Table 1:
Types of somatic data and limitations of somatic data usage for annotating germline variants in cancer predisposition genes. LOH: loss of heterozygosity.
| Somatic Data Type | Utility | Limitations | ||||
|---|---|---|---|---|---|---|
| Defined by Field with Standard Reference |
Availability of Assay | Tissue Dependent | Confounding Factors for Interpretation |
Subject to Modification with increasing Metadata |
||
| Loss of Heterozygosity | Evidence supporting second hit and consistency with Knudson Two---Hit Hypothesis | No | Algorithms to defineare assay dependent and a definition is not accepted regarding size of LOH | Requires tumor tissue an different Labs have variable requirements pertaining to amount and type | Certain tumor types are difficult to determine, i.e. hypodiploid leukemia | As more tumors sampled greater clarity will be determined regarding focal vs. diffuse LOH definitions |
| Cancer Hotspots | Mutations defined based metadata, gene size, and tumor types | Yes; cancerhotspots.com; cBioPortal.com | Data can begenerated by reference laboratories | Requires tumor tissue anddifferent labs have variable requirements pertaining to amount and type | Not all Cancer Types have beenfactored into calculation of Hotspots. At present 25,000 tumor types included | Definitions have seen changes in definition based on analysis of 11,000 tumors to 25,000 |
| RNA-‐Seq | Beneficial in determining significance of splicing variants | No | Many commercial and academic labs; but few offer clinically | Requires tumor tissue anddifferent labs have variable requirements pertaining to amount and type: can also be done on non-‐tumor tissue | Universal standard for interpretation lacking | Yes |
| Microsatellite Instability Sensor | Provides evidence consistentwith mis-‐match repair deficiency | Yes (but center dependent) | Available by some clinical labs | Yes | Tumor purity can impact interpretation | Yes |
| Chromothripsis | Provides evidence consistentwith germline TP53 mutation | Yes: signature 13 | Limited requiresWGS/WES | No | Tumor purity | No |
| Immunohistochemistry (IHC) | Absence of proteins by IHCprovides evidence of genetic abnormality, e.g. mis-‐match repair genes, SDH complex genes | For some genes, e.g., MLH1, MSH2, MSH6, PMS2, SDHA, SDHB | Commercially available, expensive | Yes | Preparation and amount oftissue available | No |
| Cancer Signatures | e.g. 3,6,9, 13 when detectedcan provide evidence of germline abnormality | Yes | Yes, but requires WGS/WES | No | Expensive, Analytic Expertise | Yes |
| Second Mutation of Alternate Allele | Evidence supporting secondhit and consistency with Knudson Two---Hit Hypothesis | No | yes, but to becomplete requires extensive | No | Depending on extent ofsequencing second mutation may or may not be missed | Yes |
| Methylation Testing | Epigenetic silencing mayindicate evidence supporting second hit and consistency with Knudson Two---Hit Hypothesis | Yes: brain tumors and sarcomas | Limited | Yes | Tumor purity and handling of sample | Yes |