Whole exome sequencing is a targeted capture platform which does not capture the entire exome. Regions not captured by the exome will not be analyzed.

• Please note, it is important to understand the absence of a reportable variant in a given gene does not mean there are not pathogenic variants in that gene.

Data sensitivity and specificity for exome testing is variable as gene coverage is not uniform throughout the exome.

The Agilent SureSelect XT Human All Exon v5 kit captures ~98% of Refseq coding base pairs, and >94% of the captured coding bases in the exome are covered at our depth-of-coverage minimum threshold (30 reads).

All test reports include the following information:

• Regions of the symptom candidate gene list which were not captured by the current exome capture platform.
• Regions of the symptom cadidate gene list which were not sequenced to a sufficient depth of coverage to make a clinical diagnosis.

You can check if genes are captured by the Agilent SureSelect v5 exome capture, and how well those genes are typically covered here.

Coverage Glossary

Symbol: Gene symbol

Chr: Chromosome

% Captured: The minimum portion of the gene captured by the Agilent SureSelect XT Human All Exon v5 kit. This includes all transcripts for a given gene.

• 100.00%=the entire gene is captured
• 0.00%=none of the gene is captured

% Covered: The minimum portion of the gene that has at least 30x average coverage when sequenced on the Illumina HiSeq2000 with 100 base pair (bp) paired-end reads for eight CEPH samples. This is the result for a typical sample, but the minimum when considering all of the different isoforms for the given gene.

% High Quality: The minimum portion of the gene we would anticipate being captured and having 30x sequence coverage or greater.

• For example, for the gene BAGE4, 94.26% of the gene is captured, 99.89% of the captured regions of the gene are covered by 30x sequencing depth, for a minimum of 94.15% of BAGE4 will be captured and sequenced to a depth required to make a clinical diagnosis.
• Please note, these are minimum values, and any gene may be better covered than the values listed in the table.

Please contact us if you have any questions regarding gene capture and coverage metrics at iihg@uiowa.edu.