Later this week, I’ll attend the Personal Genomes meeting at Cold Spring Harbor Laboratory. This is a smaller meeting (less than a hundred participants), but an excellent one by all accounts.

Keynotes

There are three keynotes, including one from NHGRI director Eric Green. His and the keynote from Stanford’s Henry Greely seem focused on applying genomic information in the clinic, a theme that will undoubtedly resonate throughout the meeting.

Greely, H. Preparing for the coming tsunami of clinical genomic information Green, E.D. Genomics in 2K10 and beyond—Charting a course for genomic medicine Hood, L. Systems genetics and systems biology

Talks

I’d heard that the talks at this meeting were of exceptional quality, and by the look of the abstracts, this trend seems likely to continue. The diversity of subject matter is impressive: there are updates on sequencing technology (J. Beechem on quantum-dot nanosequencing, Jonathan Rothberg on IonTorrent) and studies of human genetic variation in general (Conrad). I’m looking forward to a talk by my friend Matthew Bainbridge of Baylor College of Medicine, who will report on mutation discovery [likely by exome sequencing] for autosomal dominant diseases. There will be talks on sequencing to study other heritable complex diseases, such as Crohn’s disease and atherosclerosis.

Bainbridge, M. Mutation discovery for autosomal dominant diseases Beechem, J. Single molecule real-time DNA sequencing on the surface of a quantum-dot nanocrystal Brugarolas, J.B. Genome evaluation, functional studies, and research translation in renal cell carcinoma Conrad, D. Variation in genome-wide mutation rates within and between human families Dimitrova, N. Correlating genotyping and gene expression data with next-generation whole genome sequencing data Gibson, N.W. A comparison of two methods for digitally quantifying mRNAs Grimmond, S.M. Studying pancreatic cancer at single nucleotide resolution Jones, S.J. Clinical utility of genomic sequencing of a rare adenocarcinoma Jorde, L.B. Direct estimates of the human mutation rate using whole-genome sequence data Laird, P.W. Mining the cancer methylome Lunshof, J.E. Personal genomes and phenomes—Reframing health Myers, R.M. Personal functional genomics Patil, P. Refining a method for processing an individual’s whole genome to clinical utility Pérez-Llamas, C. IntOGen, Integrative OncoGenomics for personal cancer genomes Ritz, A. Algorithms for resequencing and assembly using strobe sequencing data Rothberg, J.M. PostLight sequencing with semiconductor chips Schadt, E. Enabling a more comprehensive understanding of your risk of infection from viral pathogens via the construction of a real-time disease weather map Schreiber, S. Whole genome sequence of a Crohn disease trio—A paradigm for complex disease etiology discovery Teer, J.K. Comparison and application of whole exome and genome sequencing on an individual with high risk for atherosclerosis Trevino, L.R. Screening for germline variants that predispose to cancer from next-generation sequencing data Varley, K. Allele-specific DNA methylation in a three-generation family reveals genetic influence on epigenetic regulation WANG, J. Personal genomes are personalized Wilson, R. Whole genome sequencing, analysis and diagnosis of a patient with acute promyelocytic leukemia (APL) Worthey, E. Personal genomics in a clinical setting—Experience from an academic medical college and children’s hospital Wyman, S.K. Post-transcriptional modification of microRNAs is a common, conserved mechanism that increases complexity in the microRNA transcriptome Yandell, M.D. Automated high-throughput analysis of personal genome sequences—Towards clinical interpretation

Cancer will feature prominently, with talks on pancreatic cancer, adenocarcinoma, and renal cell carcinoma. Peter Laird of USC, a member of the Cancer Genome Atlas research consortium and methylation expert, has a talk on mining the cancer methylome. Rick Wilson, director of the Genome Center at Washington University in St. Louis, will present some very recent work on sequencing and diagnosis of a patient with acute promyelotic leukemia (APL).

Posters

No matter the recent debate on the usefulness of poster sessions at scientific conferences, I’m looking forward to this one. I’ll be presenting my group’s work on somatic mutation detection by whole-genome and exome sequencing of five patients with ovarian cancer. These are pre-publication results and (in my opinion) make for an interesting comparison. The question is very pertinent: how do current exome sequencing approaches like Agilent SureSelect perform relative to whole-genome sequencing, when it comes to detecting somatic mutations in coding regions of the genome? Nathan Dees from my group has a poster on another interesting project: whole genome sequencing of a primary breast tumor, liver metastasis, and lung metastasis samples from a single patient.  There are many interesting posters, too many to talk about.  Here’s the full list:

Adams, D.R. The NIH Undiagnosed Diseases Program—Application of genome-scale sequencing to diagnostic mysteries in single families Ahn, S. Comparing and combining two next-generation sequencing technologies for human genome re-sequencing Bolser, D.M. The social, political, and economic impact of personal genomes Brodzik, A.K. Recent advances in sequence homology assessment in the difference set space with application to the analysis of human genomes Brunham, L. Differential effect of the rs4149056 variant in SLCO1B1 on myopathy associated with simvastatin and atorvastatin Calvo, S. Targeted sequencing identifies causal disease genes in individual patients with mitochondrial disease Caruccio, N. Improved methods for rRNA removal and mRNA-Seq library preparation Casals, F. Medical genomics of primary immunodeficiencies Cho, V.E. Identification of individuals within study cohorts with unusual intermediate phenotypes Choi, M. A compilation of rare functional variations from human exomes Craig, D.W. Whole-genome sequencing of autosomal recessive autism Decker, B. Clinical analysis of whole genome sequence data at the Medical College of Wisconsin Dees, N. Disease progression from primary breast tumor to liver and lung metastases Dewal, N. Haplotype specific amplification in high-throughput tumor sequence data Dimitrova, N. Multi-modal suite for disease specific analysis of next-generation sequencing data Dinwiddie, D.L. Carrier screening of recessive genetic disorders by target enrichment and next-generation sequencing Dorkins, H.R. Personal genomes and tomorrow’s doctors Gonzaga-Jauregui, C. Assessment of copy-number variation in a family using both whole genome sequencing and array CGH Gusev, A. Whole genome low-pass sequencing combined with GWAS data detects variants associated with cholesterol and hemoglobin levels in individuals from the island of Kosrae, Micronesia Hall, I.M. Capturing the full spectrum of coding variation with de novo exon assembly Hambuch, T. Experiences of whole genome sequencing in the clinical laboratory Huang, A.L. Genetic basis of human sleep behaviors—Studies from familial sleep phase syndromes Ju, Y. The fine-scale structure of genomic variants and its functional influence on gene expression Koboldt, D.C. Somatic mutation discovery in ovarian cancer by whole genome and exome sequencing Kuersten, S. Enhanced method to capture the small RNA transcriptome Lerner-Ellis, J. Implementing 2nd generation sequencing in the clinic Markello, T.C. Whole exome and whole genome sequencing in the NIH Undiagnosed Diseases Program Metzker, M.L. Molecular and biochemical characterization of novel syndromes of ketosis-prone diabetes (KPD) Parla, J. A comparative evaluation of SNP discovery in human whole exome sequence data versus human whole genome sequence data Phan, L. dbSNP and dbVar—NCBI databases of simple and structural variations Quinlan, A.R. The landscape of functional mutation in the human exome Reid, J. miRNA precursor variants and their possible effects on expression and function Repo, S. CAGI—The Critical Assessment of Genome Interpretation, a community experiment to evaluate phenotype prediction Ross, M. An approach to clinical interpretive tools for whole genome sequencing Sabo, A. The ARRA autism sequencing collaboration, Phase 1—Deep whole exome sequencing in 1000 autism cases and 1000 matched controls Saito, T.L. Managing genome databases with UTGB Toolkit Sen, S.K. Transcriptome profiling of cardiovascular disease by massively parallel short-read DNA sequencing Shah, A. Massively parallel screening of genetic alterations in common cancers Stong, N.E. Telomere analysis using next-gen sequence data Swan, M. The application of genome-wide association studies of aging in a patient-driven clinical trial West, J. Whole-genome sequencing of a family of four—Educational and ethical perspectives White, L.D. The emerging role of core sequencing facilities in the personal genomes era Xing, E.P. Exploiting a hierarchical clustering tree of gene-expression traits in eQTL analysis Xing, E.P. Leveraging genetic interaction networks for joint mapping of marginal and epistatic eQTLs Xing, E.P. MoGUL—Detecting common insertions and deletions in a population Yan, J. Using genetic information in risk prediction for alcohol dependence in the Collaborative Study on the Genetics of Alcoholism GWAS sample Yu, F. Low coverage personal genomics enabled by an integrative SNP pipeline

As many members of the NGS blogosphere are aware, CSHL has implemented some strict rules of blogging while at their meetings. Thus, I’m likely signing off until next week, when I’ll post a full report.