Page May2011

Progress report

Accomplishments in the last six months:

General:

• CNV detection in exome sequencing - developed R/C HMM script for finding windows with elevated or reduced read count in exon enriched sequencing data. (with Stefan Haas)
• Applied algorithm to XLID patients (project in collaboration with Abt Ropers, MPI-MG) to provide short candidate list of large duplications and deletions. (with Stefan Haas, Abt Ropers, et al)
• Enrichment coverage analysis of XLID project - provided figures for paper on enrichment statistics across patients, per-gene enrichment analysis (coverage against target overlap, mapability and GC-content).
• Use of the distance covariance for gene-gene or histone-histone interactions (with Julia Lasserre). Simulations of variance stabilizations for correlated count data.

Ongoing data analysis projects:

• Compare CNV detection with existing algorithms, using different enrichment protocols as background, simulate lower read counts, heterozygous CNV

Goals for the next six months

• Examine variance and artifacts in read count data (ChIPSeq, RNASeq)
• Examine the background read depth from DNAse I HS data from ENCODE project
• Extend the HMM script to find significantly elevanted reads after accounting for position-specific covariates

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