1. Sean Davis, M.D., Ph.D. Genetics Branch, Center for Cancer Research National Cancer Institute National Institutes of Health Genomics for Pediatrics An Overview of Technologies for Observing the Human Genome
6. phenotype Gene Copy Number Sequence Variation Chromatin Structure and Function Gene Expression Transcriptional Regulation DNA Methylation Patient and Population Characteristics
28. Array Comparative Genomic Hybridization (aCGH) Tumor DNA Normal DNA Hybridize (Tumor Suppressors) (Oncogenes) Normal Copy Number DNA Loss Amplification
39. Again, DNA hybridized to DNA, but designed to detect the differences in hybridization due to a SNP
40. Can be used for measuring copy number, finding stretches of uniparental disomy, risk alleles for certain conditions, and in linkage and association studies
49. Simultaneous Gene Expression and Copy Number on Tiling Arrays Annotated Genes Expression Copy Number, Sample 1 Copy Number, Sample 2 Simultaneous measurement of copy number in two samples and gene expression in one sample overlayed on map of genes in the region
50. Simultaneous Gene Expression and Copy Number on Tiling Arrays Annotated Genes Expression Copy Number, Sample 1 Copy Number, Sample 2 Increased expression in the small amplicon does not include all genes, giving clues as to the biologically important genes in the region
51. Simultaneous Gene Expression and Copy Number on Tiling Arrays Annotated Genes Expression Copy Number, Sample 1 Copy Number, Sample 2 Spikes of expression at exons of ERBB2
52. Simultaneous Expression and Copy Number Copy Number Expression Copy Number Evolutionary Conservation Expression Copy Number Opposite Strand Expression Evolutionary Conservation Expression Copy Number
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54. Why did the chicken cross the road? Darwin1: It was the logical next step after coming down from the trees. Darwin2: The fittest chickens cross the road.
64. Regions of open chromatin are necessary for transcriptional and regulatory machinery to have access to gene neighborhoods and facilitate transcription
69. Transcription factor binding sites (experimentally determined by ChIP/chip, etc.) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. The ENCODE Consortium. Nature , 2007.
83. These technologies will see increasing use in clinical medicine, but such use must be tempered by sound clinical hypotheses and testing
84. The data generated by many of these technologies necessitates improved clinical, translational, and research information systems
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87. Designing studies that evaluate the operating characteristics of new testing methods is costly and requires the appropriate patient populations
88. There are many ethical concerns associated with the enormous amounts of personal information that might be gleaned from genomic technologies applied in the clinical setting
89. The Biggest Challenge? How do we integrate all the disparate pieces of information, collected longitudinally and by many sources, to improve the health of the individual?
97. One day the zoo-keeper noticed that the orangutan was reading two books - the Bible and Darwin's The Origin of Species. In surprise he asked the ape, "Why are you reading both those books"? "Well," said the orangutan, "I just wanted to know if I was my brother's keeper or my keeper's brother." [email_address]