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  • 1
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    An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-07-18
    Description: Retrotransposition of processed mRNAs is a common source of novel sequence acquired during the evolution of genomes. Although the vast majority of retroposed gene copies, or retrogenes, rapidly accumulate debilitating mutations that disrupt the reading frame, a small percentage become new genes that encode functional proteins. By using a multibreed association analysis in the domestic dog, we demonstrate that expression of a recently acquired retrogene encoding fibroblast growth factor 4 (fgf4) is strongly associated with chondrodysplasia, a short-legged phenotype that defines at least 19 dog breeds including dachshund, corgi, and basset hound. These results illustrate the important role of a single evolutionary event in constraining and directing phenotypic diversity in the domestic dog.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748762/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2748762/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Parker, Heidi G -- VonHoldt, Bridgett M -- Quignon, Pascale -- Margulies, Elliott H -- Shao, Stephanie -- Mosher, Dana S -- Spady, Tyrone C -- Elkahloun, Abdel -- Cargill, Michele -- Jones, Paul G -- Maslen, Cheryl L -- Acland, Gregory M -- Sutter, Nathan B -- Kuroki, Keiichi -- Bustamante, Carlos D -- Wayne, Robert K -- Ostrander, Elaine A -- 1R01GM83606/GM/NIGMS NIH HHS/ -- 1R24GM082910/GM/NIGMS NIH HHS/ -- 5R01EY006855/EY/NEI NIH HHS/ -- R01 EY006855/EY/NEI NIH HHS/ -- R01 EY006855-25/EY/NEI NIH HHS/ -- Z99 HG999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):995-8. doi: 10.1126/science.1173275. Epub 2009 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19608863" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Breeding ; Chondrocytes/metabolism ; Dogs/anatomy & histology/*genetics ; Evolution, Molecular ; Extremities/*anatomy & histology ; Fibroblast Growth Factor 4/*genetics ; *Gene Duplication ; *Gene Expression Regulation ; Gene Frequency ; Genes, Duplicate ; Genome-Wide Association Study ; Haplotypes ; Humerus/metabolism ; Long Interspersed Nucleotide Elements ; Oligonucleotide Array Sequence Analysis ; Pedigree ; Phenotype ; Polymorphism, Single Nucleotide ; Regulatory Sequences, Nucleic Acid ; Retroelements/*genetics ; Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Genome-Wide Association Study of Down Syndrome-Associated Atrioventricular Septal Defects (2015)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2015-10-06
    Description: The goal of this study was to identify the contribution of common genetic variants to Down syndrome–associated atrioventricular septal defect, a severe heart abnormality. Compared with the euploid population, infants with Down syndrome, or trisomy 21, have a 2000-fold increased risk of presenting with atrioventricular septal defects. The cause of this increased risk remains elusive. Here we present data from the largest heart study conducted to date on a trisomic background by using a carefully characterized collection of individuals from extreme ends of the phenotypic spectrum. We performed a genome-wide association study using logistic regression analysis on 452 individuals with Down syndrome, consisting of 210 cases with complete atrioventricular septal defects and 242 controls with structurally normal hearts. No individual variant achieved genome-wide significance. We identified four disomic regions (1p36.3, 5p15.31, 8q22.3, and 17q22) and two trisomic regions on chromosome 21 (around PDXK and KCNJ6 genes) that merit further investigation in large replication studies. Our data show that a few common genetic variants of large effect size (odds ratio 〉2.0) do not account for the elevated risk of Down syndrome–associated atrioventricular septal defects. Instead, multiple variants of low-to-moderate effect sizes may contribute to this elevated risk, highlighting the complex genetic architecture of atrioventricular septal defects even in the highly susceptible Down syndrome population.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 3
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    Analysis of Copy Number Variants on Chromosome 21 in Down Syndrome-Associated Congenital Heart Defects (2018)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2018-01-05
    Description: One in five people with Down syndrome (DS) are born with an atrioventricular septal defect (AVSD), an incidence 2000 times higher than in the euploid population. The genetic loci that contribute to this risk are poorly understood. In this study, we tested two hypotheses: (1) individuals with DS carrying chromosome 21 copy number variants (CNVs) that interrupt exons may be protected from AVSD, because these CNVs return AVSD susceptibility loci back to disomy, and (2) individuals with DS carrying chromosome 21 genes spanned by microduplications are at greater risk for AVSD because these microduplications boost the dosage of AVSD susceptibility loci beyond a tolerable threshold. We tested 198 case individuals with DS+AVSD, and 211 control individuals with DS and a normal heart, using a custom microarray with dense probes tiled on chromosome 21 for array CGH (aCGH). We found that neither an individual chromosome 21 CNV nor any individual gene intersected by a CNV was associated with AVSD in DS. Burden analyses revealed that African American controls had more bases covered by rare deletions than did African American cases. Inversely, we found that Caucasian cases had more genes intersected by rare duplications than did Caucasian controls. We also showed that previously DS+AVSD (DS and a complete AVSD)-associated common CNVs on chromosome 21 failed to replicate. This research adds to the swell of evidence indicating that DS-associated AVSD is similarly heterogeneous, as is AVSD in the euploid population.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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