Statistical challenges arising from genome resequencing

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Workshop theme

This tutorial session precedes a research workshop on genome resequencing starting in the afternoon at the Isaac Newton Institute. The tutorial session is self-contained and open to all, including individuals not registered for the research workshop. The aim of the tutorial session is to provide an introduction to resequencing data, some experimental techniques that exploit new sequencing technologies, and statistical and computational issues in interpreting the data. It is intended principally for those new to the field at the PhD or early RA level, some familiarity with genetics and genomics will be helpful. No advance registration is required and there is no charge to attend.

Please note that the Tutorial Sessions are seperate from the main Workshop and will take place at The Centre for Mathematical Sciences (CMS), adjacent to the Isaac Newton Institute.

Cheap, fast, sequencing platforms now allow near-complete genome sequences to be quickly and affordably obtained from individual members of any species. The DNA sequences of individual humans, their pathogens and model organisms will have an enormous impact on population genetics and evolutionary theory, as well as on epidemiology, particularly our understanding of infectious disease.

The motivation for the workshop is to bring together leading mathematical and biological researchers in an interdisciplinary environment to discuss the mathematical, statistical and computational challenges that lie ahead. We plan to discuss the most pressing open problems and the most promising avenues of future research necessary to deliver the full benefits of genome resequencing.

The workshop will consist of invited talks and contributed posters, as well as some social activities and opportunities for informal discussions. We plan to organise an introductory tutorial session on the Tuesday monrning, details to be confirmed. The topics for the invited talks will cover basecalling, sequence assembly, and mapping; imputation and inference of relatedness; cancer genomics and methylation; CNV/indels, RNA-seq, ChIP-seq and pathogens.

The mathematical techniques involved will be wide-ranging, including statistical and machine-learning techniques for high-dimensional classification and regression, as well as techniques from signal processing and various mathematical models of population genetics and evolutionary processes.

Timetable

Tuesday 13th July 2010
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
13:30 to 14:10	Peter Donnelly University of Oxford Whole-genome sequencing for medical and population genetics	Room 1
14:10 to 14:50	Mario Caccamo Biotechnology and Biological Sciences Research Council (BBSRC) Challenges behind crop resequencing	Room 1
14:50 to 15:30	Andy Clark Cornell University Modeling allele-specific expression from RNA-seq data	Room 1
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:30	Phil Green University of Washington Next-generation data analysis	Room 1
16:30 to 17:00	Raphael Irizarry Johns Hopkins University What the 1000 genomes project tells us about systematic bias and batch effects in sec-gen data	Room 1
17:00 to 17:30	Yun Song University of California, Berkeley Model-based base-calling and de novo error correction algorithms for short-read sequencing	Room 1
17:30 to 18:30	Welcome Wine Reception	No Room Required
18:45 to 19:15	Dinner at Fitzwilliam College	No Room Required

Wednesday 14th July 2010
09:00 to 09:30	Kees Albers University of Cambridge Calling small indels in the 1000 Genomes low-coverage and high-coverage pilots	Room 1
09:30 to 10:00	Efficient construction of overlap assemblies using suffix array based methods	Room 1
10:00 to 10:30	Reference-free analysis of genetic variation	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:30	Jonathan Marchini University of Oxford Genotype imputation with thousands of genomes	Room 1
11:30 to 12:00	Gonçalo Abecasis University of Michigan Sequencing 1000s of Human Genomes	Room 1
12:00 to 12:30	Augie Kong DeCode genetics Phasing SNPs and sequences	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
15:30 to 16:00	Poster session	Discussion Room
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:30	Peter Campbell Wellcome Trust Sanger Institute Analysis of whole cancer genomes	Room 1
16:30 to 17:00	Sohrab Shah BC Cancer Agency Statistical models for inference of SNVs in cancer genomes	Room 1
17:00 to 17:30	Thomas Down University of Cambridge Deconvolving the epigenome: analysis strategies for genome-wide studies	Room 1
18:45 to 19:15	Dinner at Fitzwilliam College	No Room Required
19:45 to 21:30	Formal poster session	Discussion Room

Thursday 15th July 2010
09:00 to 09:30	Joe Pickrell University of Chicago Understanding variation in mRNA processing with RNA sequencing	Room 1
09:30 to 10:00	Hui Jiang Stanford University Estimating Isoform-Specific Gene Expression Using Paired-End RNA-Seq	Room 1
10:00 to 10:30	John Marioni University of Chicago De novo assembly and evolutionary analyses of liver-expressed genes in 16 mammal species	Room 1
10:30 to 11:00	Morning Coffee	No Room Required
11:00 to 11:30	Geoff Faulkner University of Edinburgh Transposed element RNAs detected by massively parallel sequencing	Room 1
11:30 to 12:00	Lachlan Coin Imperial College London Integration of sequence and array data in a population and haplotype-based model of SNPs and CNVs	Room 1
12:00 to 12:30	Steven McCarroll Harvard University Population-based analysis of genome structural variation using broad, highly parallel population sequencing	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
15:30 to 16:00	Poster session	Discussion Room
15:30 to 16:00	Afternoon Tea	No Room Required
16:00 to 16:30	Julian Parkhill Wellcome Trust Sanger Institute Population genomics of bacterial pathogens	Room 1
16:30 to 17:00	Daniel Falush University College Cork Microevolutionary analysis of metagenomic data	Room 1
17:00 to 17:30	Dominic Kwiatkowski Wellcome Trust Sanger Institute Using next-gen sequencing to get at the genetic architecture and dynamics of Plasmodium falciparum populations	Room 1
19:30 to 22:00	Conference Dinner at Emmanuel College	No Room Required

Friday 16th July 2010
09:30 to 10:00	Tomi Pastinen McGill University Cis-regulatory SNPs (cis-rSNPs) altering transcription detected by allelic expression (AE) mapping	Room 1
10:00 to 10:30	Vincent Plagnol University College London Allele specific expression analysis using high throughput DNA sequencing	Room 1
10:30 to 11:00	Jen Taylor CSIRO Plant Industry Genome-wide characteristics of sequence coverage by next-generation sequencing: how does this impact interpretation?	Room 1
11:00 to 11:30	Morning Coffee	No Room Required
11:30 to 12:00	Raphael Gottardo Fred Hutchinson Cancer Research Centre A statistical framework for the analysis of ChIP-Seq data	Room 1
12:00 to 12:30	Duncan Odom Cancer Research UK Species specific transcription in mice carrying human chromosome 21	Room 1
12:30 to 13:00	Peter Park Harvard University Identification of enriched regions in ChIP-seq and whole-genome sequencing data	Room 1
13:00 to 13:30	Lunch at Wolfson Court	No Room Required

Speakers

Gonçalo Abecasis University of Michigan
Kees Albers University of Cambridge
Mario Caccamo Biotechnology and Biological Sciences Research Council (BBSRC)
Peter Campbell Wellcome Trust Sanger Institute
Andy Clark Cornell University
Lachlan Coin Imperial College London
Peter Donnelly University of Oxford
Thomas Down University of Cambridge
Daniel Falush University College Cork
Geoff Faulkner University of Edinburgh
Raphael Gottardo Fred Hutchinson Cancer Research Centre
Phil Green University of Washington
Raphael Irizarry Johns Hopkins University
Hui Jiang Stanford University
Augie Kong DeCode genetics
Dominic Kwiatkowski Wellcome Trust Sanger Institute
Jonathan Marchini University of Oxford
John Marioni University of Chicago
Steven McCarroll Harvard University
Duncan Odom Cancer Research UK
Peter Park Harvard University
Julian Parkhill Wellcome Trust Sanger Institute
Tomi Pastinen McGill University
Joe Pickrell University of Chicago
Vincent Plagnol University College London
Sohrab Shah BC Cancer Agency
Yun Song University of California, Berkeley
Jen Taylor CSIRO Plant Industry

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Statistical challenges arising from genome resequencing

Workshop theme

Timetable

Speakers

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