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Fig. 2 | Genome Medicine

Fig. 2

From: A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases

Fig. 2

Improving the sensitivity of nucleotide variant identification for diagnosis of rare genetic diseases in approximately 35X human WGS. a. Venn diagram comparing nucleotide variants identified in WGS of sample UDT_173 (HiSeq 2500, 2 × 100 nt, 18-h run time) with previously disclosed methods for 50-h diagnostic WGS (Published WGS50 pipeline) [12], or with parameters described herein to improve sensitivity (GSNAP/GATK-VQSR). b. Pie charts showing the distribution of allele frequencies and pathogenicity of nucleotide variants reported by the three pipelines (Published WGS50, GSNAP/GATK-VQSR, and DRAGEN) in WGS of the same sample. Rare variants had allele frequencies <0.01, based on genomic sequences of approximately 3,000 internal samples. Previously reported disease causing variants are ACMG Category 1 mutations. Likely pathogenic variants are ACMG Category 2 variants (loss of initiation, premature stop codon, disruption of stop codon, whole gene deletion, frameshifting indel, disruption of splicing). Possibly pathogenic variants are ACMG Category 3 (non-synonymous substitution, in-frame indel, disruption of polypyrimidine tract, overlap with 5’ exonic, 5’ flank or 3’ exonic splice contexts, and intragenic mitochondrial variants). c Graphs of variant density versus variant allele frequency. Values for the two pipelines are plotted. Results represent the sum of approximately 40X WGS in three samples. Upper panel shows results for all variants. Lower panel shows results for ACMG Category 1–3 variants

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