Current Data And Future Analysis

Thomas Wieland, Thomas Schwarzmayr and Tim M Strom

Helmholtz Zentrum München Institute of Human Genetics

Geneva, 16/04/12

Overview

1. Current Data

– mRNA

– miRNA

– Imputation

2. Future Analysis

– Variant Calling on mRNA Data

mRNA

Our 48 samples have on average 55M reads 88% mapped (BWA; reads trimmed to 50bp)

~4% of aligned reads intersect lincRNA (from UCSC)

miRNA

miRNA

miRNA31% (+- 13%) of reads overlapping with known miRNAs (UCSC)

Imputation

info value: “a measure of the relative statistical information about the SNP allele frequency from the imputed data” (Marchini, J., & Howie, B. Nature reviews. Genetics, 2010)

Variant Calling on mRNA Data

Illumina Pipeline

Alignment BWAReference genome

Variant calling SAMtools

Variant filter SAMtools / custom

Variant annotationUCSC gene tables

dbSNP

Database

Candidate genes Linkage information

Run statistics

Inheritance model

Base Quality

Alignment Statistics

Enrichment StatisticsRefSeq genes

lincRNA,miRNAs,...

Variant Calling on mRNA Data

Variant calling SAMtools

Variant filter SAMtools / custom

Variant annotationUCSC gene tables

dbSNP

Database

Candidate genes Linkage informationInheritance model

RefSeq genes

lincRNA,miRNAs,...

pre-aligned mRNA files

• Samples• Case-Controls• Homozygous-Heterozygous

• Type of variation

• SNV call quality

• dbSNP / HapMap• Average heterozygozity

Exome database• Genes• Cases• Controls• Quality• Annotation• dbSNP• HGMD• 1000 genomes• PolyPhen Prediction, ...

Variant Calling on mRNA Data

Possible analysis: mRNA calling vs. WG genotypes mRNA calling vs. Imputation RNA editing?

Recent discussions about amount: “widespread” (M. Li et al., Science 333, 53, 2011) vs. “very few” (Schrider et al., Plos One, 2011)

Can we find known sites from literature? (e.g. Li, J. B. et al. (2009). Genome-wide identification of human RNA editing sites by parallel DNA capturing and sequencing. Science, 324(5931), 1210-3.)