Question

Find any Neurobiology PRIMARY article (short but long enough) and summarize the background leading up to research, materials and methods section, results section, and the author's conclusion.

Please include a complete reference of the article.

Answer 1

Citation: Logue MW, Lancour D, Farrell J, Simkina I, Fallin MD, Lunetta KL and Farrer LA (2018) Targeted Sequencing of Alzheimer Disease Genes in African Americans Implicates Novel Risk Variants. Front. Neurosci. 12:592. doi: 10.3389/fnins.2018.00592

Background of research

The genetic architecture of late-onset Alzheimer disease (AD) in African Americans (AAs) differs from that in persons of European ancestry. In addition to APOE, genome-wide association studies (GWASs) of AD in AA samples have implicated ABCA7, COBL, and SLC10A2 as AA-AD risk genes. Previously studies identified by whole exome sequencing a small number of AA AD cases and subsequent genotyping in a large AA sample of AD cases and controls association of AD risk with a pair of rare missense variants in AKAP9. These studies confirm the utility of examining African-descent samples to identify new AD risk variants in known AD genes as well as novel AD loci. In this study, targeted sequencing in a discovery cohort containing approximately 1,000 AAs to identify new potentially causal variants in risk genes previously implicated in AD risk in AAs (ABCA7, AKAP9, COBL, MS4A6A, PTK2B, SLC10A2, and ZCWPW1) or in AD and related traits in other populations.

Materials and Methods

The study was carried out by using the targeted gene sequencing

Samples used

a. 113 AD (Alzheimer disease) cases and 131 controls from two cohorts of AA (African Americans) is a family-based study of clinic-based AD cases and their first-degree relatives.

b. 222 AD cases and 190 controls from the Genetic and Environmental Risk Factors for Alzheimer Disease among African Americans i.e. unrelated individuals ascertained through the Henry Ford Health System.

Additionally, deep sequencing (including both introns and exons) of approximately 100 genes previously linked to AD or AD-related traits in an AA cohort of 489 AD cases and 472 controls to find novel AD risk variants were performed.

Sequencing Methods

The sequencing was done in two waves by using Illumina Hiseq2500 1T platform and Illumina HiSeq4000 platform.

Sanger Sequencing

Genotyping for the ABCA7 deletion polymorphism rs567222111 was performed by using bi-directional Sanger sequencing. Further the data were processed for quality control for duplicate removal, local realignment near indels, base quality score recalibration, and variant quality score recalibration.

Statistical Analysis

The data were analyzed by using different statistical packages like PLINK v1.9, GMMAT package and LDlink.

Results:

The results showed that there was an 11 base-pair frame-shift loss-of-function (LOF) variant in ABCA7 gene (rs567222111) for which the evidence was bolstered when combined with data from a replication AA cohort of 484 cases and 484 controls (OR = 2.42, p = 0.022).

The results also showed the association of AD with a rare 9 bp deletion (rs371245265) located very close to the AKAP9 transcription start site (rs371245265, OR = 10.75, p = 0.0053). The most significant findings were obtained with a rare protective variant in F5 (OR = 0.053, p = 6.40 × 10-5), a gene that was previously associated with a brain MRI measure of hippocampal atrophy, and two common variants in KIAA0196 (OR = 1.51, p<8.6 × 10-5). Gene-based tests of aggregated rare variants yielded several nominally significant associations with KANSL1, CNN2, and TRIM35.

Conclusion:

The present study was carried out to identify variants with supporting genetic evidence and predicted functional impact for examination in relevant biological systems. Given the previously identified relationship between loss of function mutations in ABCA7 and AD and genetic and biological evidence for a role of rare AKAP9 variants in AD, the novel ABCA7 coding region deletion (rs567222111) and the potentially regulatory AKAP9 deletion (rs371245265) are the most compelling findings for future studies. However, none of findings remain significant after correcting for the total number of tests performed in the study due to less number of samples. Hence, the present study highlights the difficulty of obtaining statistically significant results with rare variants, especially those with frequencies less than 1%. It is essential to replicate these findings in independent AA samples, and sufficiently large samples will become available eventually through the efforts of large consortia including the Alzheimer ’s disease Genetics Consortium and Alzheimer’s Disease Sequencing Project.