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Scientists map genes behind risk:
Scientists reveal a new genetic resource of the essay of the food of the mind, opening the door to precision nutrition strategies to protect cognitive function in aging adults.
Data descriptor: Mediterranean intervention for neurodegenerative delay (spirit) Essay: genetic resource for precision nutrition. In addition, Image credit: Crystal Light / Shutterstock
A recent study of data descriptor published in the journal Nutrients Describes genotyping. Nevertheless, quality control (QC) and imputation procedures to generate a new genetic resource from participants in the Mediterranean-Dash test for a neurodegenerative delay test (Spirit).
The prevalence of dementia should increase due to the gradual aging of the world’s population. In addition, scientists map genes behind risk The age -related cognitive decline varies according to individuals. Therefore, The diet is a hybrid of food approaches to stop hypertension (DASH) and Mediterranean diets with certain modifications. Therefore, The mind regime emphasizes the berries. Moreover, green leaves, beans, nuts, seafood, whole grains, wine, olive oil, poultry and limited in fat.
Studies suggest that adherence to the diet can slow down cognitive decline and reduce the risk of Alzheimer’s disease. However. For example, the main clinical trial of the mind found no significant difference in cognitive change after three years compared to a limited control diet.
This result is a key motivation for the current genetic study. For example, The variation in the metabolism of the constituents of the diet between individuals can improve. Furthermore, limit their effectiveness and, ultimately, have an impact on the response to the diet. Consequently. For example, knowledge on genetic factors contributing to this variation scientists map genes behind risk could be useful to identify the subgroups that particularly benefit from this regime and exploring the mechanisms underlying the relationship between cognitive health and the diet.
About the study – Scientists map genes behind risk
In this study. Meanwhile, researchers in the United States described the genotyping, the CQ and the imputation procedures to generate genetic data from the participants in the mental trial. However, The mental trial was a phase III randomized controlled trial (RCT) on the effects of the limited mental regime. in cognitive decline in relation to a usual diet with a similar caloric restriction. Participants were older, overweight and unarmed cognitive adults with a sub-optimal diet and family history of dementia.
Blood samples have been taken at several times. Genomic DNA was extracted from total blood samples and serum. In particular. the researchers had to overcome the challenges, in particular the closure of a laboratory due to the COVVI-19 pandemic, which required scientists map genes behind risk the use of serum for DNA extraction in many cases where total blood was not available. The genotyping of apolipoprotein E (APOE) was made using whole blood samples and serum.
Monomucleotide polymorphisms (SNP) with call rates> 95%, Hardy-Weinberg (HWE) P> 1 × 10-6 balance and the frequency of minor alleles (MAF)> 0.05 were used for the QC sample. Additionally, The discrepancies between self -depressed and genetically deduced sex have been identified.
Kinship (kinship) among the test samples. the effects of the DNA sample, the study site and the batch of tables were examined. In addition, the sample ancestry was genetically deduced using the analysis of the main components (ACP). For the SNP QC, the genotype concordance was evaluated between double pairs to estimate the reproducibility of the genotyping.
For the second QC sample. the team calculated the heterozygoty and poor quality differentiated samples from those of naturally low heterozygotia using scientists map genes behind risk statistical models to identify aberrant values.
In addition. they made a second QC SNP to keep the variants of the X chromosome and autosomal variants with MAF> 0.01, Hwe p> 1 × 10-6 and call rates> 95%. A second ACP was produced by ancestry using a carved autosomal Biallelic SNP set with MAF> 0.05 and call rates> 98%. In addition. genotypes were made for each ancestry using the Haplotype reference consortium (HRC) and 1,000 reference panels for the phase 3 project (1000g).
The APOE genotype of the participants was initially determined by sequencing the SNP RS7412 and RS429358 to APOE Exon 4. In addition, the APOE genotype was derived using imputed SNPs, and the concordance was evaluated using the APOE sequence genotype. To validate the quality of genetic data. researchers have sought to reproduce the known associations of association studies at the genome scale (Gwass) with biomarkers linked to food.
scientists map genes behind risk
Scientists map genes behind risk
Results
DNA concentrations varied between 0.12 ng / μl and 4.14 ng / μl in serum samples and 4.4 ng / μl and 277.8 ng / μl in whole blood samples. Genetic data has been generated for 602 test samples. The exclusion of pre-QC samples with call rates <90% and SNPs with MAF <0.01 led to 573 participants with genotype data for more than 1.01 million SNP. A total of 630,959 SNP were used for QC check samples. Two samples with lag between self -declared and genetically inferred sex were excluded.
Three pairs of first degree parents were identified. The main component 1 (PC1) separated white individuals from black participants. The three Asian participants and a “other” participant gathered closer to the whites. Furthermore, The team used PC1 to define a subset of European descent participants as self-identified white individuals in the six. standard deviations (SDS) scientists map genes behind risk of PC1.
Likewise, a smaller subset of African-Ancian participants has been determined. The ancestry of eight other participants could not be deduced with confidence. so their genetic data was excluded from the final set of data.
Genotypes’ concordance rates varied between 98.1% and 99.8%, indicating high coherence. After QC sample, 58 and 494 unrelated samples of the induced African and European ancestors were preserved, respectively. After a second ACP, the population’s sub-structure remained obvious in the European Ascension Group. In addition, after all QC procedures, 809,442 and 772,662 variants were preserved for 494 and 58 participants in European and African ancestry, respectively.
After the imputation with the 1000g panel, around 47.1 million variants were obtained for each ancestry. The imputation of the CRH, carried out only for the participants in the Old-Biens, resulted in 39.1 million variants. The imputation of the CHRC has demonstrated a higher quality for low frequency scientists map genes behind risk and commune variants. Moreover, The concordance of the APOE genotype was 98.2% between the genotypes of 1000 g and sequenced.
Compared to sequencing data. the gear-based genotypes have poorly classified five non-porters as E4 carriers and two E4 carriers as non-porters. Likewise, HRC’s imputation has given genotypes identical to those with the 1000g panel. The team has reproduced at least one SNP previously linked to adiponectin. alpha-linolenic acid, coffee-carrotene supply, alpha-tocopherol, tea consumption and docosahexaenoic acid in 1000g attributed data. The results were comparable to the data improved by the HRC.
Conclusions
In short, the study presents a genetic resource of the first ECR of the mental diet targeting cognitive results. The results highlight the adequacy of serum as an alternative DNA source. Although the extraction of serum DNA. genotypic performance are lower than those of total blood, the serum remains attractive in the event of a lacking or insufficient scientists map genes behind risk total blood. The HRC and 1000G reference panels have given high quality attributed data for populations of African and European ancestry.
The concordance was high between the APOE genotypes attributed and sequenced. In addition, researchers have reproduced Gwas associations known with biomarkers linked to the diet.
The authors have also noted several limitations to provide a context for future research. This is in particular that the study population was mainly of European ancestry. which can limit the generalization of the results, and that the specific criteria of the participants (for example, overweight, family history of dementia) mean that the resource is not representative of the general population. They also advise that the effects by potential lots of the type of sample. the study site should be taken into account in future analyzes.
This genetic resource allows analyzes of genetic contributions to the variability of cognitive responses to mental diet. supporting scientists map genes behind risk integrative analysis with other types of data to delimit the underlying biological mechanisms. The data will be made available to other researchers via the National Institute on the aging genetics of the. data storage site on Alzheimer’s disease (Niagads).
These efforts could ultimately clarify precision nutrition strategies and help promote cognitive health.
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