Publication Watch: In Early 2013, Nice Flow of New Papers from DNAnexus Users - Inside DNAnexus

It’s been awhile since we checked in on publications using DNAnexus, so we headed over to PubMed to provide an update. With so many great new papers coming out — more than 10 just in the past few months — we wanted to take the opportunity to look at a few of them and see how they’re making use of DNAnexus.

In the Journal of Medical Genetics, scientists from Hebrew University Medical Center and colleagues at other organizations published a paper entitled “Agenesis of corpus callosum and optic nerve hypoplasia due to mutations in SLC25A1 encoding the mitochondrial citrate transporter” (published online February 2013). Lead author Simon Edvardson et al. report on the first known patient with agenesis of corpus callosum caused by a mitochondrial citrate carrier deficiency. The team performed exome sequencing and used DNAnexus for read alignment and variant calling. Two pathogenic variants were found in a gene responsible for the mitochondrial citrate transporter, and functional studies in yeast validated the findings by displaying the same biomolecular effects of the mutated proteins.

In the January issue of Antimicrobial Agents and Chemotherapy, a journal from the American Society for Microbiology, a research team from Georgetown University Medical Center and the Institute of Microbiology in Beijing released a paper called “Azole Susceptibility and Transcriptome Profiling in Candida albicans Mitochondrial Electron Transport Chain Complex I Mutants.” In the study, the authors looked at how mitochondrial changes in yeast alter susceptibility to certain azole compounds commonly used as antifungal agents. As part of the effort, the team used RNA-seq to generate a transcriptome profile of two mutants known to increase susceptibility to azoles. Data analysis was conducted through DNAnexus. The scientists found that both mutants showed downregulation of transporter genes that encode efflux proteins, a mechanism thought to be linked to the cell energy required for azole susceptibility.

In the journal Human Mutation, a paper entitled “A Deletion Mutation in TMEM38B Associated with Autosomal Recessive Osteogenesis Imperfecta” (published online in January) comes from a research group at Ben Gurion University and the Soroka Medical Center, both in Israel. The scientists studied patients with autosomal recessive osteogenesis imperfecta, or brittle bone disease, which could not be explained by any previously known mutation. The team used genome-wide linkage analysis and whole exome sequencing to identify a single mutation common to all three patients: a homozygous deletion mutation of an exon in TMEM38B. Sequence read alignment, variant calling, and annotation were done with DNAnexus tools.

Finally, a paper published early online in February in the journal Case Reports in Genetics called “Targeted Next-generation Re-sequencing of F5 gene Identifies Novel Multiple Variants Pattern in Severe Hereditary Factor V Deficiency“ comes from a group that used DNAnexus for data quality, exome coverage, and exome-wide SNP/indel analysis. The authors — scientists from Pennsylvania State University and MS Hershey Medical Center — present a study of four people with severe factor V deficiency in which they used next-gen sequencing to study the factor V gene locus. They found five coding mutations and 75 noncoding variants, including three missense mutations previously associated with other factor V phenotypes.