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CLINICAL RESEARCH

Clinical research software in an automated pipeline for effortless project setup, automatic variant detection and annotation, and extensive cross-sample comparisons. PRICING DOWNLOAD FREE TRIAL

Set up your clinical research projects in minutes using Lasergene Genomics automated pipeline for human genome analysis.

Clinical research software has become more widely available in recent years, as the demand for workflows such as trio analysis, paired tumor-normal comparisons, and rare variant studies has grown. However, most commercially available software for human genome analysis requires extensive work up-front in preparing a project for assembly and eventual analysis. Lasergene Genomics stands apart in the field of clinical research software in part because of SeqMan NGen, our revolutionary wizard that enables you to set up your entire genome or exome resequencing project in mere minutes. SeqMan NGen automates tasks that typically require extensive manual intervention, including automatically organizing experiments and replicates, built-in access to diverse genome template packages for humans and model organisms, automatic incorporation of BED and VCF files, and automatic detection, annotation, and analysis of variants. Following assembly, the human genome analysis tools available in Lasergene Genomics make it possible to immediately begin extensive multi-sample variant comparisons, identify statistically significant variants, and explore relevant genes that intersect with variants of interest.

For research purposes only. Note that a “Commercial Services” license is required for organizations that use our software as part of an analysis pipeline that is provided as a service for others. Please request a quote or contact us for additional information.

Lasergene Genomics clinical research workflow for human genome analysis

Clinical Research Step 1

Set up

Input reads, BED/VCF files, and select human or mouse template package

Clinical Research Step 2

Assemble and identify variants

SeqMan NGen assembles sequencing data and automatically identifies, annotates, and analyzes variants

Clinical Research Step 3

Compare samples

Create and compare variant sets, apply statistical filters

Clinical Research Step 4

Analyze genes

Easily find genes that intersect with variant sets and analyze gene ontology

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Learn more about our Clinical Research Software

Resources | Tutorials | FAQs | Benchmarks | Citations | User Guide

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Resources

Please see our resources below for more information on our clinical research software for human genome analysis.

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

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

Read Blog Post

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Variant Analysis in Lasergene Genomics

Watch Webinar

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Cloud Assemblies for NGS Sequences Webinar

Watch Webinar

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Working with Variant Call Format Files in Lasergene Genomics

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

Read Blog Post

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

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

Read White Paper

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

Read White Paper

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

Read White Paper

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

Read White Paper

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SeqMan NGen Assembly of Ion Torrent Exome Data With and Without Heterozygous Indel Removal: a Comparison Using NA12878 Reference Materials

Read White Paper

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Considerations for Next-Gen Sequence Assembly and Analysis Software Selection

Read White Paper

Tutorials

Watch one of our videos or check out one of our written tutorials to learn more about using Lasergene Genomics clinical research software for human genome analysis.

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.

FAQs

What supplemental variant data is available for human genome analysis?

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.

Is there an additional cost to access the human variant databases?

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.

Does Lasergene Genomics clinical research software support both Sanger and Illumina sequence data for variant analysis?

Yes, both sequencing platforms are supported for all whole genome and targeted resequencing projects.

How long does it take to go from raw data to analysis for an exome project?

The typical exome assembly and analysis time is approximately one hour, and this includes sequence mapping, variant calling, variant cross-comparing across samples and annotating found variants with variant databases.

Can I use variant calls made in my BWA/GATK pipeline?

Yes, the VCF comparison workflow accessed in SeqMan NGen allows you to compare variants across samples and/or annotate them with the available variant databases to enhance your analysis.

What types of variant analysis are available following assembly?

Lasergene Genomics clinical research software provides a wide variety of tools for analyzing variants, including:

  • 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
  • The ability to send genes or variants of interest to SeqMan Ultra to view the read alignment at that position; or to GenVision Pro to view the assembly coverage for all samples simultaneously

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.

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.

Benchmarks

In most studies, especially when looking for rare mutations, having a reliable reference set with known variations isn’t feasible. To test the accuracy of NGS alignment and variant calling in Lasergene Genomics, we used SeqMan NGen to align whole human exome data from the Genome in a Bottle Consortium (GIAB) to the human genome. Because this is a well curated data set, we were able to compare the variant calls to the “answer” provided by GIAB. We also performed alignment and variant calling in several other software packages using the same data and comparable settings. We then looked at three metrics:

  1. Sensitivity – This is also known as the true positive rate, and is the ratio of correctly identified variants to the total known variants in the reference set. The higher the sensitivity, the greater the likelihood that a variant in the sample will be identified by the software.
  2. Specificity – Also known as the true negative rate, this is the ratio of non-variant calls to the total number of positions in the reference set that are known to be homozygous with the reference sequence. Specificity is inversely related to the number of false positives.
  3. False Discovery Rate (FDR) – This is the ratio of false positives to all variant calls made by the software. The FDR value for a variant caller allows you to understand how many variants in your project are likely to be false positives.

Because an accurate alignment is a necessary precursor to accurate variant detection, these metrics also help you understand the alignment accuracy from various software pipelines.

Results Summary:

Variant Analysis Accuracy Table
READ WHITE PAPER

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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  • Easy and fast

    “It is easy and fast to identify SNPs, structural changes, and CNVs.”

    Kirk Nelson, Qpex Biopharma Inc.

  • 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

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