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Long noncoding RNAs (lncRNAs) are increasingly recognized to play major regulatory roles in development and disease. To identify novel regulators in breast biology, we identified differentially regulated lncRNAs during mouse mammary development. Among the highest and most differentially expressed was a transcript (Zfas1) antisense to the 5' end of the(More)
MOTIVATION In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology. RESULTS We present a method for CNV detection for TR data, including whole-exome capture data.(More)
In this study, the two determinants of the rate of osteoclastic bone resorption, cell number and cell activity, were evaluated to characterize the response to two chronic resorptive stimuli, a calcium-deficient diet and a phosphorus-deficient diet, fed to rats for 8 days. The number of osteoclast nuclei was determined directly and the resorptive activity of(More)
Despite intensive efforts using linkage and candidate gene approaches, the genetic etiology for the majority of families with a multi-generational breast cancer predisposition is unknown. In this study, we used whole-exome sequencing of thirty-three individuals from 15 breast cancer families to identify potential predisposing genes. Our analysis identified(More)
Formalin-fixed, paraffin-embedded (FFPE) material tends to yield degraded DNA and is thus suboptimal for use in many downstream applications. We describe an integrated analysis of genotype, loss of heterozygosity (LOH), and copy number for DNA derived from FFPE tissues using oligonucleotide microarrays containing over 500K single nucleotide polymorphisms. A(More)
This study evaluates osteoblast and osteoclast cell numbers and cell activities determined from quantitative histology of trabecular bone in human iliac crest bone biopsies. Subjects studied were postmenopausal osteoporotic patients (aged 53-81) for whom total body calcium and urine and serum clinical data were also available. Only 39% of the osteoclasts(More)
PURPOSE Gene panel sequencing is revolutionizing germline risk assessment for hereditary breast cancer. Despite scant evidence supporting the role of many of these genes in breast cancer predisposition, results are often reported to families as the definitive explanation for their family history. We assessed the frequency of mutations in 18 genes included(More)
The breast cancer predisposition gene, BRCA2, has a large number of genetic variants of unknown effect. The variant rs11571833, an A > T transversion in the final exon of the gene that leads to the creation of a stop codon 93 amino acids early (K3326*), is reported as a neutral polymorphism but there is some evidence to suggest an association with an(More)