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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.

Can I use TogoVar in-house?

A Docker image will be released. We request your patience.

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
JGA-NGS
JGA-SNP
3.5KJPN
HGVD
ExAC

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
rs114202595 chr7:127254587 G>A 7:127254587 G A 7:g.127254587:G>A
tgv30913365
GT
G>T G T 7:g.127254587:G>T
Ins
tgv1019
1
138646
A
rs761725800 chr1:138646 dupA 1:138646 C CA 1:g.138646_138647insA
Del
tgv63
1
13486
GC
rs780379327 chr1:13486-13487 delGC 1:13485 AGC A 1:g.13486_13487del
Indel
tgv1537710
1
53676691
CTA
rs1057517525 chr1:53676691 delCinsTA 1:53676691 C TA 1:g.53676691delinsTA
Substitution
tgv675673
1
21889705
ACCA
rs786204530 chr1:21889705-21889706 AC>CA 1:21889705 AC CA 1:g.21889705_21889706delinsCA