Horizontal Well Placement Optimization in Gas Reservoirs Using Genetic Algorithms

Horizontal well placement determination within a reservoir is a significant and difficult step in the reservoir development process. Determining the optimal well location is a complex problem involving many factors including geological considerations, reservoir and fluid properties, economic costs, lateral direction, and technical ability. The most thorough approach to this problem is that of an exhaustive search, in which a simulation is run for every conceivable well position in the reservoir. Although thorough and accurate, this approach is typically not used in real world applications due to the time constraints from the excessive number of simulations. This project suggests the use of a genetic algorithm applied to the horizontal well placement problem in a gas reservoir to reduce the required number of simulations. This research aims to first determine if well placement optimization is even necessary in a gas reservoir, and if so, to determine the benefit of optimization. Performance of the genetic algorithm was analyzed through five different case scenarios, one involving a vertical well and four involving horizontal wells. The genetic algorithm approach is used to evaluate the effect of well placement in heterogeneous and anisotropic reservoirs on reservoir recovery. The wells are constrained by surface gas rate and bottom-hole pressure for each case. This project's main new contribution is its application of using genetic algorithms to study the effect of well placement optimization in gas reservoirs. Two fundamental questions have been answered in this research. First, does well placement in a gas reservoir affect the reservoir performance? If so, what is an efficient method to find the optimal well location based on reservoir performance? The research provides evidence that well placement optimization is an important criterion during the reservoir development phase of a horizontal-well project in gas reservoirs, but it is less significant to vertical wells in a homogeneous reservoir. It is also shown that genetic algorithms are an extremely efficient and robust tool to find the optimal location

Horizontal Well Placement Optimization in Gas Reservoirs Using Genetic Algorithms

Horizontal well placement determination within a reservoir is a significant and difficult step in the reservoir development process. Determining the optimal well location is a complex problem involving many factors including geological considerations, reservoir and fluid properties, economic costs, lateral direction, and technical ability. The most thorough approach to this problem is that of an exhaustive search, in which a simulation is run for every conceivable well position in the reservoir. Although thorough and accurate, this approach is typically not used in real world applications due to the time constraints from the excessive number of simulations. This project suggests the use of a genetic algorithm applied to the horizontal well placement problem in a gas reservoir to reduce the required number of simulations. This research aims to first determine if well placement optimization is even necessary in a gas reservoir, and if so, to determine the benefit of optimization. Performance of the genetic algorithm was analyzed through five different case scenarios, one involving a vertical well and four involving horizontal wells. The genetic algorithm approach is used to evaluate the effect of well placement in heterogeneous and anisotropic reservoirs on reservoir recovery. The wells are constrained by surface gas rate and bottom-hole pressure for each case. This project's main new contribution is its application of using genetic algorithms to study the effect of well placement optimization in gas reservoirs. Two fundamental questions have been answered in this research. First, does well placement in a gas reservoir affect the reservoir performance? If so, what is an efficient method to find the optimal well location based on reservoir performance? The research provides evidence that well placement optimization is an important criterion during the reservoir development phase of a horizontal-well project in gas reservoirs, but it is less significant to vertical wells in a homogeneous reservoir. It is also shown that genetic algorithms are an extremely efficient and robust tool to find the optimal location

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Abstract 15628: HeartCare: Improving Clinical Practice Through Comprehensive Cardiovascular Genetic Testing

Introduction:Cardiovascular disease (CVD) is the leading cause of mortality in the United States, leading to one in four deaths. The role of inherited susceptibility to CVD is well established, from rare monogenic disorders to polygenic traits. For many of these conditions, guidelines exist for medical interventions and other preventative care that can improve outcomes and quality of life.Methods:We developed a comprehensive genetic screen, "HeartCare", consisting of a 158 gene panel evaluating 1) Mendelian conditions including cardiomyopathies, aortopathies, arrhythmias, and dyslipidemias, 2) a coronary artery disease polygenic risk score (PRS), 3) variants in the LPA gene encoding Lipoprotein(a) that are an independent risk factor for atherosclerotic CVD events, and 4) pharmacogenetic (PGx) variants contributing to simvastatin-induced myopathy and warfarin metabolism. After sequencing in a CAP/CLIA certified laboratory, results were returned to the ordering physician after a multi-disciplinary sign-out conference and uploaded to the EMR.Results:As of June 2020, 678 individuals had completed testing with a 31% overall positive rate for Mendelian genes, elevated polygenic risk, and LPA risk alleles (excluding PGx). Of these, 8.1% had a positive finding for a Mendelian condition, the majority (60%) being dyslipidemias (e.g., FH), followed by 25% cardiomyopathies (e.g., HCM, DCM, ARVC) and 6% aortopathies (e.g., Marfan, Loeys-Dietz). Approximately 20% of individuals carried an LPA risk allele, and 9.3% belonged to the high-risk group according to their PRS. Approximately half had a PGx finding related to simvastatin and/or warfarin metabolism. Nearly one in five individuals had a finding with direct clinical care impact, including referral to specialists, imaging, laboratory studies, therapies/procedures (e.g., PCSK9i, ICD).Conclusions:To our knowledge, this is the first test of its kind assaying four distinct categories of genetic variation related to cardiovascular health. Our results demonstrate that comprehensive testing can be routinely used to identify individuals who may benefit from interventions to improve survival, reduce morbidity, and enhance quality of life

Genetic testing in ambulatory cardiology clinics reveals high rate of findings with clinical management implications

Purpose Cardiovascular disease (CVD) is the leading cause of death in adults in the United States, yet the benefits of genetic testing are not universally accepted. Methods We developed the "HeartCare" panel of genes associated with CVD, evaluating high-penetrance Mendelian conditions, coronary artery disease (CAD) polygenic risk, LPA gene polymorphisms, and specific pharmacogenetic (PGx) variants. We enrolled 709 individuals from cardiology clinics at Baylor College of Medicine, and samples were analyzed in a CAP/CLIA-certified laboratory. Results were returned to the ordering physician and uploaded to the electronic medical record. Results Notably, 32% of patients had a genetic finding with clinical management implications, even after excluding PGx results, including 9% who were molecularly diagnosed with a Mendelian condition. Among surveyed physicians, 84% reported medical management changes based on these results, including specialist referrals, cardiac tests, and medication changes. LPA polymorphisms and high polygenic risk of CAD were found in 20% and 9% of patients, respectively, leading to diet, lifestyle, and other changes. Warfarin and simvastatin pharmacogenetic variants were present in roughly half of the cohort. Conclusion Our results support the use of genetic information in routine cardiovascular health management and provide a roadmap for accompanying research

Genome Sequence of the Brown Norway Rat Yields Insights Into Mammalian Evolution

The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution

Genetic determinants of risk in pulmonary arterial hypertension: international genome-wide association studies and meta-analysis.

BACKGROUND: Rare genetic variants cause pulmonary arterial hypertension, but the contribution of common genetic variation to disease risk and natural history is poorly characterised. We tested for genome-wide association for pulmonary arterial hypertension in large international cohorts and assessed the contribution of associated regions to outcomes. METHODS: We did two separate genome-wide association studies (GWAS) and a meta-analysis of pulmonary arterial hypertension. These GWAS used data from four international case-control studies across 11 744 individuals with European ancestry (including 2085 patients). One GWAS used genotypes from 5895 whole-genome sequences and the other GWAS used genotyping array data from an additional 5849 individuals. Cross-validation of loci reaching genome-wide significance was sought by meta-analysis. Conditional analysis corrected for the most significant variants at each locus was used to resolve signals for multiple associations. We functionally annotated associated variants and tested associations with duration of survival. All-cause mortality was the primary endpoint in survival analyses. FINDINGS: A locus near SOX17 (rs10103692, odds ratio 1·80 [95% CI 1·55-2·08], p=5·13 × 10-15) and a second locus in HLA-DPA1 and HLA-DPB1 (collectively referred to as HLA-DPA1/DPB1 here; rs2856830, 1·56 [1·42-1·71], p=7·65 × 10-20) within the class II MHC region were associated with pulmonary arterial hypertension. The SOX17 locus had two independent signals associated with pulmonary arterial hypertension (rs13266183, 1·36 [1·25-1·48], p=1·69 × 10-12; and rs10103692). Functional and epigenomic data indicate that the risk variants near SOX17 alter gene regulation via an enhancer active in endothelial cells. Pulmonary arterial hypertension risk variants determined haplotype-specific enhancer activity, and CRISPR-mediated inhibition of the enhancer reduced SOX17 expression. The HLA-DPA1/DPB1 rs2856830 genotype was strongly associated with survival. Median survival from diagnosis in patients with pulmonary arterial hypertension with the C/C homozygous genotype was double (13·50 years [95% CI 12·07 to >13·50]) that of those with the T/T genotype (6·97 years [6·02-8·05]), despite similar baseline disease severity. INTERPRETATION: This is the first study to report that common genetic variation at loci in an enhancer near SOX17 and in HLA-DPA1/DPB1 is associated with pulmonary arterial hypertension. Impairment of SOX17 function might be more common in pulmonary arterial hypertension than suggested by rare mutations in SOX17. Further studies are needed to confirm the association between HLA typing or rs2856830 genotyping and survival, and to determine whether HLA typing or rs2856830 genotyping improves risk stratification in clinical practice or trials. FUNDING: UK NIHR, BHF, UK MRC, Dinosaur Trust, NIH/NHLBI, ERS, EMBO, Wellcome Trust, EU, AHA, ACClinPharm, Netherlands CVRI, Dutch Heart Foundation, Dutch Federation of UMC, Netherlands OHRD and RNAS, German DFG, German BMBF, APH Paris, INSERM, Université Paris-Sud, and French ANR