IN contributed to the de-identification software by improving its precision and adding important supplementary filtering modules to process discharge summaries.
The Lost Set was then used to identify natural language terms that might serve as supplementary search filter terms, extending search filter performance across the full PubMed database.
By comparing the SNP calls based on Illumina data from CASP12 to the existing capillary sequence data and avoiding heterozygous Y chromosome SNP calls, we could set filtering criteria (Supplementary Material) and filter our complete set of genotype calls using these.
The ingroup alignment consisted of 199,261 amino acid positions which reduced to 131,810 (66% average global identity) positions after filtering (supplementary file S1, Supplementary Material online).
The outgroup alignment contained 146,429 positions which reduced to 91,552 (66% average global identity) after filtering (supplementary file S2, Supplementary Material online).
We thus analyzed the sequence reads that aligned on the mtDNA sequence with the same method used for whole genome data analysis, but applying a supplementary fold-intensity filter (see Methods) to deal with the higher background noise.
Even though the GSF and IC values of the internodes concerned with the branching of the subgenus Anopheles, with the branchings within the A. gambiae species complex, and with the branching of A. christyi, increased as the stringency of the BS and TC filters increased, the values themselves were still lower even for the strictest filters (supplementary table S2, Supplementary Material online).
After stringent microarray data filtering (Supplementary Information S1), 572 of the initial ∼20,000 transcripts on the array remained as input for further analysis (Supplementary Information S1).
A total of 1369 ASD families comprising 1385 ASD probands (Table 1) passed quality control (QC) filters (Supplementary Material, Table S1).
The next step of the filtering strategy implemented a peak-calling strategy to distinguish between segments with bimodal BAF clusters, segments with skewed unimodal BAF deviations and constitutive regions of homozygosity (Supplementary Material, Computational Filtering).
