Genes residing in the chromosomal region suspected to be linked with the neurological disorder sensory/motor neuropathy with ataxia (SMNA) were investigated. Using massively parallel sequencing on the Genome Analyzer, and other methods of analysis, they found a nonsynonymous variant in the interferon-related developmental regulator gene 1 (IFRD1) in the suspect region (7q22-q32), which was not found in healthy controls. This gene is known to be localized to brain and spinal cord areas commonly affected in SNMA.

The authors used high-throughput phenotypic analysis, on the Genomye Analzyer, to examine whole genome variations in two yeast strains—Saccharomyces cerevisiae and S. paradoxus. They reported most of the genome sequences and found 235,127 SNPs and 14,051 indels in S. cerevisiae, 623,287 SNPs, 25,267 indels in S. paradoxus, along with 38 novel hypothetical open reading frames. They elucidated parallels between phylogenetic relationships and phenotypic variation, with a far broader variation in S. paradoxus than S. cerevisiae.

Amplification artifacts can cause duplicated sequences which can weight read coverage and effect genome assembly and variation analysis. To counter this, the authors utilized (G+C) poor, neutral, or rich genomes from Plasmodium falciparum, Escherichia coli, and Bordetella pertussis, respectively. They developed a library preparation method without PCR but with fully ligated template strands being enriched by the cluster amplification step of the Genome Analyzer II system. This improved SNP detection, especially for P. falciparum, simplified assembly, and speeded up experimentation time.

Mouse models of medulloblastomas (MBs) were used to investigate micro RNA (miRNA) contribution to tumor development. Nine miRNAs encoded by the miR-17 approximately 92 cluster (Oncomir-1) were shown to be overexpressed in cerebellar granule neuron progenitors, which some MBs originate from, as well as developing mouse cerebellum, but not in mature neurons. The authors used “Illumina sequencers” to sequence small RNAs linked to specific initiating mutations from post-natal day 6 and 1 month old mice in MB models.

The first complete sequence of a Fleckvieh breeding bull was carried out using predominantly 36-bp paired-end reads on the Genome Analyzer II. The authors covered 98% of the genome and identified 2.44 million single nucleotide polymorphisms (SNPs), 82% of which were novel, and 115,000 small indels, with a low false positive rate of 1.1%. Genotypes were determined using the BovineSNP50 BeacChip.