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VARIANT ANNOTATION DATABASE

DNASTAR's Variant Annotation Database combines data from a variety of SNP level annotation databases for easily accessible insights into their variant data.

Lasergene Genomics automatically enriches the analysis of variants detected in your human resequencing data using our custom Variant Annotation Database, which integrates information from many large variant databases, including Mastermind, dbNFSP, the 1000 Genomes Project, and the Exome Sequencing Project, into your variant report. These databases provide a wide range of relevant data, including literature citation counts, predictions for disease potential, clinical significance reporting, evolutionary conservation scores, human genotype and allele frequencies in 25 human populations and impact on protein.

This integration is part of the automated pipeline offered by Lasergene Genomics which removes the complex, extensive manual intervention often required for detecting, annotating, and analyzing variants in human sequencing data.

Incorporating the variant data from the Variant Annotation Database into your project is as simple as checking a box when you set up your sequencing project in SeqMan NGen. Following assembly, access to detailed, comprehensive data from integrated databases is available for each identified variant in ArrayStar.

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Learn more about the Variant Annotation Database in Lasergene Genomics

Components | Resources | FAQs | Citations | User Guide

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Variant Annotation Database - Sample of Included Components
DatabaseComponentDescription
Mastermind MM CountCount of articles in the Mastermind search engine reported in cDNA, DNA and protein with hyperlink to the MM database.
MastermindMM URI 3Search for articles in the Mastermind Genomic Search Engine with hyperlink to the MM database.
dbNSFP v4.1LRT predictionsPredictions are based on LRT score which is the p-value from the likelihood ration test.
dbNSFP v4.1Mutation Taster predictionsMutationTaster employs a Bayes classifier to eventually predict the disease potential of an alteration.
dbNSFP v4.1Sift predictionsSIFT predicts whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids.
dbNSFP v4.1phastConsA conservation score based on the multiple alignments of whole genomes (including human).
dbNSFP v4.1SiPhyThe estimated stationary distribution of nucleotides using the SiPhy algorithm that includes biased substitution patterns based on 29 mammalian genomes.
dbNSFP v4.1ClinVar clinical significanceThe clinical significance of the variant as reported by ClinVar.
dbNSFP v4.1ClinVar traitThe trait and/or disease associated with the variant as reported by ClinVar.
dbNSFP v4.1Interpro domainThe domain or conserved site in which the variant is located as annotated by the Interpro database.
dbNSFP v4.1Uniprot IDUniPro ID number and hyperlink to the UniPro database.
1000 Genomes Project African PopulationsMinor allele and Genotype frequencies for 7 African populations.
1000 Genomes Project American PopulationsMinor allele and Genotype frequencies for 3 American populations.
1000 Genomes ProjectEast Asian PopulationsMinor allele and Genotype frequencies for 5 East Asian populations.
1000 Genomes ProjectEuropean PopulationsMinor allele and Genotype frequencies for 5 European populations.
1000 Genomes ProjectSouth Asian PopulationsMinor allele and Genotype frequencies for 5 South Asian populations
Exome Sequencing ProjectAllele FrequenciesMinor allele frequencies of the NHLBI Exome Sequencing Project

Resources

Please see our resources below for more information on using the Variant Annotation Database in Lasergene Genomics.

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Working with Variant Call Format Files in Lasergene Genomics

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Rapid, Large-Scale Prioritizing of Human Variants with Lasergene Genomics Suite

Read Blog Post

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Identifying Candidate Variants and Their Effects on Protein Structure Starting from NGS Data or VCF Files

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Using the Variant Annotation Database for Human Samples

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FAQs

How do I use the Variant Annotation Database for my project?

To utilize the Variant Annotation Database for your clinical research project, simply click on the “Annotate with the Variant Annotation Database” option in the Analysis Options window of SeqMan NGen when you set up your project.

The Variant Annotation database will automatically be used to annotate the variants identified in your data.

Analysis Options

What supplemental variant data is available in the Variant Annotation Database?

DNASTAR’s Variant Annotation Database contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations include information about the frequency of the variant in the general population, in specific populations, and in publications, as well as information concerning the variant’s impact on functionality. The annotation information comes from several sources, including:

  • Mastermind, the comprehensive database of genomic literature from Genomenon, providing access to NGS variant data from millions of PubMed publications.
  • 1000 Genomes Project and the Exome Sequencing Project (ESP)
  • dbNSFP v 4.1 which includes:
  • Functional impact predictions from Sorting Intolerant from Tolerant (SIFT), MutationTaster, and the Likelihood Ratio Test (LRT).
  • Evolutionary conservation scores from SiPhy, PhyloP, PhastCons and GERP++.
  • Pathogenicity and clinical significance impact from ClinVar.
  • Basic amino acid sequence information, Database of Single Nucleotide Polymorphism (dbSNP) IDs, and annotations from Uniprot and Interpro.

How can I find citations for a specific variant in current publications?

Our integration with Mastermind provides a seamless way to find publications on a specific variant of interest. In ArrayStar, easily access and link to data from Mastermind in the SNP Table for each of your variants, including:

  • MM Count 1: Count of articles in the Mastermind Genomic Search Engine with cDNA matches for a specific variant
  • MM Count 2: Count of articles in the Mastermind Genomic Search Engine with variants either explicitly matching at the cDNA level or given only at protein level.
  • MM Count 3: Count of Mastermind articles in the Mastermind Genomic Search Engine, including other DNA-level variants resulting in the same amino acid change.
  • MM Gene: Genes for a variant from the Mastermind Genomic Search Engine.
  • MM HGVS: HGVS genomic notation for a variant from the Mastermind Genomic Search Engine.
  • MM ID 3: Variant identifiers in the Mastermind Genomic Search Engine, as gene:key, for MMCNT3.
  • MM URI 3: Search URI for articles in the Mastermind Genomic Search Engine, including other DNA-level variants resulting in the same amino acid change.

Is there an additional cost to access the Variant Annotation Database?

No. Access to the variant databases for human genome analysis is included with your purchase of Lasergene Genomics and remains available as long as your service plan is active.

Can the Variant Annotation Database be used with any Genome Template Package (GTP)?

No. The Variant Annotation Database is a human genome specific resource and must be used with either build 37 (GRCh37) or build 38 (GRCh38) of the human genome reference sequence. This is most easily done when setting up an assembly in SeqMan NGen where the Reference Sequence screen gives you the option to Download a Genome Package. The ensuing popup lets you choose GRCh37p.13 or GRCh38.p7, among others. (Note: When uploaded into SeqMan NGen, the Homo sapiens mitochondrion database will not work with the Variant Annotation Database).

Download Genome Template Package

Why do the 1000 Genomes minor allele frequencies (MAFs) reported in ArrayStar sometimes vary slightly between build 37 and build 38 based human genome assemblies?

In 2016, 1000 Genomes released their initial Phase 3 data set based on variant calls from 2,504 samples aligned to build 37 of the human genome (GRCh37). In 2018, an expanded data set was released of 2,548 samples aligned to build 38 of the human genome (GRCh38). 1000 Genomes has used “Phase 3” to describe both the 2,504 and 2,548 sample sets across both genome versions and four years of updates. DNASTAR is using the dataset version described in 1000 Genomes “Phase 3” callset for GRCh37 update.

The minor differences in the calculated MAFs between builds 37 and 38 are a reflection of the slight difference in total number of samples as well as potential differences in the number of samples with the specific allele being considered.

Why do the minor allele frequencies (MAFs) reported in ArrayStar sometimes vary from those on the 1000 Genomes and dbSNP websites?

As mentioned above, VAD-calculated 1000 Genome MAFs from GRCh37 and GRCh38 assemblies will differ slightly due to the slightly expanded number of samples used in the GRCh38 data set. dbSNP currently uses GRCh38 as their default reference but reports the 1000 Genomes MAFs based on the slightly smaller 2,504 sample data set. Therefore, VAD-calculated MAFs from GRCh37 based assemblies should be nearly identical with those at dbSNP except for very minor differences due to choices made for rounding. However, more noticeable differences may be seen between VAD-calculated MAFs from GRCh38-based assemblies and dbSNP due to the larger sample set used for the GRCh38 database. Reference: Announcement (2017) on Updated GRCh38 liftover.

Citations

Whole genome sequencing data for two individuals of Pakistani descent.
Khan, S., Kabir, F., M’Hamdi, O. et al. Sci Data 5, 180174 (2018) doi:10.1038/sdata.2018.174.

Novel variants in PAX6 gene caused congenital aniridia in two Chinese families.
Zhang, R., Linpeng, S., Wei, X. et al. Eye 31, 956–961 (2017) doi:10.1038/eye.2016.326.

Molecular characterization of Portuguese patients with dilated cardiomyopathy.
Sousa, Alexandra, et al. Portuguese Society of Cardiology, Volume 38, Issue 2, February 2019, Pages 129-139.

Detailed Characteristics of Tonsillar Tumors with Extrachromosomal or Integrated Form of Human Papillomavirus.
Pokrývková, B.; Saláková, M.; Šmahelová, J.; Vojtěchová, Z.; Novosadová, V.; Tachezy, R. Viruses 2020, 12, 42.

Expansion of phenotypic spectrum of MYO15A pathogenic variants to include postlingual onset of progressive partial deafness.
Chang, M.Y., Lee, C., Han, J.H. et al. BMC Med Genet 19, 29 (2018) doi:10.1186/s12881-018-0541-9.

A novel co-segregating DCTN1 splice site variant in a family with Bipolar Disorder may hold the key to understanding the etiology.
André Hallen, Arthur J.L. Cooper. bioRxiv 354100; doi: https://doi.org/10.1101/354100.

A mutation in the major autophagy gene, WIPI2, associated with global developmental abnormalities.
Musharraf Jelani, Hannah C. Dooley, Andrea Gubas, Hussein Sheikh Ali Mohamoud, Muhammad Tariq Masood Khan, Zahir Ali, Changsoo Kang, Fazal Rahim, Amin Jan, Nirmal Vadgama, Muhammad Ismail Khan, Jumana Yousuf Al-Aama, Asifullah Khan, Sharon A Tooze, Jamal Nasir. Brain, Volume 142, Issue 5, May 2019, Pages 1242–1254, https://doi.org/10.1093/brain/awz075.

Whole exome sequencing identified a novel missense mutation in EPM2A underlying Lafora disease in a Pakistani family
Aslam, Zain et al.Seizure – European Journal of Epilepsy, Volume 51, 200 – 203.

Next Generation Sequencing for Clinical Diagnostics-Principles and Application to Targeted Resequencing for Hypertrophic Cardiomyopathy
Voelkerding, Karl V. et al.The Journal of Molecular Diagnostics, Volume 12, Issue 5, 539 – 551.

A novel homozygous stop gain mutation in SLC12A3 gene cause Gitelman syndrome in Saudi consanguineous family
Naseer, Muhammad I., et al. Genet.Mol.Res. 17(1): gmr16039858.

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