Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma

RATIONALE: Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. OBJECTIVES: To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. METHODS: We performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. MEASUREMENTS AND MAIN RESULTS: We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P \u3c 3.53 × 10 CONCLUSIONS: The lack of minority data, despite a collaboration of eight universities and 13 individual laboratories, highlights the urgent need for a dedicated national effort to prioritize diversity in research. 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

Whole-genome sequencing of pharmacogenetic drug response in racially diverse children with asthma

RATIONALE: Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. OBJECTIVES: To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. METHODS: We performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. MEASUREMENTS AND MAIN RESULTS: We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P \u3c 3.53 × 10-7) and suggestive (P \u3c 7.06 × 10-6) loci near genes previously associated with lung capacity (DNAH5), immunity (NFKB1 and PLCB1), and β-adrenergic signaling (ADAMTS3 and COX18). Functional analyses of the BDR-associated SNP in NFKB1 revealed potential regulatory function in bronchial smooth muscle cells. The SNP is also an expression quantitative trait locus for a neighboring gene, SLC39A8. The lack of other asthma study populations with BDR and whole-genome sequencing data on minority children makes it impossible to perform replication of our rare variant associations. Minority underrepresentation also poses significant challenges to identify age-matched and population-matched cohorts of sufficient sample size for replication of our common variant findings. CONCLUSIONS: The lack of minority data, despite a collaboration of eight universities and 13 individual laboratories, highlights the urgent need for a dedicated national effort to prioritize diversity in research. 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

DNA fragment analysis by agarose gel electrofhoresis method

Agarozna gel elektroforeza je migracija nabijenih čestica na gelu, uslijed djelovanja električnog polja. Uobičajena je laboratorijska tehnika za odvajanje i analizu fragmenata DNA i ostalih biomolekula na temelju njihove veličine. Genomska DNA je ukupan genetički materijal jednog organizma i nalazi se u jezgrama stanica. Cilj ovog rada bio je opisati i primijeniti metodu agarozne gel elektroforeze te utvrditi veličine fragmenata DNA molekule. Pripremljene su četiri vrste gelova koncentracija: 0,8%, 1%, 2% i 3%. Prema dobivenim rezultatima utvrđeno je da su fragmenti genomske DNA veći od PCR fragmenata i sukladno s tim je zaključeno da manji fragmenti putuju brže i dalje od velikih fragmenata, što je bilo i očekivano. Zaključno, za analizu većih fragmenata genomske DNA optimalno je koristiti gel koncentracije 1% i manje, dok se za PCR fragmente najčešće koristi gel kocentracije od 2 do 3%, optimalno 2,5%.Agarose gel electrophoresis is the migration of charged particles on the gel, due to the influence of applied electric field. It is a common laboratory technique for separating and analyzing DNA fragments and other biomolecules based on their size. Genomic DNA is a total genetic material of an organism and it's found in the cell nuclei. The aim of this research was to describe and apply the agarose gel electrophoresis method and to determine the sizes of DNA molecule fragments. Four gel concentrations were prepared: 0.8%, 1%, 2% and 3%. According to the obtained results, it was determined that genomic DNA fragments are larger than PCR fragments and accordingly it was concluded that smaller fragments travel faster than the large fragments, which was expected. In conclusion, for the analysis of larger fragments of genomic DNA, it is optimal to use a gel concentration of 1% or less, while for PCR fragments, gel concentration of 2 to 3% is usually used, optimally 2,5%

DNA fragment analysis by agarose gel electrofhoresis method

Agarozna gel elektroforeza je migracija nabijenih čestica na gelu, uslijed djelovanja električnog polja. Uobičajena je laboratorijska tehnika za odvajanje i analizu fragmenata DNA i ostalih biomolekula na temelju njihove veličine. Genomska DNA je ukupan genetički materijal jednog organizma i nalazi se u jezgrama stanica. Cilj ovog rada bio je opisati i primijeniti metodu agarozne gel elektroforeze te utvrditi veličine fragmenata DNA molekule. Pripremljene su četiri vrste gelova koncentracija: 0,8%, 1%, 2% i 3%. Prema dobivenim rezultatima utvrđeno je da su fragmenti genomske DNA veći od PCR fragmenata i sukladno s tim je zaključeno da manji fragmenti putuju brže i dalje od velikih fragmenata, što je bilo i očekivano. Zaključno, za analizu većih fragmenata genomske DNA optimalno je koristiti gel koncentracije 1% i manje, dok se za PCR fragmente najčešće koristi gel kocentracije od 2 do 3%, optimalno 2,5%.Agarose gel electrophoresis is the migration of charged particles on the gel, due to the influence of applied electric field. It is a common laboratory technique for separating and analyzing DNA fragments and other biomolecules based on their size. Genomic DNA is a total genetic material of an organism and it's found in the cell nuclei. The aim of this research was to describe and apply the agarose gel electrophoresis method and to determine the sizes of DNA molecule fragments. Four gel concentrations were prepared: 0.8%, 1%, 2% and 3%. According to the obtained results, it was determined that genomic DNA fragments are larger than PCR fragments and accordingly it was concluded that smaller fragments travel faster than the large fragments, which was expected. In conclusion, for the analysis of larger fragments of genomic DNA, it is optimal to use a gel concentration of 1% or less, while for PCR fragments, gel concentration of 2 to 3% is usually used, optimally 2,5%

DNA fragment analysis by agarose gel electrofhoresis method

Agarozna gel elektroforeza je migracija nabijenih čestica na gelu, uslijed djelovanja električnog polja. Uobičajena je laboratorijska tehnika za odvajanje i analizu fragmenata DNA i ostalih biomolekula na temelju njihove veličine. Genomska DNA je ukupan genetički materijal jednog organizma i nalazi se u jezgrama stanica. Cilj ovog rada bio je opisati i primijeniti metodu agarozne gel elektroforeze te utvrditi veličine fragmenata DNA molekule. Pripremljene su četiri vrste gelova koncentracija: 0,8%, 1%, 2% i 3%. Prema dobivenim rezultatima utvrđeno je da su fragmenti genomske DNA veći od PCR fragmenata i sukladno s tim je zaključeno da manji fragmenti putuju brže i dalje od velikih fragmenata, što je bilo i očekivano. Zaključno, za analizu većih fragmenata genomske DNA optimalno je koristiti gel koncentracije 1% i manje, dok se za PCR fragmente najčešće koristi gel kocentracije od 2 do 3%, optimalno 2,5%.Agarose gel electrophoresis is the migration of charged particles on the gel, due to the influence of applied electric field. It is a common laboratory technique for separating and analyzing DNA fragments and other biomolecules based on their size. Genomic DNA is a total genetic material of an organism and it's found in the cell nuclei. The aim of this research was to describe and apply the agarose gel electrophoresis method and to determine the sizes of DNA molecule fragments. Four gel concentrations were prepared: 0.8%, 1%, 2% and 3%. According to the obtained results, it was determined that genomic DNA fragments are larger than PCR fragments and accordingly it was concluded that smaller fragments travel faster than the large fragments, which was expected. In conclusion, for the analysis of larger fragments of genomic DNA, it is optimal to use a gel concentration of 1% or less, while for PCR fragments, gel concentration of 2 to 3% is usually used, optimally 2,5%

A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma

Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the United States. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African-American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single-nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1830 Latinos (total = 2779). Finally, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p = 7.69 × 10-9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958 and rs7081864, p ≤ 5 × 10-8). Our results failed to replicate in three additional populations of 416 Latinos and 1615 African Americans. Our findings indicate that both population-specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups

A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma

Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the United States. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African-American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single-nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1830 Latinos (total = 2779). Finally, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p = 7.69 × 10-9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958 and rs7081864, p ≤ 5 × 10-8). Our results failed to replicate in three additional populations of 416 Latinos and 1615 African Americans. Our findings indicate that both population-specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups

A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma.

Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the United States. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African-American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single-nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1830 Latinos (total = 2779). Finally, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p = 7.69 × 10-9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958 and rs7081864, p ≤ 5 × 10-8). Our results failed to replicate in three additional populations of 416 Latinos and 1615 African Americans. Our findings indicate that both population-specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups

Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma

RATIONALE: Albuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response. OBJECTIVES: To identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children. METHODS: We performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR. MEASUREMENTS AND MAIN RESULTS: We identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P \u3c 3.53 × 10 CONCLUSIONS: The lack of minority data, despite a collaboration of eight universities and 13 individual laboratories, highlights the urgent need for a dedicated national effort to prioritize diversity in research. 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

Whole-Genome Sequencing of Pharmacogenetic Drug Response in Racially Diverse Children with Asthma.

RationaleAlbuterol, a bronchodilator medication, is the first-line therapy for asthma worldwide. There are significant racial/ethnic differences in albuterol drug response.ObjectivesTo identify genetic variants important for bronchodilator drug response (BDR) in racially diverse children.MethodsWe performed the first whole-genome sequencing pharmacogenetics study from 1,441 children with asthma from the tails of the BDR distribution to identify genetic association with BDR.Measurements and main resultsWe identified population-specific and shared genetic variants associated with BDR, including genome-wide significant (P < 3.53 × 10-7) and suggestive (P < 7.06 × 10-6) loci near genes previously associated with lung capacity (DNAH5), immunity (NFKB1 and PLCB1), and β-adrenergic signaling (ADAMTS3 and COX18). Functional analyses of the BDR-associated SNP in NFKB1 revealed potential regulatory function in bronchial smooth muscle cells. The SNP is also an expression quantitative trait locus for a neighboring gene, SLC39A8. The lack of other asthma study populations with BDR and whole-genome sequencing data on minority children makes it impossible to perform replication of our rare variant associations. Minority underrepresentation also poses significant challenges to identify age-matched and population-matched cohorts of sufficient sample size for replication of our common variant findings.ConclusionsThe lack of minority data, despite a collaboration of eight universities and 13 individual laboratories, highlights the urgent need for a dedicated national effort to prioritize diversity in research. 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