KVar metadata
Study
Key Terms and Definitions
SNP Single Nucleotide Polymorphism. In Kvar, this category refers to variations in the genome that include both single nucleotide variants (SNVs) and short insertions or deletions (indels) of 50 bp or less.
SV Structural Variation. Large-scale genomic alterations, typically 50 base pairs or larger, including insertions, deletions, inversions, and translocations
Metadata
Study variant type
Select one of the following study variant types to submit. - SNP - SV
Study title
A brief title of the study. Example: Analysis of Single Nucleotide Polymorphisms in the Korean Population
Study description
A description of the study. Example: We analyzed whole genome sequencing data generated on the Illumina platform from more than 100 normal Korean individuals to identify single nucleotide polymorphisms (SNPs) in the human genome.
Study type
Select one of the following study types to submit. - Case-Control - Case-Set - Collection - Control Set - Somatic - Tumor vs. Matched-Normal Note: Check only if ‘sv’ is selected in Study variant type field
SampleSet
Metadata
SampleSet ID
An appropriate ID for this sampleset. Example: Normal_1, Case_1
SampleSet size
Number of samples in sampleset. Example: 4
SampleSet type
Select one of the following sampleset types. - Case - Control Note: Check only if ‘sv’ is selected in Study variant type field
SampleSet description
Description of sampleset. Example: Korean normal population
SampleSet population
Population of Sampleset. For the subjects represented in the sampleset, indicate the: ethnicity (if human), population (if non-human primate), strain (if mouse), breed (if cattle or dog), cultivar (if plant), etc.
Example: Korean
Sample
Metadata
※ The BioSample Accession ID and Sample Name fields form a grouped requirement, where only one of the two is mandatory.
If a new BioSample is being registered as part of this submission, enter a value in the Sample Name field.
If an existing BioSample is being used, enter the appropriate BioSample Accession ID.
SampleSet ID
The SampleSet ID (from Part 2. SampleSet) to which the sample belongs.
BioSample accession ID
The accession ID of an already registered BioSample corresponding to this sample. Note: If a new BioSample is being registered, leave this field blank and fill out the "BioSample attribute" field instead.
Sample name
A unique name given by the researcher to distinguish each sample within the study. Note: This field must be completed when registering a new BioSample. If an existing BioSample accession ID is provided, this field can be left blank
NCBI taxonomy ID
NCBI’s taxonomy identifier of the organism for this sample. The NCBI taxonomy ID can be found at https://www.ncbi.nlm.nih.gov/taxonomy/. Enter 32644 (which is a taxonomy ID for unidentified organisms) for the following or similar cases: (1) when NCBI taxonomy ID is not available because NCBI taxonomy does not yet cover the organism, (2) when metagenome or environmental sample was used, whose organismal composition is unknown in advance Example: 9606 (for Homo sapiens), 452680 (for Pseudomonas sp. UK4)
Organism
The most descriptive organism name for this sample (to the species, if possible). In the case of a new species, provide the desired organism name. In the case of unidentified species, choose the appropriate Genus and include ‘sp.’, e.g. “Escherichia sp.”. When sequencing a genome from a non-metagenomic source, include a strain or isolate name too, e.g. “Pseudomonas sp. UK4” Example: Homo sapiens, Pseudomonas sp. UK4
Sample description
Description of sample
Sample population
Population of Sample
Example: Korean
Experiment
Key Terms and Definitions
Discovery Initial detection of variants using sequencing methods such as WGS or WES
Genotyping Determination of variant genotypes using sequencing-based methods such as targeted sequencing
Validation Independent confirmation of variants using alternative methods.
Metadata
Experiment ID
A unique ID to identify each of your experiments within the study. Example: snp1
Experiment type
Select one of the following experiment types. - Discovery - Genotyping - Validation
Method type
Select one of the following mehod types. - Sequencing - Oligo aCGH - SNP array - BAC aCGH - Curated - Digital array - FISH - Gene expression array - Karyotyping - MAPH - MassSpec - Merging - Multiple complete digestion - MLPA - Optical mapping - PCR - qPCR - ROMA Note: Only 'Sequencing' is available if 'Discovery' or 'Genotyping' is selected for the Experiment type field
Analysis type
Select one of the following analysis types. See the Analysis type from for details. Note: The possible values for the Analysis type field change depending on the selection in the Method type field. However, 'Manual Observation' and 'Other' are always available, regardless of the Method type selected
Reference value
The Name or accession ID of the reference sequence used for the analysis. Example: GRCh38
Method platform
Select one of the following mehod platform. See the Method platform from for details.
Method description
Description of the technique or technology used to generate the data. Example1: Whole-genome sequencing of the sample was performed using the Illumina NovaSeq 6000 platform with paired-end 150 bp reads, followed by library preparation using the TruSeq DNA PCR-Free kit.
Example2: Targeted sequencing of asthma-associated genes was conducted using a custom capture panel and the Illumina MiSeq platform with paired-end 250 bp reads.
Detection method
The specific method or assay (software package, algorithms, etc)used to detect a biological entity or feature. Example1: Single nucleotide polymorphisms (SNPs) were detected using the Genome Analysis Toolkit v.4.3.0 (GATK) HaplotypeCaller following best practices.
Example2: Structural variants (SVs) were identified using Manta Structural Variant Caller v.1.6.0 with default parameters.
Analysis type
1
Sequencing
Paired-end Mapping
2
Sequencing
Read Depth
3
Sequencing
One End Anchored Assembly
4
Sequencing
Split Read Mapping
5
Sequencing
Sequence Alignment
6
Sequencing
Serial Analysis of Gene Expression
7
SNP array, Oligo aCGH, BAC aCGH, FISH, qPCR
Probe Signal Intensity
8
SNP array
SNP Genotyping Analysis
9
Multiple Complete Digestion
MCD Analysis
10
Merging
Merging
11
Optical Mapping
Optical Mapping
12
Curated
Curated
13
-
Manual Observation
14
-
Other
Method plaotform
1
AB5500GeneticAnalyzer
2
AB 5500xl Genetic Analyzer
3
AB 5500x-Wl Genetic Analyzer System
4
AB SOLiD 3 Plus System
5
AB SOLiD 4 System
6
AB SOLiD 4hq System
7
AB SOLiD PI System
8
AB SOLiD System
9
AB SOLiD System 2.0
10
AB SOLiD System 3.0
11
BGISEQ-50
12
BGISEQ-500
13
MGISEQ-2000RS
14
AB 310 Genetic Analyzer
15
AB 3130 Genetic Analyzer
16
AB 3130xL Genetic Analyzer
17
AB 3500 Genetic Analyzer
18
AB 3500xL Genetic Analyzer
19
AB 3730 Genetic Analyzer
20
AB 3730xL Genetic Analyzer
21
Complete Genomics
22
DNBSEQ-G400
23
DNBSEQ-G400 FAST
24
DNBSEQ-G50
25
DNBSEQ-T7
26
Element AVITI
27
GS111
28
FASTASeq 300
29
GenoCare 1600
30
GenoLab M
31
Helicos HeliScope
32
HiSeq X Five
33
HiSeq X Ten
34
Illumina Genome Analyzer
35
Illumina Genome Analyzer II
36
Illumina Genome Analyzer IIx
37
Illumina HiScanSQ
38
Illumina HiSeq 1000
39
Illumina HiSeq 1500
40
Illumina HiSeq 2000
41
Illumina HiSeq 2500
42
Illumina HiSeq 3000
43
Illumina HiSeq 4000
44
Illumina HiSeq X
45
Illumina MiSeq
46
Illumina MiniSeq
47
Illumina NovaSeq 6000
48
Illumina NovaSeq X
49
Illumina NovaSeq X Plus
50
Illumina iSeq 100
51
NextSeq 1000
52
NextSeq 2000
53
NextSeq 500
54
NextSeq 550
55
Ion GeneStudio S5
56
Ion GeneStudio S5 Plus
57
Ion GeneStudio S5 Prime
58
Ion Torrent Genexus
59
Ion Torrent PGM
60
Ion Torrent Proton
61
Ion Torrent S5
62
Ion Torrent S5 XL
63
454 GS
64
454 GS 20
65
454 GS FLX
66
454 GS FLX Titanium
67
454 GS FLX+
68
454 GS Junior
69
GridION
70
MinION
71
PromethION
72
PacBio RS
73
PacBio RS II
74
Revio
75
Sequel
76
Sequel II
77
Sequel IIe
78
Onso
79
Tapestri
80
UG 100
81
Sentosa SQ301
DataSet
Metadata
Variant type
Select one of the following variant types to submit. - SNP - Variant call - Variant region
SampleSet ID
The SampleSet ID (from Part 2. SampleSet) associated with the dataset
Experiment ID
The Experiment ID (from Part 4. Experiment) associated with the dataset
Moltype
Select one of the following molecular type - Genomic - cDNA - Mito - Chloro
DataSet description
Brief description of dataset Example: Structural variations of Normal_1
Variant filename
Exact file name of the variant data. VCF is required for SNP data; VCF or Excel file (xlsx) can be used for SV data. Example: Kdata.vcf, Kdata.vcf.gz, Kdata.xlsx
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