Help

TogoVar in general

What are the objectives and utilities of TogoVar?

NGS technologies have enabled large-scale genome sequencing to capture variants at low frequencies. However, existing databases do not contain sufficient variant frequency data for Japanese populations. To address this problem, TogoVar seeks to provide a reliable frequency information by assembling variant information from the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA) and public Japanese genomic variation data.

In addition, since the reference human genome sequence can be updated, the genomic position may vary for the same variant if it refers to a different genome build. Thus, in our database, a unique ID is assigned to the same variant, thereby preventing the need to convert the positional information of the variant among different reference sequences, as done by researchers.

Do you have videos that explain TogoVar?

See TogoTV. Videos on TogoVar are here.

About the terms of use

Can I use the TogoVar for free?

You can use the TogoVar service for free. For the use of the database, refer to the Terms.

How to cite the TogoVar database in my publication?

Refer to the attribution (credit) display examples in Terms.

Can I use it for commercial purposes?

You are free to browse the TogoVar websites and use the docker images to be released for commercial purposes. For data created by third parties and imported in TogoVar, please follow the terms of use of each organization. For more details, refer to Terms.

About the data collected in TogoVar

Can I retrieve phenotype information on an individual level?

TogoVar database does not keep private information, and we do not currently provide phenotype information for each individual. For more details about phenotype information, please directly contact the research groups described in the JGA-NGS dataset and JGA-SNP dataset.

Are the data linked with information about gene expression and proteins?

Not yet but planned.

What software is used for detecting variants and how you manage the quality?

What are the targeted variant types for TogoVar?

There are five targeted variant types for TogoVar: SNV, Insertion, Deletion, Indel, and Substitution. Of 5 types that HGVS enumerated as the types of variants, Duplication is classified as Insertion, and Indels, for which the lengths of Insertion and Deletion are the same, are classified as Substitution. To identify the type of the variant, Variant Effect Predictor (VEP) is used.

How do you calculate the Consequence value?

The value of variant consequence in Variant Effect Predictor (VEP) is displayed. If there are multiple transcripts for a single variant, only the most critical consequence may be displayed.

What are SIFT and PolyPhen?

Both SIFT and PolyPhen are scores which indicate the predicted effects on the protein function when an amino acid sequence undergoes alteration due to a variant. Values calculated through Variant Effect Predictor (VEP) are displayed. The meaning of each icon is as follows.

  • SIFT
    < 0.05
    Deleterious
    ≥ 0.05
    Tolerated
  • PolyPhen
    > 0.908
    Probably Damaging
    > 0.446
    Possibly Damaging
    ≤ 0.446
    Benign
     
    Unknown

How do you calculate the value of Clinical significance?

The value of clinical significance in ClinVar is displayed.

About the TogoVar search system

What does the frequency indicator in the Frequency column of the search results represent?

The frequency indicator represents the alternative allele frequency for each dataset. The color of the frequency meter corresponds to the color allocated to the dataset. The data availability or frequency value is represented on a 9-point scale.

  Not Available
  Monomorphic (REF)
  Singleton
  < 0.0001
  < 0.001
  < 0.01
  < 0.05
  < 0.5
  ≥ 0.5
  GEM-J WGA
  JGA-NGS
  JGA-SNP
  ToMMo 8.3KJPN
  HGVD
  gnomAD genomes
  gnomAD exomes

For each variant type, how is the position, reference and alternative allele described respectively?

An example for each variant type is shown below. Note that the position of the first base in the chromosome is 1.

Variant Type

ID

Position

Ref / Alt

Description

SNV
tgv41
1
13116
TG
The 13116th base T in Chromosome 1 was replaced by G.
Ins
tgv1019
1
138646
A
A base A was inserted between the 138646th and 138647th bases in Chromosome 1.
Del
tgv63
1
13486
GC
The 13486th and 13487th bases, GC, in Chromosome 1 were deleted.
Indel
tgv1537710
1
53676691
CTA
The 53676691st base C in Chromosome 1 was deleted and TA was inserted in its place.
Substitution
tgv675673
1
21889705
ACCA
The 21889705th bases, AC, in Chromosome 1 were deleted and CA were inserted in their place.

In TogoVar, how is the variant described?

A. In TogoVar a variant is identified as a set of its genomic position, reference and alternative allele and human genome build. Examples of variant notations in TogoVar, dbSNP, VCF and HGVS are shown below.

TogoVar

dbSNP

VCF

HGVS

ID

Position

Ref / Alt

ID

Position(GRCh37)

Alleles

Position

Ref

Alt

SNV
tgv30913364
7
127254587
GA
rs114202595chr7:127254587G>A7:127254587GA7:g.127254587:G>A
tgv30913365
GT
G>TGT7:g.127254587:G>T
Ins
tgv1019
1
138646
A
rs761725800chr1:138646dupA1:138646CCA1:g.138646_138647insA
Del
tgv63
1
13486
GC
rs780379327chr1:13486-13487delGC1:13485AGCA1:g.13486_13487del
Indel
tgv1537710
1
53676691
CTA
rs1057517525chr1:53676691delCinsTA1:53676691CTA1:g.53676691delinsTA
Substitution
tgv675673
1
21889705
ACCA
rs786204530chr1:21889705-21889706AC>CA1:21889705ACCA1:g.21889705_21889706delinsCA

Q: Can I search byHGVS description(e.g. ALDH2:p.Glu504Lys)?

Yes. HGVSc (e.g.ALDH2:c.1510G>A) and HGVSp (e.g.ALDH2:p.Glu504Lys) are acceptable. Variant Recorderis used to convert an HGVS description to a GRCh37 position.

Q: What can I do with the Advanced search?

You can build a query with an alternative allele frequency, clinical significance, and other search criteria combined with the AND and/or OR operator. See"Q: Can I search for variants with different alternative allele frequencies between Japanese and other populations?" for usage.

Can I search for variants with different alternative allele frequencies between Japanese and other populations?

Yes. You can search by Advanced search

Variant sets for comparison of alternative allele frequencies are as follows:
  • For Japanese populations, variants included in either GEM-J WGA or 8.3KJPN
  • For gnomAD populations, variants included in either gnomAD genomes or gnomAD exomes

We will search for variants with an alternative allele frequency greater than 0.3 for Japanese populations and less than 0.05 for gnomAD populations.
  1. Select the Advanced search tab at the top of the home page.help-image1
  2. Select the Alternative allele frequency/count at the Add condition menu.

    help-image2

  3. Specify a dataset (GEM-J WGA) and an alternative allele frequency (>= 0.3). You can also specify the number of alternative alleles.help-image3
  4. Click the OK button. The search criteria has been set.help-image4
  5. In the same procedures, enter search criteria for the datasets, ToMMo 8.3KJPN, gnomAD genomes and gnomAD exomes.help-image5
  6. Join the search criteria for Japanese populations, GEM-J WGA and ToMMo 8.3KJPN, with the OR operator.
    1. Select the search criteria for GEM-J WGA and ToMMo 8.3KJPN. The selected criteria is enclosed by yellow borders.help-image6
    2. Select the Group menu. The selected criteria are joined with the OR operator. To change to the AND operator, click the OR icon.help-image7
  7. In the same procedures, the search criteria for the gnomAD genomes and gnomAD exomes are joined with the OR operator.help-image8

The final search criteria is as follows:

((freq(GEM-J WGA) >= 0.3) OR (freq(ToMMo 8.3KJPN) >= 0.3))
AND
(freq(gnomAD genomes) <= 0.05) OR (freq(gnomAD exomes) <= 0.05))

Each time search criteria is changed, the search is automatically executed and a list of variants that match the criteria is refreshed.help-image9

Functions in the menu bar
  • Add condition: Add search criteria to the query builder.
  • Group: Combine selected search criteria indicated by yellow borders with the OR operators. Note: click the OR icon to change to the AND operator.
  • Ungroup: Separate joined search criteria. This is a reverse operation of the Group menu.
  • Delete: Delete selected search criteria indicated by yellow borders.

Meaning of the icons
  • help-pencil:Edit search criteria
  • help-cross:Delete search criteria