Identification of Novel, Inherited Genetic Markers for Aggressive PCa in European and African Americans Using Whole Genome Sequencing

2013 ◽  
Author(s):  
Jielin Sun ◽  
Siqun L. Zheng
Keyword(s):  
African Americans ◽  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Whole Genome

0306 Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 146-146
Author(s):  
D. M. Bickhart ◽  
L. Xu ◽  
J. L. Hutchison ◽  
J. B. Cole ◽  
D. J. Null ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Copy Number ◽  
Large Scale ◽  
Copy Number Variants ◽  
Whole Genome

scholarly journals Attitudes of African Americans Toward Return of Results From Exome and Whole Genome Sequencing

2013 ◽  
Vol 161 (5) ◽  
pp. 1064-1072 ◽  
Author(s):  
Joon-Ho Yu ◽  
Julia Crouch ◽  
Seema M. Jamal ◽  
Holly K. Tabor ◽  
Michael J. Bamshad
Keyword(s):  
African Americans ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Return Of Results ◽  
Whole Genome

scholarly journals Whole genome sequencing of pharmacogenetic drug response in racially and ethnically diverse children with asthma

2017 ◽  
Author(s):  
Angel C.Y. Mak ◽  
Marquitta J. White ◽  
Zachary A. Szpiech ◽  
Walter L. Eckalbar ◽  
Sam S. Oh ◽  
...  
Keyword(s):  
African Americans ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Drug Response ◽  
Puerto Ricans ◽  
Ethnically Diverse ◽  
Asthma Prevalence ◽  
Whole Genome ◽  
Minority Children ◽  
Children With Asthma

ABSTRACTAsthma is the most common chronic disease of children, with significant racial/ethnic differences in prevalence, morbidity, mortality and therapeutic response. Albuterol, a bronchodilator medication, is the first-line therapy for asthma treatment worldwide. We performed the largest whole genome sequencing (WGS) pharmacogenetics study to date using data from 1,441 minority children with asthma who had extremely high or low bronchodilator drug response (BDR). We identified population-specific and shared pharmacogenetic variants associated with BDR, including genome-wide significant (p < 3.53 x 10-7) and suggestive (p < 7.06 x 10-6) loci near genes previously associated with lung capacity (DNAH5), immunity (NFKB1 and PLCB1), and β-adrenergic signaling pathways (ADAMTS3 and COX18). Functional analyses centered on NFKB1 revealed potential regulatory function of our BDR-associated SNPs in bronchial smooth muscle cells. Specifically, these variants are in linkage disequilibrium with SNPs in a functionally active enhancer, and are also expression quantitative trait loci (eQTL) for a neighboring gene, SLC39A8. Given the lack of other asthma study populations with WGS data on minority children, replication of our rare variant associations is infeasible. We attempted to replicate our common variant findings in five independent studies with GWAS data. The age-specific associations previously found in asthma and asthma-related traits suggest that the over-representation of adults in our replication populations may have contributed to our lack of statistical replication, despite the functional relevance of the NFKB1 variants demonstrated by our functional assays. Our study expands the understanding of pharmacogenetic analyses in racially/ethnically diverse populations and advances the foundation for precision medicine in at-risk and understudied minority populations.AUTHOR SUMMARYAsthma is the most common chronic disease among children. Albuterol, a bronchodilator medication, is the first-line therapy for asthma treatment worldwide. In the U.S., asthma prevalence is the highest among Puerto Ricans, intermediate among African Americans and lowest in Whites and Mexicans. Asthma disparities extend to mortality, which is four- to five-fold higher in Puerto Ricans and African Americans compared to Mexicans [1]. Puerto Ricans and African Americans, the populations with the highest asthma prevalence and death rate, also have the lowest albuterol bronchodilator drug response (BDR). We conducted the largest pharmacogenetic study using whole genome sequencing data from 1,441 minority children with asthma who had extremely high or low albuterol bronchodilator drug response. We identified population-specific and shared pharmacogenetic variants associated with BDR. Our findings help inform the direction of future development of asthma medications and our study advances the foundation of precision medicine for at-risk, yet understudied, racially/ethnically diverse populations.

scholarly journals Whole-genome sequencing reveals KRTAP1-1 as a novel genetic variant associated with antidepressant treatment outcomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jong-Ho Park ◽  
Shinn-Won Lim ◽  
Woojae Myung ◽  
Inho Park ◽  
Hyeok-Jae Jang ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Treatment Outcomes ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Genetic Variants ◽  
Selective Serotonin Reuptake Inhibitors ◽  
Remission Rate ◽  
Antidepressant Treatment ◽  
Whole Genome ◽  
Loss Of Function

AbstractAchieving remission following initial antidepressant therapy in patients with major depressive disorder (MDD) is an important clinical result. Making predictions based on genetic markers holds promise for improving the remission rate. However, genetic variants found in previous genetic studies do not provide robust evidence to aid pharmacogenetic decision-making in clinical settings. Thus, the objective of this study was to perform whole-genome sequencing (WGS) using genomic DNA to identify genetic variants associated with the treatment outcomes of selective serotonin reuptake inhibitors (SSRIs). We performed WGS on 100 patients with MDD who were treated with escitalopram (discovery set: 36 remitted and 64 non-remitted). The findings were applied to an additional 553 patients with MDD who were treated with SSRIs (replication set: 185 remitted and 368 non-remitted). A novel loss-of-function variant (rs3213755) in keratin-associated protein 1–1 (KRTAP1-1) was identified in this study. This rs3213755 variant was significantly associated with remission following antidepressant treatment (p = 0.0184, OR 3.09, 95% confidence interval [CI] 1.22–7.80 in the discovery set; p = 0.00269, OR 1.75, 95% CI 1.22–2.53 in the replication set). Moreover, the expression level of KRTAP1-1 in surgically resected human temporal lobe samples was significantly associated with the rs3213755 genotype. WGS studies on a larger sample size in various ethnic groups are needed to investigate genetic markers useful in the pharmacogenetic prediction of remission following antidepressant treatment.

scholarly journals Tracing the environmental footprint of theBurkholderia pseudomalleilipopolysaccharide genotypes in the tropical “Top End” of the Northern Territory, Australia

2019 ◽  
Author(s):  
Jessica R. Webb ◽  
Audrey Rachlin ◽  
Vanessa Rigas ◽  
Derek S. Sarovich ◽  
Erin P. Price ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Burkholderia Pseudomallei ◽  
Northern Territory ◽  
Whole Genome ◽  
Endemic Region ◽  
Tropical Regions ◽  
Motility Factor ◽  
Environmental Bacterium

AbstractThe Tier 1 select agentBurkholderia pseudomalleiis an environmental bacterium that causes melioidosis, a high mortality disease. Variably present genetic markers used to elucidate strain origin, relatedness and virulence inB. pseudomalleiinclude theBurkholderiaintracellular motility factor A (bimA) and filamentous hemagglutinin 3 (fhaB3) gene variants. Three lipopolysaccharide (LPS) O-antigen types inB. pseudomalleihave been described, which vary in proportion between Australian and Asian isolates. However, it remains unknown if these LPS types can be used as genetic markers for geospatial analysis within a contiguous melioidosis-endemic region. Using a combination of whole-genome sequencing (WGS), statistical analysis and geographical mapping, we examined if the LPS types can be used as geographical markers in the Northern Territory, Australia. The clinical isolates revealed that LPS A prevalence was highest in the Darwin and surrounds (n = 660; 96% being LPS A and 4% LPS B) and LPS B in the Katherine and Katherine remote and East Arnhem regions (n = 79; 60% being LPS A and 40% LPS B). Bivariate logistics regression of 999 clinicalB. pseudomalleiisolates revealed that the odds of getting a clinical isolate with LPS B was highest in East Arnhem in comparison to Darwin and surrounds (OR 19.5, 95% CI 9.1 – 42.0;p<0.001). This geospatial correlation was subsequently confirmed by geographically mapping the LPS type from 340 environmental Top End strains. We also found that in the Top End, the minoritybimAgenotypebimABmhas a similar remote region geographical footprint to that of LPS B. In addition, correlation of LPS type with multi-locus sequence typing (MLST) was strong, and where multiple LPS types were identified within a single sequence type, WGS confirmed homoplasy of the MLST loci. The clinical, sero-diagnostic and vaccine implications of geographically-basedB. pseudomalleiLPS types, and their relationships to regional and global dispersal of melioidosis, require global collaborations with further analysis of larger clinically and geospatially-linked datasets.Author SummaryBurkholderia pseudomalleiis a pathogenic soil bacterium that causes the disease melioidosis, which occurs in many tropical regions globally and in recent years has emerged in non-tropical regions. Melioidosis has been predicted to affect 165,000 people every year resulting in an estimated 89,000 deaths. Person to person transmission is rare with most cases linked to exposure to the bacterium from the environment. The genetic background ofB. pseudomalleihas been well studied and variably present genes have been linked to distinct melioidosis disease states and geographic regions, however we still need a stronger understanding of the association of genes with geography. Three lipopolysaccharide types exist inB. pseudomalleiand the prevalence of the lipopolysaccharide genes vary between melioidosis endemic regions, but it is unknown if the lipopolysaccharide genes can be used as geographical markers in a single melioidosis-endemic region. In this study, we used a combination of whole-genome sequencing, statistics and geographical mapping to elucidate if the three lipopolysaccharide genes can be used as geographical markers within the Northern Territory, Australia. We show that the three LPS types have distinct but overlapping geographical footprints within a single melioidosis region and can be used as geographic markers alongside a number of other important variably presentB. pseudomalleigenes.

scholarly journals Development of microsatellite genetic markers in Siberian larch (Larix sibirica Ledeb.) based on the de novo whole genome sequencing

2017 ◽  
Vol 53 (11) ◽  
pp. 1194-1199 ◽  
Author(s):  
N. V. Oreshkova ◽  
Yu. A. Putintseva ◽  
V. V. Sharov ◽  
D. A. Kuzmin ◽  
K. V. Krutovsky
Keyword(s):  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
De Novo ◽  
Siberian Larch ◽  
Larix Sibirica ◽  
Whole Genome

scholarly journals Genomic Sequencing To Identify Potential Causative Mutation(s) of Neurospora crassa col-4

2020 ◽  
Vol 9 (2) ◽  
Author(s):  
Thomas A. Randall
Keyword(s):  
Neurospora Crassa ◽  
Whole Genome Sequencing ◽  
Genetic Markers ◽  
Genome Sequencing ◽  
Model Organisms ◽  
Causative Mutation ◽  
Genomic Sequencing ◽  
Whole Genome ◽  
Content Type

In many cases, genes for commonly used genetic markers in model organisms have not been identified; therefore, it is of interest to identify the causative genes. Whole-genome sequencing was used to identify potential causative mutations for a col-4 allele of Neurospora crassa.

scholarly journals Su1028 – Whole-Genome Sequencing of African Americans Identifies Novel Rare Variants Associated with Inflammatory Bowel Disease

2019 ◽  
Vol 156 (6) ◽  
pp. S-488-S-489
Author(s):  
Hari K. Somineni ◽  
Talin Haritunians ◽  
Claire L. Simpson ◽  
David J. Cutler ◽  
David Okou ◽  
...  
Keyword(s):  
Inflammatory Bowel Disease ◽  
African Americans ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bowel Disease ◽  
Rare Variants ◽  
Whole Genome ◽  
Inflammatory Bowel
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