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22q11.2 microduplication in two patients with bladder exstrophy and hearing impairment.

https://arctichealth.org/en/permalink/ahliterature146325
Source
Eur J Med Genet. 2010 Mar-Apr;53(2):61-5
Publication Type
Article
Author
Johanna Lundin
Cilla Söderhäll
Lina Lundén
Anna Hammarsjö
Iréne White
Jacqueline Schoumans
Göran Läckgren
Christina Clementson Kockum
Agneta Nordenskjöld
Author Affiliation
Department of Woman and Child Health, Karolinska Institutet, Stockholm, Sweden.
Source
Eur J Med Genet. 2010 Mar-Apr;53(2):61-5
Language
English
Publication Type
Article
Keywords
Adolescent
Adult
Bladder Exstrophy - genetics
Chromosomes - ultrastructure
Chromosomes, Human, Pair 22
Comparative Genomic Hybridization
Female
Gene Duplication
Hearing Loss - genetics
Humans
In Situ Hybridization, Fluorescence
Male
Molecular Probe Techniques
Phenotype
Sweden
Syndrome
Abstract
Bladder exstrophy is a congenital malformation of the bladder and urethra. The genetic basis of this malformation is unknown however it is well known that chromosomal aberrations can lead to defects in organ development. A few bladder exstrophy patients have been described to carry chromosomal aberrations. Chromosomal rearrangements of 22q11.2 are implicated in several genomic disorders i.e. DiGeorge/velocardiofacial- and cat-eye syndrome. Deletions within this chromosomal region are relatively common while duplications of 22q11.2 are much less frequently observed. An increasing number of reports of microduplications of this region describe a highly variable phenotype. We have performed array-CGH analysis of 36 Swedish bladder exstrophy patients. The analysis revealed a similar and approximately 3 Mb duplication, consistent with the recently described 22q11.2 microduplication syndrome, in two unrelated cases with bladder exstrophy and hearing impairment. This finding was confirmed by multiplex ligation-dependent probe amplification (MLPA) and FISH analysis. Subsequent MLPA analysis of this chromosomal region in 33 bladder exstrophy patients did not reveal any deletion/duplication within this region. MLPA analysis of 171 anonymous control individuals revealed one individual carrying this microduplication. This is the first report of 22q11.2 microduplication associated with bladder exstrophy and hearing impairment. Furthermore the finding of one carrier among a cohort of normal controls further highlights the variable phenotype linked to this microduplication syndrome.
PubMed ID
20045748 View in PubMed
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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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"886-84-like" tick-borne encephalitis virus strains: Intraspecific status elucidated by comparative genomics.

https://arctichealth.org/en/permalink/ahliterature310363
Source
Ticks Tick Borne Dis. 2019 08; 10(5):1168-1172
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
08-2019
Author
Renat V Adelshin
Elena A Sidorova
Artem N Bondaryuk
Anna G Trukhina
Dmitry Yu Sherbakov
Richard Allen White Iii
Evgeny I Andaev
Sergey V Balakhonov
Author Affiliation
Irkutsk Anti-Plague Research Institute of Siberia and Far East, Trilisser 78, 664047, Irkutsk, Russia; Irkutsk State University, Irkutsk, Russia. Electronic address: adelshin@gmail.com.
Source
Ticks Tick Borne Dis. 2019 08; 10(5):1168-1172
Date
08-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Arvicolinae
Encephalitis Viruses, Tick-Borne - classification - genetics
Encephalitis, Tick-Borne - epidemiology - veterinary - virology
Genome, Viral
Genomics
Genotype
Incidence
Ixodes - virology
Rodent Diseases - epidemiology - virology
Siberia - epidemiology
Abstract
Tick-borne encephalitis virus (TBEV) can cause severe meningitis, encephalitis, and meningoencephalitis. TBEV represents a pathogen of high zoonotic potential and an emerging global threat. There are three known subtypes of TBEV: Far-Eastern, Siberian and European. Since 2001 there have been suggestions that two new subtypes may be distinguished: "178-79" and "886-84". These assumptions are based on the results of the envelope gene fragment sequencing (Zlobin et al., 2001; Kovalev and Mukhacheva, 2017) and genotype-specific probes molecular hybridization (Demina et al., 2010). There is only one full-genome sequence of "178-79" strain and two identical ones of "886-84" strain can be found in GenBank. For clarification of the intraspecific position of the "886-84-like" strains group we completely sequenced six previously unknown "886-84-like" strains isolated in Eastern Siberia. As a result of applying different bioinformatics approaches, we can confirm that "886-84-like" strains group is a distinct subtype of TBEV.
PubMed ID
31253516 View in PubMed
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A 5700 year-old human genome and oral microbiome from chewed birch pitch.

https://arctichealth.org/en/permalink/ahliterature307649
Source
Nat Commun. 2019 12 17; 10(1):5520
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
12-17-2019
Author
Theis Z T Jensen
Jonas Niemann
Katrine Højholt Iversen
Anna K Fotakis
Shyam Gopalakrishnan
Åshild J Vågene
Mikkel Winther Pedersen
Mikkel-Holger S Sinding
Martin R Ellegaard
Morten E Allentoft
Liam T Lanigan
Alberto J Taurozzi
Sofie Holtsmark Nielsen
Michael W Dee
Martin N Mortensen
Mads C Christensen
Søren A Sørensen
Matthew J Collins
M Thomas P Gilbert
Martin Sikora
Simon Rasmussen
Hannes Schroeder
Author Affiliation
The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark.
Source
Nat Commun. 2019 12 17; 10(1):5520
Date
12-17-2019
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Animals
Betula - physiology
DNA, Ancient - analysis
DNA, Bacterial - analysis
Denmark
Genome, Human
Geography
Humans
Microbiota - genetics
Mouth - microbiology
Phenotype
Radiometric Dating
Sex Determination Analysis
Time Factors
Abstract
The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.
PubMed ID
31848342 View in PubMed
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'Access arrangements' for biobanks: a fine line between facilitating and hindering collaboration.

https://arctichealth.org/en/permalink/ahliterature141708
Source
Public Health Genomics. 2011;14(2):104-14
Publication Type
Article
Date
2011
Author
S. Fortin
S. Pathmasiri
R. Grintuch
M. Deschênes
Author Affiliation
Faculty of Law, University of Montreal, Montreal, Que., Canada.
Source
Public Health Genomics. 2011;14(2):104-14
Date
2011
Language
English
Publication Type
Article
Keywords
Biological Specimen Banks - economics - organization & administration
Canada
Cooperative Behavior
Genetic Research
Genomics
Humans
Informed consent
Public Health
Public Policy
Tissue Banks - organization & administration
Abstract
This decade is witnessing the proliferation of large-scale population-based biobanks. Many biobanks have reached the stage of offering access to their collection of data and samples to the scientific community. This, however, requires that access arrangements be established to govern the relationship between biobanks and users. Access arrangements capture the convergence of all normative elements in the life cycle of a biobank: policies, laws, common practices, commitments made by the biobank to participants, the expectations of funders, and the needs of the scientific community. Furthermore, access arrangements shape new legal agreements between 'biobankers' and researchers to ensure appropriate, regulated and efficient use of biobank materials. This paper begins by examining the particularities of access arrangements, identifying the key elements of these new regulatory instruments. Second, the paper looks at various strategies used by biobanks to regulate access and surveys the underlying motivations of these strategies and the impact they can have on potential international collaboration. Third, an example of the challenges encountered in creating access policy is illustrated using the case of CARTaGENE, a biobank based in Montreal, Canada. Last, the paper presents how Public Population Project in Genomics (P(3)G) facilitates the work of biobankers and improves collaboration throughout the international human genomics research community.
PubMed ID
20689244 View in PubMed
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Accuracy of genomic selection for growth and wood quality traits in two control-pollinated progeny trials using exome capture as the genotyping platform in Norway spruce.

https://arctichealth.org/en/permalink/ahliterature299456
Source
BMC Genomics. 2018 Dec 18; 19(1):946
Publication Type
Journal Article
Date
Dec-18-2018
Author
Zhi-Qiang Chen
John Baison
Jin Pan
Bo Karlsson
Bengt Andersson
Johan Westin
María Rosario García-Gil
Harry X Wu
Author Affiliation
Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
Source
BMC Genomics. 2018 Dec 18; 19(1):946
Date
Dec-18-2018
Language
English
Publication Type
Journal Article
Keywords
Exome
Genetic markers
Genomics - methods
Genotype
Models, Genetic
Models, Statistical
Norway
Phenotype
Picea - genetics - growth & development
Plant Breeding
Pollination
Selection, Genetic
Wood - chemistry - genetics
Abstract
Genomic selection (GS) can increase genetic gain by reducing the length of breeding cycle in forest trees. Here we genotyped 1370 control-pollinated progeny trees from 128 full-sib families in Norway spruce (Picea abies (L.) Karst.), using exome capture as genotyping platform. We used 116,765 high-quality SNPs to develop genomic prediction models for tree height and wood quality traits. We assessed the impact of different genomic prediction methods, genotype-by-environment interaction (G?×?E), genetic composition, size of the training and validation set, relatedness, and number of SNPs on accuracy and predictive ability (PA) of GS.
Using G matrix slightly altered heritability estimates relative to pedigree-based method. GS accuracies were about 11-14% lower than those based on pedigree-based selection. The efficiency of GS per year varied from 1.71 to 1.78, compared to that of the pedigree-based model if breeding cycle length was halved using GS. Height GS accuracy decreased to more than 30% while using one site as training for GS prediction and using this model to predict the second site, indicating that G?×?E for tree height should be accommodated in model fitting. Using a half-sib family structure instead of full-sib structure led to a significant reduction in GS accuracy and PA. The full-sib family structure needed only 750 markers to reach similar accuracy and PA, as compared to 100,000 markers required for the half-sib family, indicating that maintaining the high relatedness in the model improves accuracy and PA. Using 4000-8000 markers in full-sib family structure was sufficient to obtain GS model accuracy and PA for tree height and wood quality traits, almost equivalent to that obtained with all markers.
The study indicates that GS would be efficient in reducing generation time of breeding cycle in conifer tree breeding program that requires long-term progeny testing. The sufficient number of trees within-family (16 for growth and 12 for wood quality traits) and number of SNPs (8000) are required for GS with full-sib family relationship. GS methods had little impact on GS efficiency for growth and wood quality traits. GS model should incorporate G?×?E effect when a strong G?×?E is detected.
PubMed ID
30563448 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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[A comparative analysis of genomes of virulent and avirulent strains of Vibrio cholerae O139].

https://arctichealth.org/en/permalink/ahliterature179953
Source
Mol Gen Mikrobiol Virusol. 2004;(2):11-6
Publication Type
Article
Date
2004
Author
G A Eroshenko
A V Osin
E Iu Shchelkanova
N I Smirnova
Author Affiliation
Mikrob Russian Research Anti-Plague Institute, Saratov.
Source
Mol Gen Mikrobiol Virusol. 2004;(2):11-6
Date
2004
Language
Russian
Publication Type
Article
Keywords
Adenosine Triphosphatases - genetics
Bacterial Outer Membrane Proteins - genetics
Bacterial Proteins - genetics
Bacterial Toxins - genetics
Cholera - microbiology
Cholera Toxin - genetics
DNA-Binding Proteins - genetics
Genome, Bacterial
Humans
Membrane Glycoproteins
Membrane Proteins - genetics
Proteins - genetics
Russia
Serine Endopeptidases - genetics
Transcription Factors - genetics
Vibrio cholerae O139 - genetics - pathogenicity
Virulence Factors - genetics
Water Microbiology
Abstract
A comparative analysis of the genome of V. cholerae O139 strains isolated in Russia's territory from patients with cholera and from the environment showed essential differences in their structures. The genome of clinical strains possessed all tested genes associated with virulence (ctxAB, zot, ace, rstC, rtxA, hap, toxR and toxT) and the at-tRS site for the CTXp phage DNA integration. As for the O139 V. cholerae chromosome strains isolated from water, 70% of the studied genes (ctxAB, zot, ace, rstC, tcpA, and toxT) and the attRS sequence were not detected in them. A lack of the key virulence genes in O139-serogroup "water" vibrios, including genes of toxin-coregulated adhesion pili. (that are receptors for the CTXp phage), and of the attachment site of the above phage are indicative of that the O139 V. cholerae strains isolated from open water sources located in different Russia's regions are epidemically negligible.
PubMed ID
15164715 View in PubMed
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[A complex approach to evaluation of human genome instability].

https://arctichealth.org/en/permalink/ahliterature168018
Source
Vestn Ross Akad Med Nauk. 2006;(4):36-41
Publication Type
Article
Date
2006
Author
Iu A Revazova
L V Khripach
I E Sidorova
V V Iurchenko
I E Zykova
Source
Vestn Ross Akad Med Nauk. 2006;(4):36-41
Date
2006
Language
Russian
Publication Type
Article
Keywords
Genome, Human - genetics
Human Genome Project
Humans
Mutagenesis - genetics
Occupational Diseases - genetics
Occupational Exposure
Oxidative Stress - physiology
Polymerase Chain Reaction
Polymorphism, Genetic - genetics
Russia
Abstract
In this study, evaluation of genome instability in individuals exposed to chemical compounds included detection of the genetic polymorphism of some xenobiotic metabolic enzymes (CYP1A1, CYP1E1, PON1, GSTM1, GSTT1), as well as measurement of oxidative state chemiluminescent variables and the level of cytogenetic damage. According to the study, the level of chromosomal aberrations in peripheral blood lymphocytes shows a strong correlation with PON54 left allele and GSTM1 null genotype, and can be described by the polynomial function of blood plasma luminol-dependent chemiluminescence. The frequencies of micronuclei in buccal epithelium displayed a weak association with GSTT1 null genotype.
PubMed ID
16889354 View in PubMed
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Actinoalloteichus fjordicus sp. nov. isolated from marine sponges: phenotypic, chemotaxonomic and genomic characterisation.

https://arctichealth.org/en/permalink/ahliterature292492
Source
Antonie Van Leeuwenhoek. 2017 Dec; 110(12):1705-1717
Publication Type
Journal Article
Date
Dec-2017
Author
Imen Nouioui
Christian Rückert
Joost Willemse
Gilles P van Wezel
Hans-Peter Klenk
Tobias Busche
Jörn Kalinowski
Harald Bredholt
Sergey B Zotchev
Author Affiliation
School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
Source
Antonie Van Leeuwenhoek. 2017 Dec; 110(12):1705-1717
Date
Dec-2017
Language
English
Publication Type
Journal Article
Keywords
Actinobacteria - chemistry - classification - genetics - isolation & purification
Animals
Bacterial Typing Techniques
Computational Biology - methods
Genes, Bacterial
Genome, Bacterial
Genomics - methods
High-Throughput Nucleotide Sequencing
Metabolomics - methods
Molecular Sequence Annotation
Multigene Family
Phenotype
Phylogeny
Porifera - microbiology
Secondary Metabolism - genetics
Abstract
Two actinobacterial strains, ADI 127-17T and GBA 129-24, isolated from marine sponges Antho dichotoma and Geodia barretti, respectively, collected at the Trondheim fjord in Norway, were the subjects of a polyphasic study. According to their 16S rRNA gene sequences, the new isolates were preliminarily classified as belonging to the genus Actinoalloteichus. Both strains formed a distinct branch, closely related to the type strains of Actinoalloteichus hoggarensis and Actinoalloteichus hymeniacidonis, within the evolutionary radiation of the genus Actinoalloteichus in the 16S rRNA gene-based phylogenetic tree. Isolates ADI 127-17T and GBA 129-24 exhibited morphological, chemotaxonomic and genotypic features distinguishable from their close phylogenetic neighbours. Digital DNA: DNA hybridization and ANI values between strains ADI 127-17T and GBA 129-24 were 97.6 and 99.7%, respectively, whereas the corresponding values between both tested strains and type strains of their closely related phylogenetic neighbours, A. hoggarensis and A. hymeniacidonis, were well below the threshold for delineation of prokaryotic species. Therefore, strains ADI 127-17T (= DSM 46855T) and GBA 129-24 (= DSM 46856) are concluded to represent a novel species of the genus Actinoalloteichus for which the name of Actinoalloteichus fjordicus sp. nov. (type strain ADI 127-17T = DSM 46855T = CECT 9355T) is proposed. The complete genome sequences of the new strains were obtained and compared to that of A. hymeniacidonis DSM 45092T and A. hoggarensis DSM 45943T to unravel unique genome features and biosynthetic potential of the new isolates.
Notes
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