Whole exome sequencing by high-throughput sequencing of target-enriched genomic DNA (exome-seq) has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. We present a comparison of three major commercial exome sequencing platforms from Agilent, Illumina and Nimblegen applied to the same human blood sample. Our results suggest that the Nimblegen platform,...

SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol. 2014 Sep;32(9):903-14. doi: 10.1038/nbt.2957. PMID:25150838  Dr. Rong Chen is in SEQC consortium. Here is the paper SEQC_NatBiotech. http://www.nature.com/nbt/journal/v32/n9/full/nbt.2957.html Abstract We present primary results from the Sequencing Quality Control (SEQC)...

Background The invention of high throughput sequencing technologies has led to the discoveries of hundreds of thousands of genetic variants associated with thousands of human diseases. Many of these genetic variants are located outside the protein coding regions, and as such, it is challenging to interpret the function of these genetic variants by traditional genetic approaches. Recent genome-wide functional genomics studies, such as FANTOM5...

The Resilience Project – Software The Resilience Project offers two software tools to the community to scan their sequencing or genotyping data for potential unexpected heroes. You can use these two Java tools to scan VCF and other files for 1) exact allele matches against the UHP core allele panel as well as 2) early terminations in a list of genes; from version 2 onwards, formats such as GFF, CNS, and samtools pileup calls will be...

2019 Glicksberg BS et al. Integrative analysis of loss-of-function variants in clinical and genomic data reveals novel genes associated with cardiovascular traits.  Supplementary Materials and Supplemental Tables revision 2018 Ayers KL, Benjamin S. Glicksberg BS, Garfield AS, Longerich S, White JA, Yang PW, Du L, Chittenden TW, Gulcher JR, Roy S, Fiedorek F, Gottesdiener K, Cohen S, North KE, Schadt EE, Li SD*, Chen R* and Van der Ploeg...