PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data. (1/79)

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MIRAGAA--a methodology for finding coordinated effects of microRNA expression changes and genome aberrations in cancer. (2/79)

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Human genome variation in health and in neuropsychiatric disorders. (3/79)

OBJECTIVES: Variation in the human genome may explain genetic contributions to complex traits and common diseases. FINDINGS: Until recently, single nucleotide polymorphisms were thought to be the most prevalent form of interindividual genetic variation. However, structural genomic rearrangements such as deletions, duplications, and inversions lead to variation in gene copy number and contribute even more to genomic diversity. Other sources of genomic variation include noncoding genes, pseudogenes, and mobile genetic elements (transposons). CONCLUSIONS: Genome dynamics, including changes in gene number and position as well as epigenetic modifications of coding and noncoding sequences, can affect regulation of gene expression and may contribute to the variability of complex phenotypes.  (+info)

UDP-glucuronosyltransferase 1A10: activity against the tobacco-specific nitrosamine, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol, and a potential role for a novel UGT1A10 promoter deletion polymorphism in cancer susceptibility. (4/79)

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Analysis of copy number variations among diverse cattle breeds. (5/79)

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DNA sequence variants and the practice of medicine. (6/79)

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Variant -and individual dependent nature of persistent Anaplasma phagocytophilum infection. (7/79)

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Characterization of missing human genome sequences and copy-number polymorphic insertions. (8/79)

The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 new insertion sequences corresponding to 720 genomic loci. We found that a substantial fraction of these sequences are either missing, fragmented or misassigned when compared to recent de novo sequence assemblies from short-read next-generation sequence data. We determined that 18-37% of these new insertions are copy-number polymorphic, including loci that show extensive population stratification among Europeans, Asians and Africans. Complete sequencing of 156 of these insertions identified new exons and conserved noncoding sequences not yet represented in the reference genome. We developed a method to accurately genotype these new insertions by mapping next-generation sequencing datasets to the breakpoint, thereby providing a means to characterize copy-number status for regions previously inaccessible to single-nucleotide polymorphism microarrays.  (+info)