Annotations available in Ion Reporter™ Software

Ion Reporter™ Software provides several annotation sources are derived from public and private annotation databases for hg19 and GRCh38. Ion Reporter™ Software also provides annotation sets. An annotation set is a collection of annotation sources that you can use to annotate variants in your analyses. You can use annotation sets that are predefined in the software, or create custom annotation sets.

Each analysis workflow uses a different version of the annotation source. The versions are available in the analysis workflow, and in the TSV file. Every analysis workflow also has an associated annotation set that lists all of the annotation sources used, along with their versions.

To add custom annotation sources to an annotation set, see Import a custom annotation source.

The following annotation are included in Ion Reporter™ Software.

Annotations

Description

Source[1]

5000 exomes

Population frequency information from the 5000 exomes project

NHLBI ESP

Allele coverage

Number of reads supporting the called allele

Ion Reporter™ Software

Allele frequency

Frequency of the allele observed from the raw data

Ion Reporter™ Software

Amino acid change

HGVS notation that represents an amino acid change

Ion Reporter™ Software

Genetic category

Unique genetic category that is used by Ion Reporter™ Software

This annotation is for use only with trio analysis workflows.

Ion Reporter™ Software

ClinVar

Assessment of the impact of the variant observed from NCBI ClinVar database

ClinVar

Coding

HGVS notation that represents a nucleotide change

Ion Reporter™ Software

Copy number

The copy number ploidy state

Ion Reporter™ Software

COSMIC

Catalog of somatic mutations in tumor tissue

COSMIC

Coverage

Total coverage for a variant

Ion Reporter™ Software

Custom

See Import a custom annotation sourcefor more information

Ion Reporter™ Software

Cytogenetic band

The cytogenetic band where the CNV was detected

This annotation is for use only with aneuploidy analysis workflows.

Ion Reporter™ Software

DRA

Disease Research Area

Ion Reporter™ Software

dbSNP

Single Nucleotide Polymorphism database. The dbSNP annotation source in Ion Reporter™ Software contains a flag carried by a subset of its SNPs that have been curated by UCSC to be "UCSC Common SNPs". In order for a variant to be annotated as a UCSC Common SNP, the variant is first annotated as being present in dbSNP, and it might also then have be classified as a UCSC Common SNP.

dbSNP

DGV

Database of Genomic Variants: A curated database of human genomic structural variation

DGV

DrugBank

List of drugs known to target the gene(s) affected by the variant

DrugBank

Note: When you create an hg19 annotation set, do not use the annotation source DrugBank version 20150107. Use instead annotation source DrugBank version 1 or DrugBank version 20161212 or 20180731, which the latest version available in Ion Reporter™ Software 5.12 for hg19. If you use the DrugBank version 20150107 in an hg19 annotation set, you will not be able to create a filter chain of DrugBank for any analysis that uses the annotation set.

ExAC

Exome Aggregation Consortium—Database catalog of variant frequencies

ExAC

Father genotype

Genotype of father.

This annotation is for use only with trio analysis workflows.

Ion Reporter™ Software

FATHMM scores

Prediction of the functional consequences of a variant. In Ion Reporter™ Software, FATHMM scores are available for COSMIC version 77 and later. These scores are populated when "COSMIC" is chosen as a part of the annotation preset that is used.

COSMIC

Gene models

Set of genes that overlap with the variant

RefSeq

Ensembl

Gene panel

Filter variants based on specific amplicon in an AmpliSeq panel. For example, Ion AmpliSeq CCP.

Ion Reporter™ Software

Gene set

Focus on variants found within a specific set of genes

Ion Reporter™ Software

Genetic category

The genetic category. For example, compound heterozygote of the variant identified.

This annotation is for use only with trio analysis workflows.

Ion Reporter™ Software

Genotype

Genotype of the sample in each position

Ion Reporter™ Software

Gene Ontology

Standardized ontology for gene and gene products. For example, functional role or localization.

GO

Grantham score

A measure of evolutionary distance. See Grantham score.

Ion Reporter™ Software

Hotspot information

Indicates whether a variant overlaps a hotspot file

Ion Reporter™ Software

Location

Position of the variant. For example, exonic.

Ion Reporter™ Software

Locus

Position of the variant.

Ion Reporter™ Software

MAF

Population frequency information from the 1000 genomes project.

MAF numbers are provided by the dbSNP in Ion Reporter™ Software, which gets the MAF numbers from 1000 genomes. Therefore, the version of dbSNP annotation sources used within the Ion Reporter™ analysis may impact these MAF values.

1000 Genomes

Mother genotype

Genotype of mother

This annotation is for use only with trio analysis workflows.

Ion Reporter™ Software

MyVariants

A personal knowledge base of genomic variants (formerly, VariantKB database)

Ion Reporter™ Software

Named Variants

A list of known variants in the CFTR gene panel

Ion Reporter™ Software

OMIM

Online Mendelian Inheritance in Man®

OMIM

p-value

p-value of the variant call

Ion Reporter™ Software

Pfam

Protein domain families in the coded protein

Pfam

PhylopP

Measure of conservation of the protein across a wide range of organisms

Cornell University

PolyPhen-2

Prediction of the functional effect of a variant on a protein

Harvard University

Reference

The reference allele (hg19)

Ion Reporter™ Software

Reference / variant coverage

Individual strand coverage information for the reference and variant calls

Ion Reporter™ Software

SIFT

Prediction of the functional effect of a variant on a protein

JCVI

Size

Size of the variant

Ion Reporter™ Software

Transcript set

Preferred transcripts used to determine coding regions of genes.

If you include a transcript file, only transcripts that are present in your selection of canonical transcripts are reported. Other transcripts are filtered out.

RefSeq canonical; Ensembl canonical

Type

Type of variant. For example, SNP, INDEL, CNV, and so on.

Ion Reporter™ Software

UCSC common SNPs

The dbSNP annotation source in Ion Reporter™ Software contains a flag carried by a subset of its SNPs that have been curated by UCSC to be "UCSC Common SNPs". In order for a variant to be annotated as a UCSC Common SNP, the variant is first annotated as being present in dbSNP, and it might also then have be classified as a UCSC Common SNP.

Ion Reporter™ Software

Variant effect

The effect of the variant on the coding sequence. For example, missense or stoploss.

Ion Reporter™ Software

1 In this table, Ion Reporter™ Software refers to either a calculation or functional annotation that is performed by the software.