Table 1.
Significant CNVR output fields description
| Column | Description |
|---|---|
| CNVR | CNV region of greatest significance and overlap coordinates. |
| CountSNPs | The number of probes available in the CNVR for this data set. In this case, contributing individual CNV calls may be larger. |
| SNP | Tag SNP for ease and clarity of reporting and replication. |
| DelTwoTailed | Two-tailed Fisher’s exact P-value based on the contingency table Cases Del/Cases Diploid/Controls Del/Controls Diploid as listed separately. |
| DupTwoTailed | Two-tailed Fisher’s exact P-value based on the contingency table Cases Dup/Cases Diploid/Controls Dup/Controls Diploid as listed separately. |
| ORDel | The odds ratio for deletion. |
| ORDup | The odds ratio for duplication. |
| Cases Del | The number of cases with a deletion detected in this region by PennCNV. |
| Cases Diploid | The number of cases without a deletion or duplication detected in this region by PennCNV. |
| Control Del | The number of control subjects with a deletion detected in this region by PennCNV. |
| Control Diploid | The number of control subjects without a deletion or duplication detected in this region by PennCNV. |
| Cases Dup | The number of cases with a duplication detected in this region by PennCNV. |
| Cases Diploid | The number of cases without a deletion or duplication detected in this region by PennCNV. |
| Control Dup | The number of control subjects with a duplication detected in this region by PennCNV. |
| Control Diploid | The number of control subjects without a deletion or duplication detected in this region by PennCNV. |
| IDsCasesDel | The sample IDs of cases corresponding to the Cases Del column for clinical data lookup. To convert to list in Excel: Data-TextToColumns-Delimited-Space then Copy-PasteSpecial-Transpose. |
| IDsCasesDup | The sample IDs of cases corresponding to the Cases Dup column for clinical data lookup. To convert to list in Excel: Data-TextToColumns-Delimited-Space then Copy-PasteSpecial-Transpose. |
| StatesCasesDel | CN states listed corresponding to IDsCasesDel [1 (CN = 0)/2 (CN = 1)]. |
| StatesCasesDup | CN states listed corresponding to IDsCasesDup [5 (CN = 3)/6 (CN = 4)]. |
| TotalStatesCases(1) | The number of cases in Cases Del with a homozygous deletion or both copies lost. |
| TotalStatesCases(2) | The number of cases in Cases Del with a hemizygous deletion or one copy lost. |
| TotalStatesCases(5) | The number of cases in Cases Dup with a hemizygous duplication or one copy gained. |
| TotalStatesCases(6) | The number of cases in Cases Dup with a homozygous duplication or two copies gained. |
| IDsDelControl | The sample IDs of control subjects corresponding to the Control Del column for clinical data lookup. |
| IDsDupControl | The sample IDs of control subjects corresponding to the Control Dup column for clinical data lookup. |
| StatesDelControl | CN states listed corresponding to IDsDelControl [1 (CN = 0)/2 (CN = 1)]. |
| StatesDupControl | CN states listed corresponding to IDsDupControl [5 (CN = 3)/6 (CN = 4)]. |
| TotalStates(1) | The number of Controls in Controls Del with a homozygous deletion or both copies lost. |
| TotalStates(2) | The number of Controls in Controls Del with a hemizygous deletion or one copy lost. |
| TotalStates(5) | The number of Controls in Controls Dup with a hemizygous duplication or one copy gained. |
| TotalStates(6) | The number of Controls in Controls Dup with a homozygous duplication or two copies gained. |
| ALLTwoTailed | All CNV states considered together P. |
| ORALL | All CNV states considered together OR. |
| ZeroTwoTailed | Only CN = 0 CNV state considered together P. |
| ORZero | Only CN = 0 CNV state considered together OR. |
| OneTwoTailed | Only CN = 1 CNV state considered together P. |
| OROne | Only CN = 1 CNV state considered together OR. |
| ThreeTwoTailed | Only CN = 3 CNV state considered together P. |
| ORThree | Only CN = 3 CNV state considered together OR. |
| FourTwoTailed | Only CN = 4 CNV state considered together P. |
| ORFour | Only CN = 4 CNV state considered together OR. |
| Gene | The closest proximal gene based on UCSC Genes, which includes both RefSeq Genes and Hypothetical Gene transcripts. |
| Distance | The distance from the CNVR to the closest proximal gene annotated. If the value is 0, the CNVR resides directly on the gene. |
| Description | The gene description delimited by ‘/’ for multiple gene transcripts or multiple genes listed. |
| Pathway | Annotated pathway membership of gene with reference compiled from Gene Ontology database, BioCarta database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (definition files in GeneRef folder). |
| AverageNumsnpsCaseDel | The average numsnp of CNV calls contributing to Case Del CNVR. Allows for much more informative CNV size (confidence) filtering post hoc. |
| AverageLengthCaseDel | The average length of CNV calls contributing to Case Del CNVR. Allows for much more informative CNV size (confidence) filtering post hoc. |
| CNVRangeCaseDel | Alternative larger CNV Range Case Del definition compared with minimal common overlap definition of CNVR. |
| AverageNumsnpsControlDel | The average numsnp of CNV calls contributing to Control Del CNVR. Allows for much more informative CNV size (confidence) filtering post hoc. |
| AverageLengthControlDel | The average length of CNV calls contributing to Control Del CNVR. Allows for much more informative CNV size (confidence) filtering post hoc. |
| CNVRangeControlDel | Alternative larger CNV Range Control Del definition compared with minimal common overlap definition of CNVR. |
| CNVType | Deletion or duplication CNVR significant in combined report. |
| Cytoband | Cytoband genomic landmark designations. |
| redFlagCount | Count red flag from association review (see text, briefly: Segmental Duplications, Database of Genomic Variants, Centromere/Telomere, GC base content, Probe Count, Population Frequency, Peninsula, Inflated). |
| redFlagReasons | The failing metrics for association review and their values. |