56 research outputs found
Comprehensive characterization of PTEN mutational profile in a series of 34,129 colorectal cancers
Loss of expression or activity of the tumor suppressor PTEN acts similarly to an activating mutation in the oncogene PIK3CA in elevating intracellular levels of phosphatidylinositol (3,4,5)-trisphosphate (PIP3), inducing signaling by AKT and other pro-tumorigenic signaling proteins. Here, we analyze sequence data for 34,129 colorectal cancer (CRC) patients, capturing 3,434 PTEN mutations. We identify specific patterns of PTEN mutation associated with microsatellite stability/instability (MSS/MSI), tumor mutational burden (TMB), patient age, and tumor location. Within groups separated by MSS/MSI status, this identifies distinct profiles of nucleotide hotspots, and suggests differing profiles of protein-damaging effects of mutations. Moreover, discrete categories of PTEN mutations display non-identical patterns of co-occurrence with mutations in other genes important in CRC pathogenesis, including KRAS, APC, TP53, and PIK3CA. These data provide context for clinical targeting of proteins upstream and downstream of PTEN in distinct CRC cohorts.Loss of the tumour suppressor gene PTEN leads to the activation of pro-tumourigenic signalling pathways. Here, the authors analyse sequencing data from a large cohort of colorectal cancer patients harbouring PTEN mutations and identify distinct patterns of associations with genomic and clinical features
Spectroscopic Target Selection in the Sloan Digital Sky Survey: The Quasar Sample
We describe the algorithm for selecting quasar candidates for optical
spectroscopy in the Sloan Digital Sky Survey. Quasar candidates are selected
via their non-stellar colors in "ugriz" broad-band photometry, and by matching
unresolved sources to the FIRST radio catalogs. The automated algorithm is
sensitive to quasars at all redshifts lower than z=5.8. Extended sources are
also targeted as low-redshift quasar candidates in order to investigate the
evolution of Active Galactic Nuclei (AGN) at the faint end of the luminosity
function. Nearly 95% of previously known quasars are recovered (based on 1540
quasars in 446 square degrees). The overall completeness, estimated from
simulated quasars, is expected to be over 90%, whereas the overall efficiency
(quasars:quasar candidates) is better than 65%. The selection algorithm targets
ultraviolet excess quasars to i^*=19.1 and higher-redshift (z>3) quasars to
i^*=20.2, yielding approximately 18 candidates per square degree. In addition
to selecting ``normal'' quasars, the design of the algorithm makes it sensitive
to atypical AGN such as Broad Absorption Line quasars and heavily reddened
quasars.Comment: 62 pages, 15 figures (8 color), 8 tables. Accepted by AJ. For a
version with higher quality color figures, see
http://archive.stsci.edu/sdss/quasartarget/RichardsGT_qsotarget.preprint.p
Photometric Redshifts of Quasars
We demonstrate that the design of the Sloan Digital Sky Survey (SDSS) filter
system and the quality of the SDSS imaging data are sufficient for determining
accurate and precise photometric redshifts (``photo-z''s) of quasars. Using a
sample of 2625 quasars, we show that photo-z determination is even possible for
z<=2.2 despite the lack of a strong continuum break that robust photo-z
techniques normally require. We find that, using our empirical method on our
sample of objects known to be quasars, approximately 70% of the photometric
redshifts are correct to within delta z = 0.2; the fraction of correct
photometric redshifts is even better for z>3. The accuracy of quasar
photometric redshifts does not appear to be dependent upon magnitude to nearly
21st magnitude in i'. Careful calibration of the color-redshift relation to
21st magnitude may allow for the discovery of on the order of 10^6 quasars
candidates in addition to the 10^5 quasars that the SDSS will confirm
spectroscopically. We discuss the efficient selection of quasar candidates from
imaging data for use with the photometric redshift technique and the potential
scientific uses of a large sample of quasar candidates with photometric
redshifts.Comment: 29 pages, 8 figures, submitted to A
High-Redshift Quasars Found in Sloan Digital Sky Survey Commissioning Data II: The Spring Equatorial Stripe
This is the second paper in a series aimed at finding high-redshift quasars
from five-color (u'g'r'i'z') imaging data taken along the Celestial Equator by
the Sloan Digital Sky Survey (SDSS) during its commissioning phase. In this
paper, we present 22 high-redshift quasars (z>3.6) discovered from ~250 deg^2
of data in the spring Equatorial Stripe, plus photometry for two previously
known high-redshift quasars in the same region of sky. Our success rate of
identifying high-redshift quasars is 68%. Five of the newly discovered quasars
have redshifts higher than 4.6 (z=4.62, 4.69, 4.70, 4.92 and 5.03). All the
quasars have i* < 20.2 with absolute magnitude -28.8 < M_B < -26.1 (h=0.5,
q_0=0.5). Several of the quasars show unusual emission and absorption features
in their spectra, including an object at z=4.62 without detectable emission
lines, and a Broad Absorption Line (BAL) quasar at z=4.92.Comment: 28 pages, AJ in press (Jan 2000), final version with minor changes;
high resolution finding charts available at
http://www.astro.princeton.edu/~fan/paper/qso2.htm
Weak Lensing with SDSS Commissioning Data: The Galaxy-Mass Correlation Function To 1/h Mpc
(abridged) We present measurements of galaxy-galaxy lensing from early
commissioning imaging data from the Sloan Digital Sky Survey (SDSS). We measure
a mean tangential shear around a stacked sample of foreground galaxies in three
bandpasses out to angular radii of 600'', detecting the shear signal at very
high statistical significance. The shear profile is well described by a
power-law. A variety of rigorous tests demonstrate the reality of the
gravitational lensing signal and confirm the uncertainty estimates. We
interpret our results by modeling the mass distributions of the foreground
galaxies as approximately isothermal spheres characterized by a velocity
dispersion and a truncation radius. The velocity dispersion is constrained to
be 150-190 km/s at 95% confidence (145-195 km/s including systematic
uncertainties), consistent with previous determinations but with smaller error
bars. Our detection of shear at large angular radii sets a 95% confidence lower
limit , corresponding to a physical radius of
kpc, implying that galaxy halos extend to very large radii. However, it is
likely that this is being biased high by diffuse matter in the halos of groups
and clusters. We also present a preliminary determination of the galaxy-mass
correlation function finding a correlation length similar to the galaxy
autocorrelation function and consistency with a low matter density universe
with modest bias. The full SDSS will cover an area 44 times larger and provide
spectroscopic redshifts for the foreground galaxies, making it possible to
greatly improve the precision of these constraints, measure additional
parameters such as halo shape, and measure the properties of dark matter halos
separately for many different classes of galaxies.Comment: 28 pages, 11 figures, submitted to A
The Sloan Digital Sky Survey Quasar Catalog I. Early Data Release
We present the first edition of the Sloan Digital Sky Survey (SDSS) Quasar
Catalog. The catalog consists of the 3814 objects (3000 discovered by the SDSS)
in the initial SDSS public data release that have at least one emission line
with a full width at half maximum larger than 1000 km/s, luminosities brighter
than M_i^* = -23, and highly reliable redshifts. The area covered by the
catalog is 494 square degrees; the majority of the objects were found in SDSS
commissioning data using a multicolor selection technique. The quasar redshifts
range from 0.15 to 5.03. For each object the catalog presents positions
accurate to better than 0.2" rms per coordinate, five band (ugriz) CCD-based
photometry with typical accuracy of 0.05 mag, radio and X-ray emission
properties, and information on the morphology and selection method. Calibrated
spectra of all objects in the catalog, covering the wavelength region 3800 to
9200 Angstroms at a spectral resolution of 1800-2100, are also available. Since
the quasars were selected during the commissioning period, a time when the
quasar selection algorithm was undergoing frequent revisions, the sample is not
homogeneous and is not intended for statistical analysis.Comment: 27 pages, 4 figures, 4 tables, accepted by A
Colors of 2625 Quasars at 0<z<5 Measured in the Sloan Digital Sky Survey Photometric System
We present an empirical investigation of the colors of quasars in the Sloan
Digital Sky Survey (SDSS) photometric system. The sample studied includes 2625
quasars with SDSS photometry. The quasars are distributed in a 2.5 degree wide
stripe centered on the Celestial Equator covering square degrees.
Positions and SDSS magnitudes are given for the 898 quasars known prior to SDSS
spectroscopic commissioning. New SDSS quasars represent an increase of over
200% in the number of known quasars in this area of the sky. The ensemble
average of the observed colors of quasars in the SDSS passbands are well
represented by a power-law continuum with (). However, the contributions of the bump
and other strong emission lines have a significant effect upon the colors. The
color-redshift relation exhibits considerable structure, which may be of use in
determining photometric redshifts for quasars. The range of colors can be
accounted for by a range in the optical spectral index with a distribution
(95% confidence), but there is a red tail in the
distribution. This tail may be a sign of internal reddening. Finally, we show
that there is a continuum of properties between quasars and Seyfert galaxies
and we test the validity of the traditional division between the two classes of
AGN.Comment: 66 pages, 15 figures (3 color), accepted by A
Sloan Digital Sky Survey Imaging of Low Galactic Latitude Fields: Technical Summary and Data Release
The Sloan Digital Sky Survey (SDSS) mosaic camera and telescope have obtained
five-band optical-wavelength imaging near the Galactic plane outside of the
nominal survey boundaries. These additional data were obtained during
commissioning and subsequent testing of the SDSS observing system, and they
provide unique wide-area imaging data in regions of high obscuration and star
formation, including numerous young stellar objects, Herbig-Haro objects and
young star clusters. Because these data are outside the Survey regions in the
Galactic caps, they are not part of the standard SDSS data releases. This paper
presents imaging data for 832 square degrees of sky (including repeats), in the
star-forming regions of Orion, Taurus, and Cygnus. About 470 square degrees are
now released to the public, with the remainder to follow at the time of SDSS
Data Release 4. The public data in Orion include the star-forming region NGC
2068/NGC 2071/HH24 and a large part of Barnard's loop.Comment: 31 pages, 9 figures (3 missing to save space), accepted by AJ, in
press, see http://photo.astro.princeton.edu/oriondatarelease for data and
paper with all figure
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