Whole exome data filtering schema for DNA variants.

Genomic DNAs from five pairs of leiomyomas and corresponding myometrial samples underwent whole exome enrichment and sequencing. After sequence alignment, each pair of leiomyoma and corresponding myometrium was independently analyzed using NextGENe software (represented by each row in the table; SoftGenetics, State College, PA). The DNA variants in each tissue (leiomyoma/normal myometrium) were compared to reveal mutations which were unique to the leiomyoma. After filtering against the Single Nucleotide Polymorphism database v132 (dbSNP132; http://www.ncbi.nlm.nih.gov/projects/SNP/) and applying protein prediction software tools, PolyPhen-2 and SIFT (http://genetics.bwh.harvard.edu/pph2/; http://sift.jcvi.org/), we identified MED12 as the only gene commonly mutated in two or more leiomyomas. The minimum base coverage threshold was 20 sequencing reads per base-pair for variant filtering.aAll DNA variants in exons and within 10 base-pairs (bps) of exon-intron junctions in introns.bDNA variants unique to the leiomyoma in exons and within 10 bps of exon-intron junctions in introns.cDNA variants unique to the leiomyoma in exons and within 10 bps of exon-intron junctions in introns which were not found in dbSNP132.dExonic single nucleotide variants (SNVs) unique to the leiomyoma which caused a change in the protein sequence and were not found in dbSNP132.eSNVs unique to the leiomyoma located in introns within 10 bps of exon-intron junctions which were not found in dbSNP132.fExonic deletions/insertion-deletions (dels/indels) unique to the leiomyoma which were not found in dbSNP132.gDels/indels unique to the leiomyoma located in introns within 10 bps of exon-intron junctions which were not found in dbSNP132.hDNA variants unique to the leiomyoma in exons and within 10 bps of exon-intron junctions in introns which were predicted to be damaging to the protein, not found in dbSNP132.iLeiomyomas L2 and L3 harbored missense SNVs in exon 2 of MED12 which were detected by exome sequencing and predicted to be damaging. L1 contained a 42 bp deletion in exon 2 of MED12 which was undetected by exome sequencing but revealed via Sanger sequencing.