27 research outputs found
Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing
Background: Targeted next generation sequencing (NGS) technology to assess the mutational status of multiple genes on formalin-fixed, paraffin embedded (FFPE) tumors is rapidly being adopted in clinical settings, where quality control (QC) practices are required. Establishing reliable FFPE QC materials for NGS can be challenging and/or expensive. Here, we established a reliable and cost-effective FFPE QC material for routine utilization in the Ion AmpliSeqâ„¢ Cancer Hotspot Panel v2 (CHP2) assay.
Methods: The performance characteristics of the CHP2 assay were determined by sequencing various cell line mixtures and 55 different FFPE tumors on the Ion Torrent PGM platform. A FFPE QC material was prepared from a mixture of cell lines derived from different cancers, comprising single nucleotide variants and small deletions on actionable genes at different allelic frequencies. Results: The CHP2 assay performed with high precision and sensitivity when custom variant calling pipeline parameters where established. In addition, all expected somatic variants in the QC material were consistently called at variant frequencies ranging from 9.1 % (CV = 11.1 %) to 37.9 % (CV = 2.8 %).
Conclusions: The availability of a reliable and cost-effective QC material is instrumental in assessing the performance of this or any targeted NGS assay that detects somatic variants in fixed solid tumor specimens
Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing
Background Targeted next generation sequencing (NGS) technology to assess the mutational status of multiple genes on formalin-fixed, paraffin embedded (FFPE) tumors is rapidly being adopted in clinical settings, where quality control (QC) practices are required. Establishing reliable FFPE QC materials for NGS can be challenging and/or expensive. Here, we established a reliable and cost-effective FFPE QC material for routine utilization in the Ion AmpliSeq™ Cancer Hotspot Panel v2 (CHP2) assay. Methods The performance characteristics of the CHP2 assay were determined by sequencing various cell line mixtures and 55 different FFPE tumors on the Ion Torrent PGM platform. A FFPE QC material was prepared from a mixture of cell lines derived from different cancers, comprising single nucleotide variants and small deletions on actionable genes at different allelic frequencies. Results The CHP2 assay performed with high precision and sensitivity when custom variant calling pipeline parameters where established. In addition, all expected somatic variants in the QC material were consistently called at variant frequencies ranging from 9.1 % (CV = 11.1 %) to 37.9 % (CV = 2.8 %). Conclusions The availability of a reliable and cost-effective QC material is instrumental in assessing the performance of this or any targeted NGS assay that detects somatic variants in fixed solid tumor specimens
One of the closest exoplanet pairs to the 3:2 Mean Motion Resonance: K2-19b \& c
The K2 mission has recently begun to discover new and diverse planetary
systems. In December 2014 Campaign 1 data from the mission was released,
providing high-precision photometry for ~22000 objects over an 80 day timespan.
We searched these data with the aim of detecting further important new objects.
Our search through two separate pipelines led to the independent discovery of
K2-19b \& c, a two-planet system of Neptune sized objects (4.2 and 7.2
), orbiting a K dwarf extremely close to the 3:2 mean motion
resonance. The two planets each show transits, sometimes simultaneously due to
their proximity to resonance and alignment of conjunctions. We obtain further
ground based photometry of the larger planet with the NITES telescope,
demonstrating the presence of large transit timing variations (TTVs), and use
the observed TTVs to place mass constraints on the transiting objects under the
hypothesis that the objects are near but not in resonance. We then
statistically validate the planets through the \texttt{PASTIS} tool,
independently of the TTV analysis.Comment: 18 pages, 10 figures, accepted to A&A, updated to match published
versio
Planetary system LHS 1140 revisited with ESPRESSO and TESS
Context. LHS 1140 is an M dwarf known to host two transiting planets at orbital periods of 3.77 and 24.7 days. They were detected with HARPS and Spitzer. The external planet (LHS 1140 b) is a rocky super-Earth that is located in the middle of the habitable zone of this low-mass star. All these properties place this system at the forefront of the habitable exoplanet exploration, and it therefore constitutes a relevant case for further astrobiological studies, including atmospheric observations. Aims. We further characterize this system by improving the physical and orbital properties of the known planets, search for additional planetary-mass components in the system, and explore the possibility of co-orbitals. Methods. We collected 113 new high-precision radial velocity observations with ESPRESSO over a 1.5-yr time span with an average photon-noise precision of 1.07 m s-1. We performed an extensive analysis of the HARPS and ESPRESSO datasets and also analyzed them together with the new TESS photometry. We analyzed the Bayesian evidence of several models with different numbers of planets and orbital configurations. Results. We significantly improve our knowledge of the properties of the known planets LHS 1140 b (Pb ∼ 24.7 days) and LHS 1140 c (Pc ∼ 3.77 days). We determine new masses with a precision of 6% for LHS 1140 b (6.48 ± 0.46 Mpdbl) and 9% for LHS 1140 c (mc = 1.78 ± 0.17 Mpdbl). This reduces the uncertainties relative to previously published values by half. Although both planets have Earth-like bulk compositions, the internal structure analysis suggests that LHS 1140 b might be iron-enriched and LHS 1140 c might be a true Earth twin. In both cases, the water content is compatible to a maximum fraction of 10-12% in mass, which is equivalent to a deep ocean layer of 779 ± 650 km for the habitable-zone planet LHS 1140 b. Our results also provide evidence for a new planet candidate in the system (md = 4.8 ± 1.1Mpdbl) on a 78.9-day orbital period, which is detected through three independent methods. The analysis also allows us to discard other planets above 0.5 Mpdbl for periods shorter than 10 days and above 2 Mpdbl for periods up to one year. Finally, our co-orbital analysis discards co-orbital planets in the tadpole and horseshoe configurations of LHS 1140 b down to 1 Mpdbl with a 95% confidence level (twice better than with the previous HARPS dataset). Indications for a possible co-orbital signal in LHS 1140 c are detected in both radial velocity (alternatively explained by a high eccentricity) and photometric data (alternatively explained by systematics), however. Conclusions. The new precise measurements of the planet properties of the two transiting planets in LHS 1140 as well as the detection of the planet candidate LHS 1140 d make this system a key target for atmospheric studies of rocky worlds at different stellar irradiations.With funding from the Spanish government through the "MarÃa de Maeztu Unit of Excellence" accreditation (MDM-2017-0737
Quality control material for the detection of somatic mutations in fixed clinical specimens by next-generation sequencing
Evidence of a Functional Role for p21 Down- Regulation in Synergistic Antileukemic Interactions between the Histone Deacetylase Inhibitor Sodium Butyrate and Flavopiridol
ABSTRACT The functional significance of disruption of p21 WAF1/CIP1 induction by flavopiridol (FP) in human leukemia cells (Jurkat) exposed to the histone deacetylase (HDAC) inhibitor sodium butyrate (SB) was investigated. Coexposure of leukemic cells to FP blocked SB-mediated induction of p21 WAF1/CIP1 and resulted in a marked increase in mitochondrial injury, activation of procaspases-3 and -8, Bid cleavage, and PARP degradation. in Jurkat cells inducibly expressing p21 WAF1/CIP1 under the control of a doxycycline-responsive promoter) partially but significantly reduced cytochrome c and apoptosis-inducing factor release, loss of mitochondrial membrane potential, caspase-3 and -8 activation, Bid cleavage, poly(ADP-ribose)polymerase (PARP) degradation, and apoptosis in response to SB/FP. Furthermore, increasing expression of p21 WAF1/CIP1 (i.e., by culturing cells in the presence of higher concentrations of doxycycline) rendered cells more resistant to SB/FP-mediated lethality. Enforced expression of p21 WAF1/CIP1 did not modify SB/FP-mediated JNK activation or generation of reactive oxygen species. Consistent with these results, Jurkat cells stably expressing a p21 WAF1/CIP1 nuclear localization mutant (p21⌬NLS) were also resistant to SB/FP-mediated mitochondrial injury, activation of procaspases-3 and -8, PARP cleavage, and apoptosis. Finally, enforced expression of full-length or ectopic expression of ⌬NLS p21 WAF1/CIP1 increased the amount of p21 WAF1/CIP1 coimmunoprecipitating with procaspase-3. Together, these findings suggest that interruption of HDAC-mediated p21 WAF1/CIP