scholarly journals Highly parallel genome variant engineering with CRISPR/Cas9 in eukaryotic cells

2017 ◽  
Author(s):  
Meru J. Sadhu ◽  
Joshua S. Bloom ◽  
Laura Day ◽  
Jake J. Siegel ◽  
Sriram Kosuri ◽  
...  
Keyword(s):  
Essential Genes ◽  
Protein Domain ◽  
Eukaryotic Cells ◽  
Sequence Variants ◽  
Large Classes ◽  
Premature Termination Codons ◽  
A Genome ◽  
Functional Consequences ◽  
Dna Sequence Variants ◽  
High Throughput Manner

AbstractDirect measurement of functional effects of DNA sequence variants throughout a genome is a major challenge. We developed a method that uses CRISPR/Cas9 to engineer many specific variants of interest in parallel in the budding yeast Saccharomyces cerevisiae, and to screen them for functional effects. We used the method to examine the functional consequences of premature termination codons (PTCs) at different locations within all annotated essential genes in yeast. We found that most PTCs were highly deleterious unless they occurred close to the C-terminal end and did not interrupt an annotated protein domain. Surprisingly, we discovered that some putatively essential genes are dispensable, while others have large dispensable regions. This approach can be used to profile the effects of large classes of variants in a high-throughput manner.

Abstract P255: Genetic Variation in Chromosome 8p23 is Associated With Sedentary Behavior in Humans

Circulation ◽  
2014 ◽  
Vol 129 (suppl_1) ◽  
Author(s):  
Tuomo Rankinen ◽  
Mark A Sarzynski ◽  
Barbara Sternfeld ◽  
Steve Sidney ◽  
Claude Bouchard
Keyword(s):  
African Americans ◽  
Sedentary Behavior ◽  
Dna Sequence ◽  
Sedentary Time ◽  
Sitting Time ◽  
Sequence Variants ◽  
Replication Studies ◽  
Genome Wide ◽  
A Genome ◽  
Dna Sequence Variants

Sedentary behavior, usually quantified as sitting time, has been shown to be associated with several adverse health outcomes, even among individuals who meet the current recommendations for physical activity. Both twin and family studies have shown that sedentary behavior aggregates in families and is a heritable trait. However, little is known about genes and DNA sequence variants that contribute to propensity to be sedentary. The purpose of our study was to conduct a genome-wide association study to identify genomic regions and DNA sequence variants associated with sedentary time. A total of 67,530 Caucasians (56% female, mean age 62.1 years [SD 12.5]) from the Kaiser Permanente Research Program on Genes, Environment, and Health (RPGEH) cohort were used for the discovery analyses. Other RPGEH ethnicities (African-Americans: N=2,500; East Asians: N=6,300; Hispanics: N=8,800) were used for replication studies. Information on daily sitting time outside of work was obtained by a questionnaire. A custom panel of 657,184 autosomal single nucleotide polymorphisms (SNPs) was genotyped using Affymetrix platform. Associations between sedentary time (dichotomized; cases 3 hours or more, controls less than 3 hours per day) and the SNPs were tested with PLINK logistic model using age, sex, BMI and admixture principal components as covariates. The strongest evidence of association was detected on chromosome 8p23.1. A total of 24 SNPs within a 1.34 Mb region were associated with sedentary time at genome-wide significance level (p<5x10 -8 ), with SNP rs11774552 showing the peak association (OR=0.924, p= 1.7x10 -12 ). Sex-specific analyses confirmed that the associations were present both in men and women. The same SNPs were not associated with sedentary time in other ethnicities. However, SNP rs28754712, which is located in the immediate vicinity (+456 bp) of rs11774552, showed a significant association with sedentary time (OR=0.795, p=1.2x10 -3 ) in African-Americans. In summary, our results provide the first evidence of genomic region and DNA sequence variants associated with sedentary behavior in humans. If confirmed in additional replication studies, these findings will advance our understanding of biological mechanisms contributing to propensity to be sedentary.

scholarly journals A rapid solubility assay of protein domain misfolding for pathogenicity assessment of rare DNA sequence variants

2020 ◽  
Vol 22 (10) ◽  
pp. 1642-1652 ◽  
Author(s):  
Corey L. Anderson ◽  
Tim C. Routes ◽  
Lee L. Eckhardt ◽  
Brian P. Delisle ◽  
Craig T. January ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Protein Domain ◽  
Sequence Variants ◽  
Dna Sequence Variants

Evidence for association of DNA sequence variants in the phosphatidylinositol-4-phosphate 5-kinase IIα gene (PIP5K2A) with schizophrenia

2006 ◽  
Vol 11 (9) ◽  
pp. 837-846 ◽  
Author(s):  
S G Schwab ◽  
M Knapp ◽  
P Sklar ◽  
G N Eckstein ◽  
C Sewekow ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Sequence Variants ◽  
Dna Sequence Variants ◽  
Phosphatidylinositol 4

scholarly journals Genome-wide mapping of unexplored essential regions in the Saccharomyces cerevisiae genome: evidence for hidden synthetic lethal combinations in a genetic interaction network

2014 ◽  
Vol 42 (15) ◽  
pp. 9838-9853 ◽  
Author(s):  
Saeed Kaboli ◽  
Takuya Yamakawa ◽  
Keisuke Sunada ◽  
Tao Takagaki ◽  
Yu Sasano ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Interaction ◽  
Interaction Network ◽  
Essential Genes ◽  
Genetic Interactions ◽  
Lethal Gene ◽  
Synthetic Lethal ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale

Abstract Despite systematic approaches to mapping networks of genetic interactions in Saccharomyces cerevisiae, exploration of genetic interactions on a genome-wide scale has been limited. The S. cerevisiae haploid genome has 110 regions that are longer than 10 kb but harbor only non-essential genes. Here, we attempted to delete these regions by PCR-mediated chromosomal deletion technology (PCD), which enables chromosomal segments to be deleted by a one-step transformation. Thirty-three of the 110 regions could be deleted, but the remaining 77 regions could not. To determine whether the 77 undeletable regions are essential, we successfully converted 67 of them to mini-chromosomes marked with URA3 using PCR-mediated chromosome splitting technology and conducted a mitotic loss assay of the mini-chromosomes. Fifty-six of the 67 regions were found to be essential for cell growth, and 49 of these carried co-lethal gene pair(s) that were not previously been detected by synthetic genetic array analysis. This result implies that regions harboring only non-essential genes contain unidentified synthetic lethal combinations at an unexpectedly high frequency, revealing a novel landscape of genetic interactions in the S. cerevisiae genome. Furthermore, this study indicates that segmental deletion might be exploited for not only revealing genome function but also breeding stress-tolerant strains.

Effects of Selection at Linked Sites on Patterns of Genetic Variability

2021 ◽  
Vol 52 (1) ◽  
pp. 177-197
Author(s):  
Brian Charlesworth ◽  
Jeffrey D. Jensen
Keyword(s):  
Genetic Variability ◽  
Population Genetic ◽  
Selective Sweeps ◽  
Recombination Rates ◽  
Frequency Distributions ◽  
A Genome ◽  
Demographic Processes ◽  
Dna Sequence Variants ◽  
Genomic Regions ◽  
Functional Components

Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.

scholarly journals The functional impact of alternative splicing in cancer

2016 ◽  
Author(s):  
Héctor Climente-González ◽  
Eduard Porta-Pardo ◽  
Adam Godzik ◽  
Eduardo Eyras
Keyword(s):  
Alternative Splicing ◽  
Negative Correlation ◽  
Protein Interactions ◽  
Somatic Mutations ◽  
Protein Domain ◽  
Protein Protein Interactions ◽  
Systematic Analysis ◽  
Functional Impact ◽  
Functional Consequences ◽  
Functional Transformations

SummaryAlternative splicing changes are frequently observed in cancer and are starting to be recognized as important signatures for tumor progression and therapy. However, their functional impact and relevance to tumorigenesis remains mostly unknown. We carried out a systematic analysis to characterize the potential functional consequences of alternative splicing changes in thousands of tumor samples. This analysis revealed that a subset of alternative splicing changes affect protein domain families that are frequently mutated in tumors and potentially disrupt protein protein interactions in cancer-related pathways. Moreover, there was a negative correlation between the number of these alternative splicing changes in a sample and the number of somatic mutations in drivers. We propose that a subset of the alternative splicing changes observed in tumors may represent independent oncogenic processes that could be relevant to explain the functional transformations in cancer and some of them could potentially be considered alternative splicing drivers (AS-drivers).

scholarly journals A genome-wide meta-analysis identifies 53 sequence variants associating with carpal tunnel syndrome

2022 ◽  
Author(s):  
Astros Skuladottir ◽  
Gyda Bjornsdottir ◽  
Egil Ferkingstad ◽  
Gudmundur Einarsson ◽  
Lilja Stefansdottir ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Carpal Tunnel Syndrome ◽  
Carpal Tunnel ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Missense Variant ◽  
Sequence Variants ◽  
Genome Wide ◽  
A Genome ◽  
Tunnel Syndrome

Abstract Carpal tunnel syndrome (CTS) is the most common entrapment neuropathy and has a largely unknown underlying biology. In a genome-wide association study of CTS (Ncases = 48,843, Ncontrols = 1,190,837), we found 53 sequence variants at 50 loci that associate with the syndrome. The most significant association is with a missense variant (p.Glu366Lys) in SERPINA1 that protects against CTS (P = 2.9 × 10−24, OR = 0.76). Through various functional analyses, we conclude that at least 22 genes mediate CTS risk and highlight the role of 19 CTS variants in the biology of the extracellular matrix. We show that the genetic component to the risk is higher in recurrent/persistent cases than nonrecurrent/nonresistant cases. Anthropometric traits including height and BMI are genetically correlated with CTS, in addition to early hormonal-replacement therapy, osteoarthritis, and restlessness. Our findings suggest that the components of the extracellular matrix play a key role in the pathogenesis of CTS.

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