Boletín de Segovia: Número 68 - 1874 junio 8

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Additional file 2: of Molgenis-impute: imputation pipeline in a box

Computation of IMPUTE2’s info metric

Additional file 4: Table S4. of GAVIN: Gene-Aware Variant INterpretation for medical sequencing

The tools used to evaluate our benchmark variant set and the web addresses used through which they were accessed. (XLSX 51 kb

Resolving variants of unknown significance through reanalysis of 4,978 public RNA-seq samples

<p>Presentation given at the European Society of Human Genetics (ESHG) 2014 conference.</p

Additional file 2: Table S2. of GAVIN: Gene-Aware Variant INterpretation for medical sequencing

Detailed overview of all benchmark results. Each combination of tool and dataset is listed. We provide the raw counts of true positives (TP), true negatives (TN), false positives (FP), and false negatives (FN), as well as of pathogenic and benign variants that were “missed,” i.e. not correctly identified as such. From these numbers, we calculated the sensitivity and specificity. (XLSX 58 kb

Additional file 3: Table S3. of GAVIN: Gene-Aware Variant INterpretation for medical sequencing

Estimate of the practical impact in clinical diagnostics of using methods of different sensitivity and specificity on a dataset with 100 benign and 10 pathogenic variants. (XLSX 50 kb

Final Review

Overview of the number of variants detected at each filter step for each patient. (DOC 128 kb

Correlation between the NC statistic and PolyPhen2 predictions.

<p>Within each minor allele count, derived missense alleles are positively correlated (Spearman's ) with PolyPhen2 predictions (pph2_prob), while no such correlation exists for ancestral missense alleles. P-values are 1-sided (alternative hypothesis ).</p

Cartoon presentation of the NC statistic.

<p>The NC statistic aims to capture the length of the haplotype carrying a variant. For a given variant (called the index variant, shown in the middle of the figure), the value of the NC statistic is the base-10 logarithm of the sum of physical distances measured up-stream (5′ direction) and down-stream (3′ direction) from the index variant to the closest variant that is either beyond a recombination spot (example shown on the left) or is linked to the index variant but is rarer than the index variant (example shown on the right). The red arrow in the figure illustrates that sum of the two distances.</p

Discrimination of derived missense alleles by the NC statistic.

<p>Missense alleles are sub-classified info categories based on <i>PolyPhen-2</i> predictions. Effect sizes were calculated as standard deviations from the mean of the NC statistic for synonymous variants at the same minor allele count (MAC). Within each MAC class, P-values were calculated by 1-sided Mann-Whitney test. Combined P-values for MAC 2–6 were computed by meta-analysis (Methods).</p