The Habitable Zone Planet Finder Reveals a High Mass and Low Obliquity for the Young Neptune K2-25b

Using radial velocity data from the Habitable Zone Planet Finder, we have measured the mass of the Neptune-sized planet K2-25b, as well as the obliquity of its M4.5 dwarf host star in the 600–800 Myr Hyades cluster. This is one of the youngest planetary systems for which both of these quantities have been measured and one of the very few M dwarfs with a measured obliquity. Based on a joint analysis of the radial velocity data, time-series photometry from the K2 mission, and new transit light curves obtained with diffuser-assisted photometry, the planet's radius and mass are 3.44 ± 0.12 R_⊕ and 24.5_(-5.2)^(+5.7) M_⊕. These properties are compatible with a rocky core enshrouded by a thin hydrogen–helium atmosphere (5% by mass). We measure an orbital eccentricity of e = 0.43 ± 0.05. The sky-projected stellar obliquity is λ = 3° ± 16°, compatible with spin–orbit alignment, in contrast to other "hot Neptunes" that have been studied around older stars

The Habitable-zone Planet Finder Reveals A High Mass and a Low Obliquity for the Young Neptune K2-25b

Using radial-velocity data from the Habitable-zone Planet Finder, we have measured the mass of the Neptune-sized planet K2-25b, as well as the obliquity of its M4.5-dwarf host star in the 600-800MYr Hyades cluster. This is one of the youngest planetary systems for which both of these quantities have been measured, and one of the very few M dwarfs with a measured obliquity. Based on a joint analysis of the radial velocity data, time-series photometry from the K2 mission, and new transit light curves obtained with diffuser-assisted photometry, the planet's radius and mass are $3.44\pm 0.12 \mathrm{R_\oplus}$ and $24.5_{-5.2}^{+5.7} \mathrm{M_\oplus}$. These properties are compatible with a rocky core enshrouded by a thin hydrogen-helium atmosphere (5% by mass). We measure an orbital eccentricity of $e=0.43 \pm 0.05$. The sky-projected stellar obliquity is $\lambda=3 \pm 16^{\circ}$, compatible with spin-orbit alignment, in contrast to other "hot Neptunes" that have been studied around older stars.Comment: Accepted for publication in AJ, 31 pages, 14 figure

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.

Sequencing bacterial genomes from DNA isolated directly from clinical samples offers the promise of rapid and precise acquisition of informative genetic information. In the case of Chlamydia trachomatis, direct sequencing is particularly desirable because it obviates the requirement for culture in mammalian cells, saving time, cost and the possibility of missing low abundance strains. In this proof of concept study, we developed methodology that would allow genome-scale direct sequencing, using a multiplexed microdroplet PCR enrichment technology to amplify a 100 kb region of the C. trachomatis genome with 500 1.1-1.3 kb overlapping amplicons (5-fold amplicon redundancy). We integrated comparative genomic data into a pipeline to preferentially select conserved sites for amplicon design. The 100 kb target region could be amplified from clinical samples, including remnants from diagnostics tests, originating from the cervix, urethra and urine, For rapid analysis of these data, we developed a framework for whole-genome based genotyping called binstrain. We used binstrain to estimate the proportion of SNPs originating from 14 C. trachomatis reference serotype genomes in each sample. Direct DNA sequencing methods such as the one described here may have an important role in understanding the biology of C. trachomatis mixed infections and the natural genetic variation of the species within clinically relevant ecological niches

Direct Amplification, Sequencing and Profiling of <i>Chlamydia trachomatis</i> Strains in Single and Mixed Infection Clinical Samples

<div><p>Sequencing bacterial genomes from DNA isolated directly from clinical samples offers the promise of rapid and precise acquisition of informative genetic information. In the case of <i>Chlamydia trachomatis</i>, direct sequencing is particularly desirable because it obviates the requirement for culture in mammalian cells, saving time, cost and the possibility of missing low abundance strains. In this proof of concept study, we developed methodology that would allow genome-scale direct sequencing, using a multiplexed microdroplet PCR enrichment technology to amplify a 100 kb region of the <i>C. trachomatis</i> genome with 500 1.1–1.3 kb overlapping amplicons (5-fold amplicon redundancy). We integrated comparative genomic data into a pipeline to preferentially select conserved sites for amplicon design. The 100 kb target region could be amplified from clinical samples, including remnants from diagnostics tests, originating from the cervix, urethra and urine, For rapid analysis of these data, we developed a framework for whole-genome based genotyping called <i>binstrain</i>. We used <i>binstrain</i> to estimate the proportion of SNPs originating from 14 <i>C. trachomatis</i> reference serotype genomes in each sample. Direct DNA sequencing methods such as the one described here may have an important role in understanding the biology of <i>C. trachomatis</i> mixed infections and the natural genetic variation of the species within clinically relevant ecological niches.</p></div

Phylogeny of 100

<p>Tree calculated in the same manner as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099290#pone-0099290-g002" target="_blank">Figure 2</a> but instead based on the 100 kb region of the <i>C. trachomatis</i> genome selected for targeted amplification. The colors are the same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099290#pone-0099290-g003" target="_blank">Figure 3</a>.</p

Primer design strategy.

<p>Diverse <i>C. trachomatis</i> genomes were aligned using Whole Genome Alignment (WGA) software against the <i>C. trachomatis D/UW3/CX</i> reference sequence and SNPs (hash lines) were identified (a small number of indels were also identified but were omitted from the figure to make it simpler). The genome was divided into 100 bp blocks. Blocks with a threshold of two or more SNPs are labeled in black and correspond to gray regions in the genome). Starts and ends for primers (amplicon regions in dashed lines) were designed to avoid variable blocks (the black portions of the barcode). Primers were designed to allow approximately 5-fold overlapping amplicon coverage.</p

Summary of <i>binstrain</i> analysis of selected gDNA and clinical sample data.

<p>Format is the same as <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099290#pone-0099290-g002" target="_blank">Figure 2</a>. Note that for a potential mixed infection, we would not be able to currently distinguish between multiple the presence of recombinant and non-recombinant strains, just the proportion of the genotype specific SNPs represented by the <b>β</b> values.</p