Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals

Abstract

Massively parallel sequencing technologies have identified a broad spectrum of human genome diversity. Here we deep sequenced and correlated 18 genomes and 17 transcriptomes of unrelated Korean individuals. This has allowed us to construct a genome-wide map of common and rare variants and also identify variants formed during DNA-RNA transcription. We identified 9.56 million genomic variants, 23.2% of which appear to be previously unidentified. From transcriptome sequencing, we discovered 4,414 transcripts not previously annotated. Finally, we revealed 1,809 sites of transcriptional base modification, where the transcriptional landscape is different from the corresponding genomic sequences, and 580 sites of allele-specific expression. Our findings suggest that a considerable number of unexplored genomic variants still remain to be identified in the human genome, and that the integrated analysis of genome and transcriptome sequencing is powerful for understanding the diversity and functional aspects of human genomic variants.

RNA Editing in RHOQ Promotes Invasion Potential in Colorectal Cancer

“…Genomewide detection of potential A-to-I editing site candidates in HCC was made possible by next-generation sequencing of the transcriptome Chen et al, 2013). Recent advances in transcriptome sequencing and bioinformatic analysis have facilitated identification of novel RNA editing sites (Ju et al, 2011;Li et al, 2011;Bahn et al, 2012;Ramaswami et al, 2013). These advances will promote future studies that will enhance our understanding of the role of RNA editing in cancer.…”

“…The RNA and whole-genome sequencing reads were aligned to the NCBI human reference genome assembly (build 36.1) using GSNAP (Wu and Nacu, 2010) with allowance for 5% mismatches. In the same manner, the RNA sequencing reads were also aligned to a cDNA set consisting of 161,250 mRNA sequences obtained from public databases (36,742 RefSeq,73,671 UCSC,and 161,214 Ensembl) to decrease the false positives and false negatives in variant detection from RNA sequencing data (Ju et al, 2011).…”

A Chimeric RNA Characteristic of Rhabdomyosarcoma in Normal Myogenesis Process

“…Paired-end sequencing was then conducted using Hiseq 2000 (Illumina). The 101-bp RNA-seq data were then analyzed as described previously ( 27 ). For the detection of fusion genes, we used defuse as described before ( 15 ).…”

RNA editing of protein sequences: A rare event in human transcriptomes

“…Until recently this mechanism that alters RNA sequences at specific sites was considered relatively rare in human cells, mainly restricted to brain-specific substrates and repetitive regions of the genome (Bass 2002). During the last years, however, the development of bioinformatics prediction tools (Levanon et al 2004) started to challenge this view, followed by the application of deep-sequencing approaches, which allow the study of this phenomenon at a genome-wide scale (Li et al 2009bBahn et al 2011;Ju et al 2011;Rosenberg et al 2011;Peng et al 2012;Ramaswami et al 2012). Current estimates range from several hundred (Li et al 2009b) to several thousand (Levanon et al 2004;Bahn et al 2011;Ju et al 2011;Li et al 2011;Peng et al 2012;Ramaswami et al 2012) edited sites throughout the genome, suggesting that RNA editing is an abundant process contributing greatly to complexity at both the transcriptome and the proteome levels.…”