Whole Exome/Whole Genome Sequencing Analysis

WHOLE EXOME/WHOLE GENOME SEQUENCING ANALYSIS

Assemble whole genome, whole exome, and gene panel sequencing data against a reference sequence, then identify and compare variants.

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Let Lasergene Genomics do the heavy lifting of whole genome and whole exome sequencing analysis so you can focus on the results.

The sheer volume of data generated from whole exome sequencing and whole genome sequencing presents a challenge for many researchers faced with the prospect of assembling and analyzing it. Whether you are working with whole genome, whole exome, or other targeted sequencing data, the resulting amount of information requires a significant amount of data processing and analysis. Lasergene Genomics enables you to align resequencing data from all major NGS platforms against a reference sequence with unsurpassed ease and speed. Comprehensive post-assembly analysis options make it easy to identify and compare genetic variants as well as structural and non-coding variants. Advanced gene filtering offers the ability to determine the level of disruption to each gene caused by variations. Handling large volumes of data is what Lasergene Genomics was designed to do – let us do the heavy lifting, so you can focus on the results.

Whole exome/whole genome sequence analysis in 4 simple steps

Step 1

Align data to a genomic template

Step 2

Identify and compare variants of interest

Step 3

Analyze variants within context of annotation data and read alignment

Step 4

Evaluate assembly coverage for all sample simultaneously

Learn more about Whole Genome/Whole Exome Sequencing Analysis

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Resources

Please see our resources below for more information on whole genome/whole exome sequencing analysis.

DNASTAR’s SeqMan NGen vs. Four Alternative Pipelines: Variant Detection Comparison Using Illumina Data from NA12878

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SeqMan NGen vs. CLC Bio Genomics Workbench: Variant Detection Comparison Using Data from NA12878

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SeqMan NGen vs. Two BWA+GATK Workflows: Variant Detection Comparison Using Illumina Data from NA12878

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SeqMan NGen vs. Geneious: Variant Detection Comparison Using Data from NA12878

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Considerations for Next-Gen Sequence Assembly and Analysis Software Selection

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Identifying Candidate Variants and Their Effects on Protein Structure

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A Next-Gen Sequencing Software Workflow for Gene Panel Validation Control

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Automating Workflows in DNASTAR’s Lasergene Genomics Suite for High-Throughput Applications

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Cloud Assemblies for NGS Sequences Webinar

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How Much Disk Space Do I Need For My Templated Genome Assembly?

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

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Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about whole genome sequence analysis and whole exome sequencing analysis.

Exome Analysis Tutorial

See how to align exome resequencing data from all major NGS platforms against a reference sequence with unsurpassed ease and speed in Lasergene Genomics. Comprehensive post-assembly analysis options make it easy to identify and compare genetic variants as well as structural and non-coding variants. Advanced gene filtering offers the ability to determine the level of disruption to each gene caused by variations.

Visualizing Genes and SNPS from ArrayStar in GenVision Pro

This quick tip video demonstrates how to visualize groups of genes or SNPs from ArrayStar in GenVision Pro.

Sanger Validation for NGS Assemblies

If you are working with next-gen sequencing, you may wish to use Sanger sequencing data to validate the results of the assembly or variant calls. Lasergene Genomics supports this validation, allowing you to combine both data types into a single project in SeqMan NGen.

Multiple Genome Assembly and Variant Analysis

In this video, learn how to align next-gen sequencing data for multiple samples to a genomic reference then perform variant analysis for all samples.

Using the Exome Coverage Report

This video guides you through using the Exome Coverage Report in SeqMan Pro.

Using the Variant Annotation Database

This video demonstrates how to use the Variant Annotation Database for human samples in Lasergene Genomics.

FAQs

How long does it take to assemble and call variants?

This depends whether you are doing the assembly on your local computer or are using DNASTAR Cloud Assembly. Depending on hardware and depth of sequences, local whole genome…

This depends whether you are doing the assembly on your local computer or are using DNASTAR Cloud Assembly. Depending on hardware and depth of sequences, local whole genome resequencing can take as little as 5 minutes for a bacterial assembly to 24+ hours for a mammalian genome. A typical whole exome sequencing assembly takes between 30 and 90 minutes. Regardless of workflow, cloud assemblies are much faster and multiple assemblies can also be run simultaneously.

How do I compare variants between exomes?

Multiple sample whole exome sequencing analysis is done in ArrayStar. Variant samples can be compared and filtered into sets of interest using customizable tables, a filter wizard, Venn diagram, heat map or scatter plot.

How many exomes can I compare simultaneously?

At least 100 human exome data sets can be uploaded to a single ArrayStar project for comparison.

What types of files can I import for whole genome/whole exome sequencing analysis?

ArrayStar supports the import of SeqMan NGen assemblies (.assembly), files from other ArrayStar projects (.astar, .dmaproj), SeqMan Pro SNP files (.txt), VCF SNP files (.vcf), other text (.txt) and comma-separated value (.csv) files.

What supplemental data is available for variant analysis in whole exome/whole genome sequencing projects?

For human resequencing data, DNASTAR provides access to the Variant Annotation Database, which contains variant information using coordinates from GRCh37 (hg19) and GRCh38. Annotations…

For human resequencing data, DNASTAR provides access to the Variant Annotation Database, which 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.

Does Lasergene Genomics support BED or VCF files for targeted sequencing?

Yes. SeqMan NGen can read and utilize BED and VCF files in the assembly and can also create and export a VCF file during assembly. ArrayStar can export BED and VCF files. SeqMan Pro can export VCF files.

Can I import other annotation data into my whole genome sequence analysis project?

Yes, you can import most any annotation data in text format, including gene and SNP level annotation data.

What types of variant analysis are available post-assembly?

Large-scale SNP comparisons across individuals and groups
Advanced gene filtering based on the level of disruption to each gene caused by variations
Comparison…

Large-scale SNP comparisons across individuals and groups
Advanced gene filtering based on the level of disruption to each gene caused by variations
Comparison of groups of variants using text filters, tabular data, or graphical representations that include Venn diagrams, scatter plots and heat maps
Send genes or variants of interest to SeqMan Pro to view the read alignment at that position; or GenVision Pro to view the assembly coverage for all samples simultaneously

What is the difference between whole genome sequencing and whole exome sequencing?

Whole exome sequencing analysis includes only the protein-coding region of genes in the assembly. Whole genome sequence analysis includes the entire genome in the assembly. Lasergene Genomics applications can handle both types of assembly and analysis.

Can Lasergene Genomics detect structural variations in genomic resequencing data?

Yes, Lasergene Genomics can detect copy number variation (CNV) and other structural variants as part of gene panel, whole exome and whole genome sequence analysis. Simply check the box for Calculate Copy Number Variation during assembly setup in SeqMan NGen. You can then view, filter and analyze CNVs and other structural variants using ArrayStar and SeqMan Pro.

Can I analyze VCF data for my whole exome/whole genome sequence analysis project?

Yes, you can analyze both raw sequencing data as well as VCF variant data for genome resequencing projects in Lasergene. When starting from VCF data, Lasergene will classify called variants by their effect on coding regions, relative to the imported reference genome.

Benchmarks

Lasergene Genomics Reference-Guided Genome Alignment Benchmarks
Data Set	Sequence Technology	Coverage	Assembly Time
Yeast Genome (ERX009559)*	Illumina	22X	2 Minutes
Yeast Genome (srx1484451)*	Ion Torrent	22X	3 Minutes
Drosophila Genome (SRX1961013)*	Illumina	23X	23 Minutes
Human Exome (SRR701474)*	Illumina	81X	53 Minutes
Mouse Rna-seq (SRX2013345)*	Ion Torrent Proton	NA	1.3 Hours
Human Rna-seq (SEQC-UHRR & Brain)	Illumina	NA	1.6 Hours
Rice Genome (Srx179262)*	Illumina	34X	1.6 Hours
Human Exome (SRX1873412)*	Ion Torrent Proton	162X	3.9 Hours
Human Genome (SRP000239)*	Illumina	36X	23 Hours

Citations

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.

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.

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.

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.

Zika Virus MB16-23 in Mosquitoes, Miami-Dade County, Florida, USA, 2016
Mutebi, John-Paul et al. Emerging infectious diseases, vol. 24,4 808–810. 17 Apr. 2018, doi:10.3201/eid2404.171919.

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A very powerful application
“It is a very powerful application; A run can be assembled with a reference genome in few minutes. SeqMan NGen is one of the best software applications of DNASTAR.”
Elisabeth Navarro, CNRS
Easy and fast
“It is easy and fast to identify SNPs, structural changes, and CNVs.”
Kirk Nelson, Qpex Biopharma Inc.

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