Table 1.
Coding fields used for reviewing papers.
| Topic | Coding fields |
|---|---|
| Publication | Pubmed ID; Journal; Year; Author; Title; Abstract; |
| Study general | Goal; Study design; Source of individuals; Cancer type; Ethnicity; Sequencing Center; Data repository; |
| Number of individuals sequenced in discovery | Number of cases, controls, families, and cases per family sequenced in discovery phase; |
| Sequencing technique | Samples type; Exome and/or genome; Capture kit; Sequencer; Coverage/depth; |
| Processing of raw-data | Aligner; Reference genome; Variant caller and calling QC; Annotation software and sources; |
| Technical validation | Yes/No; Validation technology; Number of cases, controls, families, and cases per family sequenced in validation phase; variants/genes validated; |
| Independent replication | Yes/No; Replication technology and analysis; Number of cases, controls, families, and cases per family sequenced in replication phase; variants/genes replicated; |
| Functional validation | In silico functional analyses; Experimental functional study; |
| Variants and genes data analysis | Candidate analysis approach; Filtering strategy overall; Analytical methods; |
| Variants and genes identification | Yes/No; Identified variants and genes; Number of cases, controls, families carrying the identified variants and genes; |
| Authors comments and conclusions | Challenges; Suggested next steps; Conclusions; |
| Derived filtering criteria/categories shown in Figure 1 | f_1: variant passing quality control metrics |
| f_2: heterozygous variant | |
| f_3: homozygous variant | |
| f_4: variant located in a coding region | |
| f_5: nonsynonymous or splice variant | |
| f_6: variant damaging according to in silico algorithms | |
| f_7: truncating variant | |
| f_8: variant altering protein properties according to molecular modeling | |
| f_9: not hypervariable gene | |
| f_10: variant absent from Minor Allele Frequency (MAF) databases | |
| f_11: variant rare in MAF databases | |
| f_12: variant segregating with disease status in the family | |
| f_13: variant present in multiple families or independent cases | |
| f_14: variant enriched in cases compared to controls | |
| f_15: gene mutated in multiple families or independent cases | |
| f_16: gene enriched in cases compared to controls | |
| f_17: variant present in disease related databases | |
| f_18: gene known to be linked to disease | |
| f_19: genetic region known to be linked to disease | |
| f_20: biological or molecular pathway known to be linked to disease | |
| f_21: pathway analysis indicating a gene-disease link | |
| f_22: variant confirmed through technical validation | |
| f_23: variant or gene replicating in independent cases | |
| f_24: variant loss of heterozygosity (LOH) observed in tumor | |
| f_25: relevant somatic mutations observed in tumor | |
| f_26: gene-disease link supported by functional experiments | |
| f_27: variant splicing supported by experiment | |
| f_28: variant-disease link supported by functional experiment |