April Newsletter


VarSeq 2.2.3 Release
By Julia Love
Genomic Curator and Product Quality Scientist

The front and center features for this release are the updates made for VarSeq-CNV. New filters and quality flags were incorporated into the CNV calling algorithms to ensure that high quality, true positive CNV events are being analyzed in whole-exome workflows. In the same vein, users can use the new “Create Low-Quality Target Regions” wizard to define a set of targets... Read More

 Following the AMP Guidelines with VSClinical: Part I

Support for the Interpretation of Non-coding and Splice Site Variants
By Nate Fortier, PhD
VP of Research

While VarSeq has always had excellent support for variant interpretation and analysis, we continue to find new edge cases in the clinical literature that improve our interpretation capabilities. In this blog, we will be covering some of the new improvements in VarSeq to support the interpretation of non-coding and splice site variants... Read More

Automating & Standardizing Your NGS Workflow

Featured in the Journal of Precision Medicine: Implementing the ACMG Guidelines for CNV in a Commerical Software Solution

We are excited to share our latest publication with The Journal of Precision Medicine, “Implementing the ACMG Guidelines for CNV in a Commercial Software Solution”.“In 2020, ACMG in collaboration with the ClinGen working group developed a new set of guidelines for the clinical interpretation of CNVs. While these guidelines provide a robust set of rules for interpreting intragenic deletions and duplications, the implementation of these guidelines in a clinical setting can be quite complex... Read More

 Following the AMP Guidelines with VSClinical: Part I

Webcast Recap: Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Capabilities 
By Gabe Rudy
VP of Product and Engineering

Thank you to those who attended the recent webcast, “Exome Analysis with VS-CNV & VSClinical: Updated Strategies & Expanded Capabilities”. In this webcast, we covered the capabilities and updates that have been incorporated into VarSeq that enhance whole-exome sequencing workflows. The new features and updates for VarSeq 2.2.3 that were discussed fall into three main categories... Read More

 Following the AMP Guidelines with VSClinical: Part I

1st Place Abstract Winner - Vinnery Gupta Webcast on Juvenile Open-Angle Glaucoma
By Dr. Viney Gupta
All India Institute of Medical Sciences

Juvenile open angle glaucoma(JOAG) is an uncommon but severe form of glaucoma, whose prevalence is high in South Asia and Africa. The currently known genes for this disease explain only 10-15% cases, depending on the population studied. While earlier, JOAG was considered an autosomal dominant disorder, recent studies have shown it to be autosomal recessive as well as occurring de novo, in some populations. We reported the disease to be genetically heterogenous... Watch Now

 Following the AMP Guidelines with VSClinical: Part I

LifeCell Case Study Announced

Phani Nagaraja Setty is working as a scientist at LifeCell. Setty obtained his Master’s degree in biochemistry and then received his Ph.D. in genomics with a concentration in Type 2 diabetes. For the last three and a half years, he has managed the lab operations for NGS tests in Lifecell diagnostics. While working on NGS-based clinical exome panels, he realized the need for an efficient genotype-phenotype correlation database orienting to the Indian population. LifeCell committed to a goal: to democratize genetic testing across the country thus... Read More

Become a Genomic Curator

We are now accepting applications to become a Genomic Curator! We are looking for experienced variant interpretation scientists with a background in oncology and targeted molecular therapy reporting. Just send us your resume and a sample of your writing and we would love to get in touch! Apply Here



CEO Corner
New eBook: Clinical Variant Analysis for Cancer

As I mentioned in last month's newsletter, we are continuing to improve our industry-leading CNV solution for analyzing NGS data. Our recent webcast featuring the latest release of VS-CNV had record attendance. If you missed this live event, I invite you to view the on-demand recording here. We are also so grateful for the recent publication in the Journal of Precision Medicine which outlines a few detailed design decisions of VS-CNV. Finally, we recently published a new case study of one of our very good customers in India, LifeCell International, who are expert users of VS-CNV. Please check out their story in the case study here.

Upcoming Webcast

High Precision Exome CNV Detection with VS-CNV  
May 5, 2021 | 12:00 PM Eastern

The detection of CNVs using exome sequencing data presents unique challenges that require specific considerations and strategies.  Over the past several months, our team has made numerous improvements to our CNV calling capabilities on exome sequencing data. In this webcast we will cover these improvements and provide guidance on developing best-practice workflows for CNV calling from whole exome coverage data. The improvements covered in this webcast include:

  • GC correction
  • New settings for adjusting sensitivity and precision
  • Target quality assessment and filtering capabilities
  • Updates flags for filtering false positive calls

Golden Helix is unique in our support for all stages of the CNV calling and interpretation process and we are constantly striving to improve our CNV analysis capabilities. Please join us for this exploration of VarSeq's improved CNV calling capabilities for exome sequencing data.

Customer Success

Our customers have published a number of fascinating articles throughout the month! To highlight just a couple:


Venous thromboembolism is caused by prothrombin p.Arg541Trp mutation in Japanese individuals

Yamamoto, J., Yamamoto, M., Takano, K. et al. Venous thromboembolism is caused by prothrombin p.Arg541Trp mutation in Japanese individuals. Hum Genome Var 8, 13 (2021). https://doi.org/10.1038/s41439-021-00145-x


Integrative sequencing discovers an ATF1-motif enriched molecular signature that differentiates hyalinizing clear cell carcinoma from mucoepidemoid carcinoma

M.E. Heft Neal, E. Gensterblum-Miller, A.D. Bhangale, A. Kulkarni, J. Zhai, J. Smith, C. Brummel, S.K. Foltin, D. Thomas, H. Jiang, J.B. McHugh, J.C. Brenner, Integrative sequencing discovers an ATF1-motif enriched molecular signature that differentiates hyalinizing clear cell carcinoma from mucoepidemoid carcinoma, Oral Oncology, Volume 117,2021,105270, ISSN 1368-8375,https://doi.org/10.1016/j.oraloncology.2021.105270.


Rare Germline Pathogenic Variants Identified by Multigene Panel Testing and the Risk of Aggressive Prostate Cancer

Nguyen-Dumont, T.; Dowty, J.G.; MacInnis, R.J.; Steen, J.A.; Riaz, M.; Dugué, P.-A.; Renault, A.-L.; Hammet, F.; Mahmoodi, M.; Theys, D.; et al. Rare Germline Pathogenic Variants Identified by Multigene Panel Testing and the Risk of Aggressive Prostate Cancer. Cancers 2021, 13, 1495. https://doi.org/ 10.3390/cancers13071495


Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss

Ascari, G., Rendtorff, N., De Bruyne, M., De Zaeytijd, J., Van Lint, M., Bauwens, M., Van Heetvelde, M., Arno, G., Jacob, J., Creytens, D., Van Dorpe, J., Van Laethem, T., Rosseel, T., De Pooter, T., De Rijk, P., De Coster, W., Menten, B., Rey, A., Strazisar, M., Bertelsen, M., Tranebjaerg, L. and De Baere, E., 2021. Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss. Frontiers in Cell and Developmental Biology, 9.


Read more about the articles published over the month on our blog!

About Golden Helix

Golden Helix has been delivering industry-leading bioinformatics solutions for the advancement of life science research and translational medicine for over 20 years with 1,000s of users around the world. Their innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from NGS sequencers and microarrays. With their solutions, hundreds of the world's top hospitals, testing labs, pharmaceutical, biotech, and academic research organizations can harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine.