Talk notes

• Debbie Nickerson again; DN: there are 2,500 Mendelian diseases in which we still don’t know the causative gene; sequencing will change that. U. Wash will be tackling 20 Mendelian diseases (160–200 exomes) in 2010; also 7,000 exomes for complex trait. using evolutionary constraint to score candidate disease genes; powerful approach for filtering out false positives. also crucial to integrate information from “normal” individuals to filter out non-disease-causing variation. Details here.
• Stacey Gabriel on exome sequncing. Including capture cost an exome should cost 1/15X of a genome. SG done 120 cancer genomes deep seq — need to do 500 of the same tumor type 2 find 3% _ this is the plan for the ICGC projects. Details here.
• Arend Sirow, Stanford: Sequences do not determine phasing: phasing different in different (related) cell types. Use sequence start sites to measure nucleosome binding sites. See Antony’s notes.
• Carlos Bustamante from the Broad; African- and Mexican-American samples display wide variation in degree of European ancestry. People are not always what think they are. 1st principal component of worlwide variation is essentially a perfect measure of African/European admixture. Details via Antony.
• Jim Knight on de novo assembly of Bonobo genome. Assembled 24X 454 sequence into max 90kb contigs/1.6Mb scafolds
• In the Microbiome session, Julie Segre asks if sequencing can tell us more than culture in identify skin bacteria? The microbiome of your left arm is no more similar to your right arm than someone else’s. why do we sterilize our outsde (purell) and infect our inside (probiotic yogurt)? See details.
• Metagenomic approaches to pathogen discovery – David Wang. Their lab looking at Respiratory and GI infections–5m deaths annually, 40% from unknown agents. Antony’s notes.
• M.Stromberg, BC, “Novel Mobile Element Insertions detected inhuman pop..”
• Charlie Rose, Novel viruses have been present forever- human interconnectivity is what has changed. Risks higher than ever. Monitor airline cabin crews as early warning for new virus threats
• Good ol’ Monsanto: Enjoyed the bit from the Monsanto Rep: Deforestation of Africa and Brazil is “Visionary” and opportunity for growth
• Notes from Thomas Briese’s talk “New Frontiers in Molecular Diagnosis of Infectious Diseases”
• Notes from Penny Chisholm’s talk “From Single Cells to Global Metagenomics”:
• Notes from Elliot Margules – Sequencing and analysis of matched tumor and normal genomes from a melanoma patient
• Notes from Kristian Cibulskis on ITector: Accurate Somatic Mutation Detection in Whole Genome and Exome Capture:
• Vanessa Hayes is discussing the work published this week in Nature on African genomes. VH just demonstrated the four different click sounds in Bushman languages as a preliminary to discussing their genomes. Desmund Tutu has a very thorough genome sequence: 30x SOliD, 7.2X Illumina, 16X 454, and a 1M Illumina chip. African genomes yields a huge number of novel variants. ow building a new Affymetrix SNP chip to target the 1.3 million novel SNPs discovered in this project. Also see notes on Bustamante talk.
• Margret Hoehe (Max Planck) is up now, discussing detailed genetic analysis of the human MHC gene cluster.
• Daniel MacArthur, “Loss-of-Function Mutations in Healthy Human Genomes: Implications for Clinical Genome Sequencing”. loss of function variants in the 1000 Genomes Project. 1656 genes that contain loss-of-function variants in the 1KG data. Individuals have ~50–100 genes knocked out each (!). Can make a classifier for LOF-tolerant and non-LOF-tolerant genes; useful in search for Mendelian disorder genes. Notes here
• Stephan Zuchner (U. Miami) on using exome sequencing to track down mutations in spastic paraplegia. he definition of the exome is still unclear – how many protein-coding exons actually exist? current exome designs don’t include functionally important non-coding regions (promoters, untranslated regions).
• Notes from Timothy Triche – Children’s Hospital Los Angeles, Unraveling the Complexity of Primary and Metastatic Ewing’s Sarcoma Using Helicos Singele Molecule Sequencing
• Notes from Ian Bosdet – Mutational Profiling of Pre and Post-Treatement Lung Tumors.
• Notes from Ogan Abaan – NIH/NCI, “Identification of novel cancer mutations in sarcomas”