Tetralogy of Fallot (TOF) is the most common of cyanotic heart diseases. The authors used 114 TOF ‘trios’ (one proband and unaffected parents) and found 11 de novo copy number variants (CNVs) in probands that were absent/rare in 2265 controls. Found CNVs at chromosome 1q21 present in 1% of 512 sporadic, nonsyndromic TOF cases. Used Genome Analyzer to assess malformed right ventricular out?ow tract to show four possible genes that could be disease-associated.

High-throughput deep sequencing technology (Illumina/Solexa digital gene expression system (DGE)) was used to examine transcriptome changes caused by mycobacterium infection of zebrafish. Among other results they found that DGE data sets enabled detection of transcript isoform switching regulated by mycobacterium. They also found induced expression during infection of a number of novel gene products. This technique both confirmed and added to the knowledge gained from microarrays.

Micro RNAs (miRNAs) are involved in gene regulation. The authors used high-throughput sequencing (using GA) to build a small RNA library of sequences from 18 to 26 nt to examine miRNAs in Gossypium hirsutum (cotton) for the first time. Using the Genome Analyzer system, they sequenced nearly 1.4 million unique small RNAs and found 34 conserved miRNA families and eight conserved miRNA encoding loci.

To determine which strand is transcribed during high-throughput cDNA sequencing, the authors used a protocol that involved incorporating deoxy-UTP during second strand cDNA synthesis, and then destruction of the strand containing uridine in the sequencing library. They carried out paired-end sequencing using the Genome Analyzer system. Using Saccharomyces cerevisiae and mouse brain transcriptomes, it was found that knowledge of transcription orientation could identify new genes, examine promoter-associated and antisense transcription, and enable more accurate determination of gene structure and expression.

The authors investigated mouse brain cortex taken at embryonic day 18 (E18) and postnatal day 7 (P7). They identified mRNAs of >16,000 genes and found 3758 genes whose expression levels changed between these two periods, including some known to be associated with neurogenesis. The Illumina Genome Analyzer system was used for high-throughput sequencing, along with RMAP. This paper is particularly useful to show the differences in information gained between single- and paired-end reads.