Project description:We couple long-read sequence assembly, full-length cDNA sequencing, and a multi-platform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies where most genes are complete, gaps are closed, and novel gene models are identified. We further analyzed the overlap between structural variants in the human genome and gene expression differences in human and chimpanzee cells, including iPS-derived organoid radial glia cells.
Project description:We performed shallow whole genome sequencing (WGS) on circulating free (cf)DNA extracted from plasma or cerebrospinal fluid (CSF), and shallow WGS on the tissue DNA extracted from the biopsy in order to evaluate the correlation between the two biomaterials. After library construction and sequencing (Hiseq3000 or Ion Proton), copy number variations were called with WisecondorX.
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
Project description:Although Great Basin paleoclimate history has been examined for more than a century, the orbital-scale paleoclimate forcings remain poorly understood. Here we show - by a detailed phasing analysis of a well-dated stalagmite ?18O time series - that Great Basin paleoclimate is linearly related to, but lagged, the 23,000?yr precession cycle in northern hemisphere summer insolation by an average of 3240 years (-900 to 6600?yr range) over the last two glacial cycles. We interpret these lags as indicating that Great Basin climate is sensitive to and indirectly forced by changes in the cryosphere, as evidenced by fast and strong linkages to global ice volume and Arctic paleoclimate indicators. Mid-latitude atmospheric circulation was likely impacted by a northward shifted storm track and higher pressure over the region arising from decreased sea ice and snow cover. Because anthropogenic warming is expected to reduce northern hemisphere snow and ice cover, continued increase in atmospheric greenhouse gases is likely to result in warming and drying over coming centuries that will amplify a warming trend that began ~2400 years ago.
Project description:We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
Project description:We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
Project description:We evaluated linked-read whole genome sequencing (WGS) for detection of structural chromosomal rearrangements in primary samples of varying DNA quality from 12 patients diagnosed with ALL. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements, aneuploidy assessment and gene deletions. Additional RNA-sequencing and copy number aberrations (CNA) data from Illumina Infinium arrays were also generated and assessed against the linked-read WGS data. RNA-sequencing data was used to support structural chromosomal rearrangements detected in the linked-read WGS data by detecting expressed fusion genes as a consequence of the rearrangements. Illumina Infinium arrays (450k array and/or SNP array) were used to assess CNA status to further support the findings in the linked-read WGS data. The processed CNA data from the primary ALL patient samples has been deposited to GEO. RNA-sequencing, linked-read WGS data, and raw SNP array data from the primary ALL patient samples will not be deposited because the patient/parent consent does not cover depositing data that may be used for large-scale determination of germline variants in a repository. The ALL samples were collected 10-20 years ago from pediatric patients aged 2-15 years, some whom have deceased. The linked-read WGS data and the RNA-sequencing data sets generated in the study are available upon reasonable request from the corresponding author Jessica.Nordlund@medsci.uu.se.
Project description:In the spring of 2018, a 10-day field study was conducted in Colorado's Denver-Julesburg oil and natural gas production basin to improve information on well pad pneumatic controller (PC) populations and identify PCs with potential maintenance issues (MIs) causing excess emissions through a novel optical gas imaging (OGI) survey approach. A total of 500 natural gas-emitting PCs servicing 102 wells (4.9 PCs/well) were surveyed at 31 facilities operated by seven different companies. The PCs were characterized by their designed operational function and applications, with 83% of the PC population identified as intermittent PCs (IPCs). An OGI inspection protocol was used to investigate emissions on 447 working PCs from this set. OGI detected continuous emissions from 11.3% of observed IPCs and these were classified as experiencing some level of MIs. OGI imaging modes were observed to have a significant effect on emission detectability with high sensitivity mode detection rates being approximately 2 times higher compared to auto mode. Fourteen snapshot emission measurements (not including actuations) were conducted on IPCs in this category using a high-volume sampling device with augmented quality assurance procedures with observed emissions rates ranging from 0.1 up to 31.3 scf/hr (mean = 2.8 scf/hr). For PCs with continuous depressurization type (CPC), 36.8% had continuous emissions observed by OGI. Four supporting emission measurements were conducted on CPCs with one unit exceeding the low bleed regulatory emission threshold with an emission rate of 9.9 scf/hr (mean = 4.2 scf/hr). Additional information was collected on PC actuation events, as observed with OGI, which showed a strong correlation between observed actuation events and facility production compared to observed continuous emissions caused by MIs which did not correlate with facility production.Implications: A novel survey approach of pneumatic controllers at oil and natural gas production facilities in the Denver-Julesburg basin, using optical gas imaging and supporting emission measurements, was demonstrated as an effective method to identify controllers with potential maintenance issues causing excess emissions. The results of the pneumatic controller and optical gas imaging surveys improved information on pneumatic controller populations within the basin and also demonstrated the significant effect optical gas imaging modes have on emission detections.
Project description:Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.