Diagnosis; Mutation Confirmation; Pre-symptomatic; Predictive; Risk Assessment

It is estimated that 80% of families with LFS will harbour an identifiable TP53 mutation.

Establish or confirm diagnosis

Predictive risk information for patient and/or family members

All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that … All coding exons and 20 bp of flanking intronic sequence are enriched using an LHSC custom targeted hybridization protocol (Roche Nimblegen), followed by high throughput sequencing (Illumina). This chemistry and analysis pipeline provides a highly sensitive and specific detection of sequence and copy number alterations in a single assay that exceeds the previous gold standard of Sanger sequence and MLPA. Sequence variants and copy number changes are assessed and interpreted using clinically validated algorithms and commercial software (SoftGenetics: Nextgene, Geneticist Assistant, Mutation Surveyor; and Alamut Visual). All genes have >1000x mean read depth coverage, with a minimum 200x coverage at a single nucleotide resolution. Mitochondrial DNA testing is validated for heteroplasmy detection sensitivity of 2-5%. All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request. View more

All positive results and known familial mutations are confirmed by a second independent method

Direct sequence of all coding exons

Tests performed
Entire test performed in-house

The LHSC NGS protocol is predicted to detect in excess of 99% of mutations present within the genes listed. Mutation detection rates in the patient are dependent on the clinical presentation including age of onset, specific diagnostic features, and family history.

Is proficiency testing performed for this test? Help
No

Software used to interpret novel variations Help
ALAMUT, integrating other programs (Polyphen-2, Mutation Taster, Alignment, ExPASy, BLAST)

Laboratory's policy on reporting novel variations Help
All variants interpreted as either ACMG category 1, 2, or 3 (pathogenic, likely pathogenic, VUS; PMID: 25741868) are confirmed using Sanger sequencing, MLPA, or other assays. ACMG category 4 and 5 variants (likely benign, benign) are not reported, but are available upon request.