ALFRED: an allele frequency resource for research and teaching

Rajeevan, Haseena; Soundararajan, Usha; Kidd, Judith R.; Pakstis, Andrew J.; Kídd, Kenneth K.

doi:10.1093/nar/gkr924

Cited by 87 publications

(70 citation statements)

References 24 publications

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“…The distributions of the allele and genotype frequencies, and the short-long genotype classification are consistent with prior research with Caucasian and European samples (Hutchison et al, 2003; van der Zwaluw et al, 2012) as well as with European samples reported in the Allele Frequency Database (Rajeevan et al, 2012). We did not collect data on ancestry informative markers and relied on self-reports of ethnicity.…”

Section: Resultssupporting

confidence: 86%

DRD4 and susceptibility to peer influence on alcohol use from adolescence to adulthood

Mrug

Windle

2014

Drug and Alcohol Dependence

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Background The long allele of DRD4 is associated with greater susceptibility to peer influences on alcohol use in young adulthood, but it is unclear whether this increased susceptibility extends to other developmental periods. This study examined the interactive effects of DRD4 polymorphism and friends' alcohol use from adolescence to adulthood. Methods Participants (N=340; 59% female; 98% White) reported on their own and their friends' alcohol use at four time points between mean ages 17 and 33. Autoregressive cross-lagged models evaluated reciprocal relationships between friends' alcohol use and participants' own alcohol use and frequency of heavy drinking over time. Multigroup modeling tested differences in model paths and covariances across high vs. low risk DRD4 polymorphisms. Results Alcohol use at age 33 was predicted by previous friends' alcohol use and correlated with current friends' alcohol use only for carriers of the DRD4 long allele. Regardless of DRD4 genotype, friends' alcohol use at age 17 predicted greater alcohol use and more frequent heavy drinking at age 23. Alcohol use and/or heavy drinking predicted greater friends' alcohol use at later time points for both genotype groups across adolescence and adulthood. Conclusions The long allele of DRD4 is associated with increased susceptibility to peer influences on alcohol use in young adulthood, but not earlier in development. Adults with the long allele of DRD4 may benefit from interventions educating them about this risk and equipping them with strategies to reduce affiliations with and influence of drinking friends.

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Section: Resultssupporting

confidence: 86%

DRD4 and susceptibility to peer influence on alcohol use from adolescence to adulthood

Mrug

Windle

2014

Drug and Alcohol Dependence

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“…This follows from the ALFRED (The ALlele FREquency Database) expected heterozygosities (rs61764370) for persons of European descent 24 are 0.05-0.25. Chin LJ 1 reported that in the general population the frequency of the G-allele of KRAS-LCS6 is 5.8% and about 7.6% in populations of European descent, based on the genotyping of 2.433 samples (representing 46 geographic populations).…”

Section: Discussionmentioning

confidence: 96%

Comparison of the prevalence of KRAS-LCS6 polymorphism (rs61764370) within different tumour types (colorectal, breast, non-small cell lung cancer and brain tumours). A study of the Czech population

Uvírová¹,

Šimová²,

Kubova³

et al. 2015

BIOMED PAP

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, Petr Dite a,bAims. A germline SNP (rs61764370) is located in a let-7 complementary site (LCS6) in the 3'UTR of KRAS oncogene, and it was found to alter the binding capability of the mature let-7 microRNA to the KRAS mRNA. The aim of the study was to evaluate the frequency of the KRAS-LCS6 variant allele in different cancer types that included patients with colorectal cancer (CRC), breast cancer (BC), non-small cell lung cancer (NSCLC) and brain tumour patient subgroups from the Czech Republic. The occurrence of this genetic variant was correlated with the presence of selected somatic mutations representing predictive biomarkers in the respective tumours. Methods. DNA of tumour tissues was isolated from 428 colorectal cancer samples, 311 non-small cell lung cancer samples, 195 breast cancer samples and 151 samples with brain tumour. Analysis of SNP (rs61764370) was performed by the PCR+RFLP method and direct sequencing. KRAS, BRAF and EGFR mutation status was assessed using real-time PCR. The status of the HER2 gene was assessed using the FISH method. Results. The KRAS-LCS6 TG genotype has been detected in 16.4% (32/195) of breast cancer cases (in HER2 positive breast cancer 3.3%, in HER2 negative breast cancer 20.1%), in 12.4% (53/428) of CRC cases (KRAS/BRAF wild type CRC in 10.6%, KRAS mutant CRC in 10.1%, BRAF V600E mutant CRC in 18.5%), in 13.2% (41/311) of NSCLC samples, (EGFR mutant NSCLC patients in 8%, EGFR wild type NSCLC in 12.9%), and 17.9% (27/151) of brain tumour cases. The KRAS-LCS6 TG genotype was not significantly different across the studied tumours. In our study, the GG genotype has not been found among the cancer samples. Conclusions. Based on the findings, it is concluded that the occurrence of the KRAS-LCS6 TG genotype was statistically significantly different in association with status of the HER2 gene in breast cancer. Furthermore, significant association between the mutation status of analysed somatic variants in genes of the EGFR signalling pathway (KRAS, BRAF, EGFR) and the KRAS-LCS6 genotype in colorectal cancer and NSCLC has not been established.

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“…In support of this theory, a genome-wide association study (GWAS) in Mexicans identified a protective allele for asthma that was more common on Native American haplotypes. 8 In addition, the protective allele for the SNP rs907092 associated with asthma in a previous GWAS in GALA II 28 is more common Native American populations (40.0%) from North and South America than in populations from Africa (11.2%) according to The ALlele FREquency Database (ALFRED) 36 and in the Human Genome Diversity Project. 37 Interestingly, the SNP rs907092 is an expression quantitative trait loci (eQTL) for several genes in the region 17q21 (http://www.ebi.ac.uk/Tools/geuvadis-das), especially for ORMDL3 ( p =9.1×10 −44 ).…”

Section: Discussionmentioning

confidence: 96%

Genetic ancestry influences asthma susceptibility and lung function among Latinos

Pino-Yanes

Thakur

Gignoux³

et al. 2015

Journal of Allergy and Clinical Immunology

117

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Background Childhood asthma prevalence and morbidity varies among Latinos in the United States, with Puerto Ricans having the highest and Mexicans the lowest. Objective To determine whether genetic ancestry is associated with the odds of asthma among Latinos, and secondarily whether genetic ancestry is associated with lung function among Latino children. Methods We analyzed 5,493 Latinos with and without asthma from three independent studies. For each participant we estimated the proportion of African, European, and Native American ancestry using genome-wide data. We tested whether genetic ancestry was associated with the presence of asthma and lung function among subjects with and without asthma. Odds ratios (OR) and effect sizes were assessed for every 20% increase in each ancestry. Results Native American ancestry was associated with lower odds of asthma (OR=0.72, 95% confidence interval [CI]: 0.66–0.78, p=8.0×10−15), while African ancestry was associated with higher odds of asthma (OR=1.40, 95%CI: 1.14–1.72, p=0.001). These associations were robust to adjustment for covariates related to early life exposures, air pollution and socioeconomic status. Among children with asthma, African ancestry was associated with lower lung function, including both pre- and post-bronchodilator measures of forced expiratory volume in the first second (−77±19 ml, p=5.8×10−5 and −83±19 ml, p=1.1×10−5, respectively) and forced vital capacity (−100±21 ml, p=2.7×10−6 and −107±22 ml, p=1.0×10−6, respectively). Conclusion Differences in the proportions of genetic ancestry can partially explain disparities in asthma susceptibility and lung function among Latinos.

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ALFRED: an allele frequency resource for research and teaching

Cited by 87 publications

References 24 publications

DRD4 and susceptibility to peer influence on alcohol use from adolescence to adulthood

DRD4 and susceptibility to peer influence on alcohol use from adolescence to adulthood

Comparison of the prevalence of KRAS-LCS6 polymorphism (rs61764370) within different tumour types (colorectal, breast, non-small cell lung cancer and brain tumours). A study of the Czech population

Genetic ancestry influences asthma susceptibility and lung function among Latinos

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