This analysis further questions the pathogenic role of at least some of the variants present in ESP.
ANK3 and CACNA1C non-synonymous variants present in the coding exons were identified using the Knome VARIANTS software (Knome Inc).
The allelic variants present in an existing population have already been subject to natural selection.
Despite rapid advances in sequencing technologies, accurately calling genetic variants present in an individual genome from billions of short, errorful sequence reads remains challenging.
First, the variants present in any of the SCCs were gathered in a comprehensive list of interesting positions, which was specific to each individual.
Dr Tishkoff reconstructed the recent history of G6PD by examining the variants present in more than 450 Africans.
Inflated true positive, false positive, and false negative estimates can result when we ignore the fact that some variants present in the sample are missing in the GIB gold standard set results.
Variants present in at least two of the eight geographic regions included 2,684,863 SNPs and 370,258 small indels, which together covered 5.7 Mb of the reference genome (Supplementary Fig. 1).
To remove false positive sites that were germline polymorphisms, we further filtered those that overlapped with germline variants present in > 10 of the 6500 non-cancer individuals sequenced by NHLBI GO Exome Sequencing Project (ESP, http://evs.gs.washington.edu/EVS/).edu/EVS/
In each experiment, the authors used mRNA from just 50 neurons from the brains of people with or without sporadic Alzheimer's, because averaging across large neuronal populations could mask variants present in only a few cells.
Two of these variants, present in one proband with familial AF, were located at adjacent nucleotides in the Kozak sequence and reduced expression of an engineered reporter.
