Clinical analysis of genome next-generation sequencing data using the Omicia platform

Abstract

Aims: Next-generation sequencing is being implemented in the clinical laboratory environment for the purposes of candidate causal variant discovery in patients affected with a variety of genetic disorders. The successful implementation of this technology for diagnosing genetic disorders requires a rapid, user-friendly method to annotate variants and generate short lists of clinically relevant variants of interest. This report describes Omicia's Opal platform, a new software tool designed for variant discovery and interpretation in a clinical laboratory environment. The software allows clinical scientists to process, analyze, interpret and report on personal genome files.

Materials & methods: To demonstrate the software, the authors describe the interactive use of the system for the rapid discovery of disease-causing variants using three cases.

Results & conclusion: Here, the authors show the features of the Opal system and their use in uncovering variants of clinical significance.

Figure 1. Omicia score

Receiver operating characteristic curve of the performance of different variant impact assessment algorithms on 10,000 test variants, including Human Gene Mutation Database disease-causing mutations and benign high frequency mutations from dbSNP.

Figure 2. Opal Variant Miner webpage

The Variant Miner consists of the variant annotation grid and filtering options by knowledge sets or variant properties. To the left of the table are the multiple available filtering options (in the collapsible windows). The bottom of the table lists the number of variants (items) left after each filtering step. Each variant is listed per table row, and ordered numerically by chromosome number and position. Hyperlinks to additional information are available for the Gene (in blue), Position/dbSNP (in blue), and Evidence (boxed) columns. Quality and Coverage information comes from the next-generation sequencing data file, if available. The allele frequency is from the 1000 Genomes frequency data. Red numbers and words in the Omicia/Polyphen/SIFT columns indicate predicted damaging variants, yellow indicates the prediction of a potentially damaging variant and green indicates a benign variant.

Figure 3. Gene summary window

This window will open if the Gene symbol hyperlink is used from the variant annotation grid. The window contains the gene structure figure with the variant positions marked, a Gene Overview with the NCBI gene summary, and the Relevant Reference Resources has a number of hyperlinks. Any other variants found in the patient for this gene are listed under Personal Variants with the variant in the row where the gene link was instigated highlighted in yellow.

Figure 4. Variant filtering windows

The selections available in each of the various collapsible windows (found on the Variant Miner page) used for data filtering are displayed.

Figure 5. Filtering results for clinical test case 3

The three genes remaining after heuristic filtering in clinical test case 3 are shown in the variant miner view.

Figure 6. Variant Annotation, Analysis and Selection Tool Trio report

Shown is the Variant Annotation, Analysis and Selection Tool data report from the trio analysis performed with the simulated clinical data described in Case 1. The ATP8B1 compound heterozygous changes rank 2nd and 3rd in this report for the Variant Annotation, Analysis and Selection Tool G-score.