Genome-Wide Analysis of the Odorant-Binding Protein Gene Family in Drosophila melanogaster

Olfaction is of considerable importance to many insects in behaviors critical for survival and reproduction, including location of food sources, selection of mates, recognition of colony con-specifics, and determination of oviposition sites. An ubiquitous, but poorly understood, component of the insect's olfactory system is a group of odorant-binding proteins (OBPs) that are present at high concentrations in the aqueous lymph surrounding the dendrites of olfactory receptor neurons. OBPs are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Here we show that the Drosophila genome carries 51 potential OBP genes, a number comparable to that of its odorant-receptor genes. We find that the majority (73%) of these OBP-like genes occur in clusters of as many as nine genes, in contrast to what has been observed for the Drosophila odorant-receptor genes. Two of the presumptive OBP gene clusters each carries an odorant-receptor gene. We also report an intriguing subfamily of 12 putative OBPs that share a unique C-terminal structure with three conserved cysteines and a conserved proline. Members of this subfamily have not previously been described for any insect. We have performed phylogenetic analyses of the OBP-related proteins in Drosophila as well as other insects, and we discuss the duplication and divergence of the genes for this large family. [The sequence data from this study have been submitted to FlyBase. Annotations for these sequences are available as supplementary material at http://www.genome.org.

Blood collection in cell-stabilizing tubes does not impact germline DNA quality for pediatric patients.

Liquid biopsy technologies allow non-invasive tumor profiling for patients with solid tumor malignancies by sequencing circulating tumor DNA. These studies may be useful in risk-stratification, monitoring for relapse, and understanding tumor evolution. The quality of DNA obtained for these studies is improved when blood samples are collected in tubes that stabilizing white blood cells (WBC). However, ongoing germline research in pediatric oncology generally requires obtaining blood samples in EDTA tubes, which do not contain a WBC-stabilizing preservative. In this study, we explored whether blood samples collected in WBC-stabilizing tubes could be used for both liquid biopsy and germline studies simultaneously, minimizing blood collection volumes for pediatric patients.Blood was simultaneously collected from three patients in both EDTA and Streck Cell-Free DNA BCT® tubes. Germline DNA was extracted from all blood samples and subjected to whole-exome sequencing and microarray profiling.Quality control metrics of DNA quality, sequencing library preperation and whole-exome sequencing alignment were virtually identical regardless of the sample collection method. There was no discernable difference in patterns of variant calling for paired samples by either whole-exome sequencing or microarray analysis.Our study demonstrates that high-quality genomic studies may be performed from germline DNA obtained in Streck tubes. Therefore, these tubes may be used to simultaneously obtain samples for both liquid biopsy and germline studies in pediatric patients when the volume of blood available for research studies may be limited

Mutation pattern is not effected by sample collection.

<p><b>(A-B)</b> Lego plot of single-nucleotide variants plotted by sequence context for variants with allelic fractions > 0.05 and < 0.95. Samples collected in <b>A)</b> EDTA tubes and <b>B)</b> Streck tubes were combined and plots show the sum of the three samples.</p

DNA extraction and sequencing metrics.

<p>DNA extraction and sequencing metrics.</p

Microarray results.

<p>Microarray results.</p

Sequencing coverage is not effected by sample collection tube.

<p><b>(A-B)</b> Box plots of the read coverage for target regions binned by GC content for samples collected in <b>A)</b> EDTA tubes or <b>B)</b> Streck tubes. For all box plots, the central box indicates values in the range 25^th-75^th percentile of all values for that subset of data with the central line indicating the median. Whiskers extend 1.5x from the lower and upper boundaries of the central box with points outside that range indicated as black circles.</p

WES variant calls.

<p>WES variant calls.</p