European ancestry have increased risk of breast cancer. We combined an admixture mapping and genome-wide association mapping approach to search for genomic regions that may explain this observation. Latina women with breast cancer (n= 1497) and Latina controls (n= 1272) were genotyped using Affymetrix and Illumina arrays. We inferred locus-specific genetic ancestry and compared the ancestry between cases and controls. We also performed single nucleotide polymorphism (SNP) association analyses in regions of interest. Correction for multiple-hypothesis testing was conducted using permutations (P(corrected)). We identified one region where genetic ancestry was significantly associated with breast cancer risk: 6q25 [odds ratio (OR) per Indigenous American chromosome 0.75, 95% confidence interval (CI): 0.65-0.85, P= 1.1 × 10(-5), P(corrected)= 0.02]. A second region on 11p15 showed a trend towards association (OR per Indigenous American chromosome 0.77, 95% CI: 0.68-0.87, P= 4.3 × 10(-5), P(corrected)= 0.08). In both regions, breast cancer risk decreased with higher Indigenous American ancestry in concordance with observations made on global ancestry. The peak of the 6q25 signal includes the estrogen receptor 1 (ESR1) gene and 5' region, a locus previously implicated in breast cancer. Genome-wide association analysis found that a multi-SNP model explained the admixture signal in both regions. Our results confirm that the association between genetic ancestry and breast cancer risk in US Latinas is partly due to genetic differences between populations of European and Indigenous Americans origin. Fine-mapping within the 6q25 and possibly the 11p15 loci will lead to the discovery of the biologically functional variant/s behind this association.
Notes
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PubMed ID
22228098 View in PubMed
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Alterations in KLRB1 gene expression and a Scandinavian multiple sclerosis association study of the KLRB1 SNP rs4763655.

https://arctichealth.org/en/permalink/ahliterature134204
Source
Eur J Hum Genet. 2011 Oct;19(10):1100-3
Publication Type
Article
Date
Oct-2011
Author
Helle Bach Søndergaard
Finn Sellebjerg
Jan Hillert
Tomas Olsson
Ingrid Kockum
Magdalena Lindén
Inger-Lise Mero
Kjell-Morten Myhr
Elisabeth G Celius
Hanne F Harbo
Jeppe Romme Christensen
Lars Börnsen
Per Soelberg Sørensen
Annette Bang Oturai
Author Affiliation
Department of Neurology, Danish Multiple Sclerosis Center, University Hospital Rigshospitalet, Copenhagen, Denmark. hbs@rh.dk
Source
Eur J Hum Genet. 2011 Oct;19(10):1100-3
Date
Oct-2011
Language
English
Publication Type
Article
Keywords
Case-Control Studies
Female
Gene Expression Regulation
Gene Frequency
Genetic Predisposition to Disease
Genome-Wide Association Study
Humans
Male
Multiple Sclerosis - epidemiology - genetics
NK Cell Lectin-Like Receptor Subfamily B - genetics - metabolism
Polymorphism, Single Nucleotide
Scandinavia - epidemiology
Abstract
Multiple sclerosis (MS) is a complex autoimmune disease affecting genetically susceptible individuals. A genome-wide association study performed by the International MS Genetics Consortium identified several putative susceptibility genes; among these, the KLRB1 gene is represented by the single-nucleotide polymorphism rs4763655. We could confirm a marginally significant association between rs4763655 and MS (P=0.046, odds ratio=1.06 (1.00-1.13)) in a large Scandinavian case-control study of 5367 MS patients and 4485 controls. The expression of KLRB1 in blood from MS patients was higher compared with healthy controls (P
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PubMed ID
21610746 View in PubMed
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An algorithm for detecting high frequency copy number polymorphisms using SNP arrays.

https://arctichealth.org/en/permalink/ahliterature133202
Source
J Comput Biol. 2011 Aug;18(8):955-66
Publication Type
Article
Date
Aug-2011
Author
Bjarni V Halldórsson
Daníel F Gudbjartsson
Author Affiliation
School of Science and Engineering, Reykjavík University, Reykjavík, Iceland. bjarnivh@ru.is
Source
J Comput Biol. 2011 Aug;18(8):955-66
Date
Aug-2011
Language
English
Publication Type
Article
Keywords
Algorithms
Alleles
Base Pairing
Cluster analysis
Computational Biology - methods
DNA Copy Number Variations
Fluorescent Dyes - analysis
Gene Frequency
Genome, Human
Genome-Wide Association Study
Genotype
Humans
Iceland
Markov Chains
Microsatellite Repeats
Normal Distribution
Oligonucleotide Array Sequence Analysis - instrumentation - methods
Polymorphism, Single Nucleotide
Abstract
We present a general algorithm for the detection of genomic variants using the Illumina iSelect platform. The Illumina iSelect platform is designed to detect SNPs, but our algorithm allows for the detections of more general forms of variations, including copy number polymorphisms and microsatellites. The algorithm does not rely on a priori information of the type of polymorphism being studied and is designed to genotype call a large number of individuals simultaneously. The algorithm proceeds by initially normalizing intensity and correcting for batch effects. Then each marker is clustered using a modified Gaussian mixture model where we account for variances in the expression of an individuals and the variance measured in bead level intensities of a probe/marker pair. Finally, these clusters are used to determine genotypes. The algorithm was then run on a dataset of 35,000 Icelandic individuals.
PubMed ID
21728861 View in PubMed
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[Analysis of clusterin gene (CLU/APOJ) polymorphism in Alzheimer's disease patients and in normal cohorts from Russian populations].

https://arctichealth.org/en/permalink/ahliterature140492
Source
Mol Biol (Mosk). 2010 Jul-Aug;44(4):620-6
Publication Type
Article
Author
S A Golenkina
A Iu Gol'tsov
I L Kuznetsova
A P Grigorenko
T V Andreeva
D A Reshetov
S S Kunizheva
L I Shagam
I Iu Morozova
I V Goldenkova-Pavlova
Kh Shimshilashvili
A O Viacheslavova
G. Faskhutdinova
A É Gareeva
A G Zainullina
É K Khusnutdinova
V P Puzyrev
V A Stepanov
A V Kolotvin
L M Samokhodskaia
N D Selezneva
S I Gavrilova
E I Rogaev
Source
Mol Biol (Mosk). 2010 Jul-Aug;44(4):620-6
Language
Russian
Publication Type
Article
Keywords
Adult
Aged
Aged, 80 and over
Alleles
Alzheimer Disease - epidemiology - genetics
Clusterin - genetics
Cohort Studies
Female
Gene Frequency - genetics
Genome-Wide Association Study
Humans
Male
Middle Aged
Polymorphism, Genetic - genetics
Russia - epidemiology
Abstract
Three genes mutations in which cause familial forms of Alzheimer's disease are known to date:PSEN1, PSEN2 and APP; and APOE gene polymorphism is a strong risk factor for Alzheimer's disease. We have evaluated allele and genotype frequency distribution of rs11136000 polymorphism in clusterin (CLU) gene (or apolipoprotein J, APOJ) in populations of three Russian regions and i nAlzheimhner's diseasepatients. Genome-wideassociation studies in samples from several European populations have recently revealed highly significant association o fCLU gene with AD (p = 8.5 x 10(-10)). We found no differences in allele and genotype frequencies of rs11136000 between populations from Moscow, Ural and Siberia regions. The allele frequencies are close to those in European populations. The genetic association analysis in cohort of Alzheimer's disease patients and normal individuals (>500 individuals ineach group) revealed no significant association of the rs11136000 polymorphism in CLU with Alzheimer's disease in Russian populations. Although our resultsdo not confirm the role of CLU gene as a majorgenetic factor forcommon form of Alzheimer's disease, the data do not rule out the possibility of modest effect of CLU and interaction between CLU and APOE genotypes in etiology of Alzheimer's disease.
PubMed ID
20873220 View in PubMed
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Analysis of East Asia genetic substructure using genome-wide SNP arrays.

https://arctichealth.org/en/permalink/ahliterature153881
Source
PLoS One. 2008;3(12):e3862
Publication Type
Article
Date
2008
Author
Chao Tian
Roman Kosoy
Annette Lee
Michael Ransom
John W Belmont
Peter K Gregersen
Michael F Seldin
Author Affiliation
Department of Biochemistry, Rowe Program in Human Genetics, University of California Davis, Davis, California, United States of America.
Source
PLoS One. 2008;3(12):e3862
Date
2008
Language
English
Publication Type
Article
Keywords
Asian Continental Ancestry Group - genetics
Far East - ethnology
Genetic Markers - genetics
Genetic Predisposition to Disease
Genetics, Population
Genome, Human
Genome-Wide Association Study
Genotype
Humans
Oligonucleotide Array Sequence Analysis
Polymorphism, Single Nucleotide
Principal Component Analysis
Abstract
Accounting for population genetic substructure is important in reducing type 1 errors in genetic studies of complex disease. As efforts to understand complex genetic disease are expanded to different continental populations the understanding of genetic substructure within these continents will be useful in design and execution of association tests. In this study, population differentiation (Fst) and Principal Components Analyses (PCA) are examined using >200 K genotypes from multiple populations of East Asian ancestry. The population groups included those from the Human Genome Diversity Panel [Cambodian, Yi, Daur, Mongolian, Lahu, Dai, Hezhen, Miaozu, Naxi, Oroqen, She, Tu, Tujia, Naxi, Xibo, and Yakut], HapMap [ Han Chinese (CHB) and Japanese (JPT)], and East Asian or East Asian American subjects of Vietnamese, Korean, Filipino and Chinese ancestry. Paired Fst (Wei and Cockerham) showed close relationships between CHB and several large East Asian population groups (CHB/Korean, 0.0019; CHB/JPT, 00651; CHB/Vietnamese, 0.0065) with larger separation with Filipino (CHB/Filipino, 0.014). Low levels of differentiation were also observed between Dai and Vietnamese (0.0045) and between Vietnamese and Cambodian (0.0062). Similarly, small Fst's were observed among different presumed Han Chinese populations originating in different regions of mainland of China and Taiwan (Fst's
Notes
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PubMed ID
19057645 View in PubMed
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An evolutionary genomic approach to identify genes involved in human birth timing.

https://arctichealth.org/en/permalink/ahliterature134886
Source
PLoS Genet. 2011 Apr;7(4):e1001365
Publication Type
Article
Date
Apr-2011
Author
Jevon Plunkett
Scott Doniger
Guilherme Orabona
Thomas Morgan
Ritva Haataja
Mikko Hallman
Hilkka Puttonen
Ramkumar Menon
Edward Kuczynski
Errol Norwitz
Victoria Snegovskikh
Aarno Palotie
Leena Peltonen
Vineta Fellman
Emily A DeFranco
Bimal P Chaudhari
Tracy L McGregor
Jude J McElroy
Matthew T Oetjens
Kari Teramo
Ingrid Borecki
Justin Fay
Louis Muglia
Author Affiliation
Department of Pediatrics, Vanderbilt University School of Medicine and Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, Tennessee, United States of America.
Source
PLoS Genet. 2011 Apr;7(4):e1001365
Date
Apr-2011
Language
English
Publication Type
Article
Keywords
Adult
African Americans - genetics
Animals
Case-Control Studies
Cohort Studies
Evolution, Molecular
Female
Finland
Gene Frequency
Genome-Wide Association Study
Genotype
Humans
Linkage Disequilibrium
Models, Genetic
Parturition - genetics
Polymorphism, Single Nucleotide
Premature Birth - genetics
Receptors, FSH - genetics
Risk factors
Young Adult
Abstract
Coordination of fetal maturation with birth timing is essential for mammalian reproduction. In humans, preterm birth is a disorder of profound global health significance. The signals initiating parturition in humans have remained elusive, due to divergence in physiological mechanisms between humans and model organisms typically studied. Because of relatively large human head size and narrow birth canal cross-sectional area compared to other primates, we hypothesized that genes involved in parturition would display accelerated evolution along the human and/or higher primate phylogenetic lineages to decrease the length of gestation and promote delivery of a smaller fetus that transits the birth canal more readily. Further, we tested whether current variation in such accelerated genes contributes to preterm birth risk. Evidence from allometric scaling of gestational age suggests human gestation has been shortened relative to other primates. Consistent with our hypothesis, many genes involved in reproduction show human acceleration in their coding or adjacent noncoding regions. We screened >8,400 SNPs in 150 human accelerated genes in 165 Finnish preterm and 163 control mothers for association with preterm birth. In this cohort, the most significant association was in FSHR, and 8 of the 10 most significant SNPs were in this gene. Further evidence for association of a linkage disequilibrium block of SNPs in FSHR, rs11686474, rs11680730, rs12473870, and rs1247381 was found in African Americans. By considering human acceleration, we identified a novel gene that may be associated with preterm birth, FSHR. We anticipate other human accelerated genes will similarly be associated with preterm birth risk and elucidate essential pathways for human parturition.
Notes
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PubMed ID
21533219 View in PubMed
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An intronic LINE-1 insertion in MERTK is strongly associated with retinopathy in Swedish Vallhund dogs.

https://arctichealth.org/en/permalink/ahliterature286513
Source
PLoS One. 2017;12(8):e0183021
Publication Type
Article
Date
2017
Author
Richard Everson
Louise Pettitt
Oliver P Forman
Olivia Dower-Tylee
Bryan McLaughlin
Saija Ahonen
Maria Kaukonen
András M Komáromy
Hannes Lohi
Cathryn S Mellersh
Jane Sansom
Sally L Ricketts
Source
PLoS One. 2017;12(8):e0183021
Date
2017
Language
English
Publication Type
Article
Keywords
Animals
Dogs
Finland
Genome-Wide Association Study
Genotype
Introns
Long Interspersed Nucleotide Elements
Mutagenesis, Insertional
Polymorphism, Single Nucleotide
Proto-Oncogene Proteins - genetics
Receptor Protein-Tyrosine Kinases - genetics
Retinal Diseases - genetics
United Kingdom
Abstract
The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA). In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs. Using 24 retinopathy cases and 97 controls with no clinical signs of retinopathy, we replicated the chromosome 17 association in Swedish Vallhunds from the UK and aimed to elucidate the causal variant underlying this association using whole genome sequencing (WGS) of an affected dog. This revealed a 6-8 kb insertion in intron 1 of MERTK that was not present in WGS of 49 dogs of other breeds. Sequencing and BLASTN analysis of the inserted segment was consistent with the insertion comprising a full-length intact LINE-1 retroelement. Testing of the LINE-1 insertion for association with retinopathy in the UK set of 24 cases and 97 controls revealed a strong statistical association (P-value 6.0 x 10-11) that was subsequently replicated in the original Finnish study set (49 cases and 89 controls (P-value 4.3 x 10-19). In a pooled analysis of both studies (73 cases and 186 controls), the LINE-1 insertion was associated with a ~20-fold increased risk of retinopathy (odds ratio 23.41, 95% confidence intervals 10.99-49.86, P-value 1.3 x 10-27). Our study adds further support for regulatory disruption of MERTK in Swedish Vallhund retinopathy; however, further work is required to establish a functional overexpression model. Future work to characterise the mechanism by which this intronic mutation disrupts gene regulation will further improve the understanding of MERTK biology and its role in retinal function.
Notes
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PubMed ID
28813472 View in PubMed
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