TarCET hereditary cancer panel

• APC(NM_000038.6): Selected region of promoter 1B is covered for sequence changes and selected region of promoter 1A is covered for both sequence changes and CNVs.
• CDKN2A: Analysis is performed for transcripts NM_000077.5 and NM_058195.4 that encode the p16INK4a and p14ARF proteins respectively.
• EPCAM(NM_002354.3): Analysis is limited to CNV analysis.
• GREM1(NM_013372.7): Analysis is limited to CNV analysis of the 40 kb 5’ upstream regulatory region.
• HOXB13: Analysis is limited to NM_006361.6: c.251G>A (p.G84E) variant.
• MLH1(NM_000249.4): Selected region of the promoter is covered for sequence changes.
• MSH2(NM_000251.3): Selected region of the promoter is covered for sequence changes.
• PTEN(NM_000314.8): Selected region of the promoter is covered for both sequence changes and CNVs.
• TP53(NM_000546.6): Selected region of the promoter is covered for CNVs.

• Genomic regions not covered by this test:
  • BMPR1A (NM_004329.3): exon 13
  • CHEK2 (NM_007194.4): exons 12-15
  • DICER1 (NM_177438.3): exon 27
  • FANCA (NM_000135.4): exon 15
  • FANCD2 (NM_001018115.30): exons 12-17 and 19-28
  • PMS2 (NM_000535.7): exons 11-15
  • POLE (NM_006231.4): exon 1
  • PTEN (NM_000314.8): exon 9
  • RB1 (NM_000321.3): exon 15
  • SDHC (NM_003001.5): exon 6
  • SMARCA4 (NM_001387283.1): exons 27, 30

This test aims to detect all variants relevant to hereditary cancer predisposition in the genes (MANE and/or canonical transcripts) listed above, by targeting the exons, 20 bp of adjacent intronic sequence, selected untranslated regions (UTR) and promoter regions. Variants that fall outside of the targeted regions are not intended to be detected by this assay. Unless otherwise noted, sequence changes (SNVs and INDELS) in the promoter and other deep intronic regions are not covered by this assay. Certain sequence changes (SNVs and INDELS) in non-coding regions of selected genes that are of clinical significance are also included in the analysis. In cases where two variants are identified in a gene, the test does not distinguish whether these are on one chromosome (in cis) or on different chromosomes (in trans). Certain sequence changes (SNVs and INDELS) in targeted regions containing repeats, sequences of high homology such as segmental duplications and pseudogenes, as well as regions of high/low GC-content may not be detected.

Copy Number Variations (CNVs) are calculated using high quality, de-duplicated and uniquely aligned sequencing reads. CNVs are detected for a subset of the targeted regions using a depth of sequencing coverage approach by applying GC-content normalization. Genomic regions are called as variants if their normalized depth of coverage deviates significantly from the expected normalized coverage which is estimated from a set of reference clinical samples. The test can detect CNVs down to a few exons level resolution. The test cannot detect CNVs at genomic regions with either low capability or containing repeats, pseudogenes and high/low GC-content. Detection of CNVs using NGS has lower sensitivity/specificity than orthogonal quantification methods, therefore the absence of reported CNVs does not guarantee the absence of CNVs. The lack of disease-causing variants in the targeted genes diminishes but does not exclude the possibility of a disease associated syndrome. Although the test is highly accurate there is still a possibility for false positive or false negative results.