17 research outputs found
The Characterization of Twenty Sequenced Human Genomes
We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs) discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways
A Search for Technosignatures Around 11,680 Stars with the Green Bank Telescope at 1.15-1.73 GHz
We conducted a search for narrowband radio signals over four observing
sessions in 2020-2023 with the L-band receiver (1.15-1.73 GHz) of the 100 m
diameter Green Bank Telescope. We pointed the telescope in the directions of 62
TESS Objects of Interest, capturing radio emissions from a total of ~11,680
stars and planetary systems in the ~9 arcminute beam of the telescope. All
detections were either automatically rejected or visually inspected and
confirmed to be of anthropogenic nature. In this work, we also quantified the
end-to-end efficiency of radio SETI pipelines with a signal injection and
recovery analysis. The UCLA SETI pipeline recovers 94.0% of the injected
signals over the usable frequency range of the receiver and 98.7% of the
injections when regions of dense RFI are excluded. In another pipeline that
uses incoherent sums of 51 consecutive spectra, the recovery rate is ~15 times
smaller at ~6%. The pipeline efficiency affects calculations of transmitter
prevalence and SETI search volume. Accordingly, we developed an improved Drake
Figure of Merit and a formalism to place upper limits on transmitter prevalence
that take the pipeline efficiency and transmitter duty cycle into account.
Based on our observations, we can state at the 95% confidence level that fewer
than 6.6% of stars within 100 pc host a transmitter that is detectable in our
search (EIRP > 1e13 W). For stars within 20,000 ly, the fraction of stars with
detectable transmitters (EIRP > 5e16 W) is at most 3e-4. Finally, we showed
that the UCLA SETI pipeline natively detects the signals detected with AI
techniques by Ma et al. (2023).Comment: 22 pages, 9 figures, submitted to AJ, revise
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Mapping copy number variation by population-scale genome sequencing.
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies
Mapping copy number variation by population-scale genome sequencing
Genomic structural variants (SVs) are abundant in humans, differing from other forms of variation in extent, origin and functional impact. Despite progress in SV characterization, the nucleotide resolution architecture of most SVs remains unknown. We constructed a map of unbalanced SVs (that is, copy number variants) based on whole genome DNA sequencing data from 185 human genomes, integrating evidence from complementary SV discovery approaches with extensive experimental validations. Our map encompassed 22,025 deletions and 6,000 additional SVs, including insertions and tandem duplications. Most SVs (53%) were mapped to nucleotide resolution, which facilitated analysing their origin and functional impact. We examined numerous whole and partial gene deletions with a genotyping approach and observed a depletion of gene disruptions amongst high frequency deletions. Furthermore, we observed differences in the size spectra of SVs originating from distinct formation mechanisms, and constructed a map of SV hotspots formed by common mechanisms. Our analytical framework and SV map serves as a resource for sequencing-based association studies. © 2011 Macmillan Publishers Limited. All rights reserved.Link_to_subscribed_fulltex