Our latest news

News about events we take part in, projects' news.
52nd European Human Genetics Conference

Developement of New Lysosomal Storage Disorders Assay

VariFind™ LSDs (Lysosomal Storage Disorders) Assay is intended for confirmatory molecular diagnostics following mass spectrometry analysis in newborn screening. The assay includes 19 genes associated with Glycogen storage disease type II, several types of Mucopolysaccharidoses and Sphingolipidoses.
Complex design of CDSs and clinically significant hot spots will allow to achieve high analytical and diagnostic characteristics of assay.
Additionally VariFind™ LSDs Assay will covers CNVs in GALC (30-kb DEL) and HEXB (16-kb DEL) by Parseq fusion-amplicon technolgy. These validated CNVs do not require confirmation via MLPA.
52nd European Human Genetics Conference
Metabolic disorders assay for confirmative diagnostics

Metabolic disorders often have similar and overlapping symptoms. They may be difficult to subtype without definitive information on the causative mutations and genes. This assay includes 5 seperate panels devided by groups of diseases.
The panel assesses 112 genes comprehensive enough to cover the majority of known monogenic metabolic syndromes. In addition to targeting all coding regionsand 20 bp padding in addition covers all clinically significant variants from ClinVar database. This assay was developed for confirmative diagnostics of results received by Tandem mass spectrometry. The assay was validated on whole blood and dried blood spots. and implemented in newborn screening programm.
52nd European Human Genetics Conference

Novel One-tube Multiple Libraries Preperation Protocol for HLA Typing
New version VariFind HLA Solution ptotocol brings unprecedented speed and simplicity to HLA typing. During multiplex LR-PCR all HLA loci are amplified in 1 tube. This single multiplex reaction amplifies 5 HLA loci (HLA-A, HLA-B, HLA-C, HLA-DQB1, HLA-DRB1) completely removing the need for amplicon pooling. Samples are transferred directly to library preparation and made ready for sequencing in a single workday. Specific barcodes allow to sequence up to 384 samples in one run. VariFind Software provides totally automated and unambigous alle typing.
52nd European Human Genetics Conference
MiCo Milano Congressi, Milan, Italy

ESHG2018 Welcome Back

The 52nd European Human Genetics Conference had finished with great results for Parseq Lab team. Thanks to all our customers and new potential clients who visited our booth.

See you next year in
Gothenburg (Sweden)!
52nd European Human Genetics Conference
Saint Petersburg, Russia

Parseq Arrow Disgnostics Workshop

From 26th till 28th of March Parseq Lab had organised 3-days Workshop for Arrow Diagnostics in Saint Petersburg.

Arrow Diagnostics participants Dr. Giampaolo Filice wet lab training on NGS libraries preparation and sequencing. Current projetcs in area of newborn screening programms specific for Italian marketwere discussed with Dr. Fabio Benzi.

Participants had impoved their skill in VariFind™ Software and Parseq products market strategy.
52nd European Human Genetics Conference
Parseq Lab Laboratory, Saint Petersburg, Russia

Parseq Biovendor Workshop

From 19th till 22nd of March Parseq Lab had organised 5-days Workshop for Biovendor Group in Saint Petersburg.

Biovendor participants Jiri Smuthny and Barbora Ruzichkova had passed wet lab training on NGS libraries preparation and sequencing.

Furthermore, the participants had impoved their skill in VariFind™ Software and Parseq products market strategy.
52nd European Human Genetics Conference

Participation in ESHG2018

From 16th till 19th of June Parseq Lab's team members Natalia Malashikhina and Alexander Pavlov will be attending the 52nd European Human Genetics Conference held in Milan, Italy.

We are happy to prepare to this event because such events help us to stay up to date and to deliver the news about our products and services. Due to the huge variety of conference topics that will cover all aspects of human genetics, we are awaiting to meet interest to our products from our potential clients.

Welcome to learn more about our products at our website, the updates and new products releases are coming soon.

Meet us at booth 582. Drop a line to nmalashikhina@parseq.pro or info@parseq.pro to get in touch before the event and to book a meeting.


Participation in all-Russian scientific-practical conference "New technologies
of diagnostics of hereditary diseases"

On 27th of October Parseq Lab participated in the round table named "The Interpretation of data obtained by next-generation sequencing", which was held within the framework of the conference "New technologies of diagnostics of hereditary diseases" (Moscow, October 27th and 28th, 2017).

The meeting was devoted to the discussion of the first results of the work
in accordance with the Consensus Paper for genome data interpretation obtained from next-generation sequencing method within newborn screening program. This Consensus Paper was adopted in December 2016 at Cystic Fibrosis Consensus. It's entry is due to the increased use of sequencing technologies and the urgent need to standardize approaches to research, analysis and interpretation of data. This is the first document in Russia regulating the procedure of interpreting the results and determining the necessary qualitative and quantitative characteristics of the sequencing results.

In the recommended scheme of the screening program are included our kits for the diagnostics of hereditary diseases — VariFindNeoscreen assay.

At the meeting there were also discussed the prospects of expanding the screening programme via inclusion diseases associated with hereditary metabolic disorders —
we are developing a panel for screening of such diseases: the panel will combine the methods of genetic diagnostics and tandem mass spectrometry.


International conference and workshop Bioinformatics: from algorithms
to applications (BIATA-2017)

The Parseq Lab team participated in the international scientific conference "Bioinformatics: from algorithms to applications" (BIATA-2017), which took place in St. Petersburg from 1st till 5th of August.

First three days of the conference was dedicated to presentations from scientists and discussions of the latest developments in bioinformatics. The focus was on SPAdes — the leading application in the field of bacterial genomes assembly — which was developed by scientists of St. Petersburg state University. On the 4th and 5th of August master-classes was held where participants could practice data analysis.
The head of Parseq Lab's bioinformatics department, Anton Bragin, held a presentation about the new product: genome browser Concentrate — the new tool based on a new approach to the visualization of genomic data.
To try the browser and to read more, please follow the link on the GitHub wiki.

This conference was the first, but we hope that it will be held annually.

Parseq Lab: VariFind™ HIS Solution. Human identification for forensics.

Parseq Lab at ISMB/ECCB 2017

Parseq Lab team of developers takes part at the 25th conference on Intelligent Systems for Molecular Biology (ISMB) and the 16th European conference on Computational Biology (ECCB) on 21—25 July, Prague, at Prague congress centre.

ISMB/ECCB is held for scientists from computer science, molecular biology, mathematics, statistics and related fields and devoted to issues of development and application of advanced computational methods for biological problems. Strong scientific and technical program that showcases the best international developments in bioinformatics and computational biology will level us up to provide you better products and services.

On Monday during a poster-session our team will present a new open-source genome browser Concentrate.
The browser bases on the new approach of graphical genome data visualization, it has strong features such as rich filtering capabilities and graphical information, that distinguishes it from existing genomiс browsers.

See you on 21—25 July.

Venue: Prague congress centre.
Parseq Lab: VariFind™ AIP assay, autoimmune diseases diagnostics.

Genetic diagnostics of autoimmune diseases

Diagnostics of autoimmune diseases using VariFind AIP assay

Parseq Lab has completed the new product — VariFind AIP assay — designed for the genetic diagnostics of hereditary autoimmune diseases, such as, for example, family Mediterranean fever. Test system was verified on the samples of the 1000 genomes project (1000 Genomes) and NIST whole genome standard sample (National Institute of Standards and Technology, USA).

Diagnostic panel includes more than 1000 clinically relevant variants in 12 genes analyzed:

· NOD2
· IL10RA
· IL10RB
· IL10

The test system includes not only reagents for targeted DNA enrichment and libraries preparation, but also the VariFind Software, which can be used to analyze high-throughput sequencing data and to annotate the detected genetic variants using information from its own databases and external sources, including specialized databases.

Clinically relevant variants can be included in a custom PDF-report.

Read more about other available test systems and how to place an order.
Parseq Lab: VariFind™ HIS Solution. Human identification for forensics.

VariFind HID project news

On April 19, during the "Molecular Diagnostics 2017" conference (Moscow) Vasiliy Pekhov (the employee of the department of medical and biological research of the organization of the forensic-criminal activity of the Main Criminalistics Department of the Investigative Committee of the Russian Federation) presented the results of molecular genetic expertise conducted by means of the VariFind HID solution developed by Parseq Lab.

The VariFind HID is a complex solution for human identification based on high-performance sequencing technology designed to resolve cases where currently used capillary electrophoresis (CE) methods are not sufficient to obtain reliable results. This solution fits for analysis of low quality DNA samples, DNA mixtures from two or more contributors, stain samples in cases without any known suspects.

Vasily Pekhov reported about several examinations conducted by the Investigative Committee, where the VariFind HID solution was used to obtain additional information about samples.

In two examinations MPS technology was applied to deal with two-contributors DNA mixtures where minor contributor's genotype was especially interesting for investigation, but the minor component ratio was below the level acceptable for CE analysis.

Another example given in the report was the use of the VariFind HID solution to identify bone remains. In this case strongly degraded DNA was isolated from bone samples and then sequenced. Genetic profile obtained was sufficient for comparison with known relatives.

In addition, the solution was used in molecular-genetic expertise for phenotype prediction. Most probable suspect's eye and hair colors were estimated based on crime scene stain DNA samples.

Based on the completed work, it was concluded that the high-throughput sequencing method allows obtaining additional information in cases that cannot be resolved by traditional approaches and extends the capabilities of forensic DNA expertise.

The VariFind HID solution includes reagent kits to examine a large number of specially selected loci, an infrastructure for data storage and management — Genome Server — and software for analysis of sequencing results, forensic hypothesis testing, and subsequent report generation. The solution consists of three modules that are designed for human identification, human ancestry estimation, and phenotype prediction.

Read more on the VariFind HID solution page.
Parseq Lab: VariFind™ Neoscreen assay for Ion Torrent and Illumina

Renewed VariFind™ Neoscreen assay

Renewed VariFind Neoscreen assay is available for purchase — the assay for detection of hereditary diseases (cystic fibrosis, galactosemia and phenylketonuria) is redesigned for the Ion Torrent platform and includes everything required for the analysis: reagents for targeted DNA enrichment, reagents for libraries preparation, reagents for barcoding, and control DNA sample — so the full list of features, that assay for Illumina platform has.

Since sequencing is a multistage process, which requires many components and each component usually had to be ordered separately, taking into account logistics, controlling date of reagents expiry and interacting with different suppliers — VariFind™ Neoscreen assay relieves from these issues and gives easy handling, unified protocols and clear algorithm of actions.

The solution includes reagents, a DNA control sample, and an application, that processes the data, finds and annotates genetic variants in targeted regions. The app works with the built-in annotated database that is supervised by our expert and is regularly updated. Variants of interest can be included in the PDF-report that you can save or print.

VariFind Neoscreen assay ensures easy work with the wet lab due to clear instructions and protocols; fast data analysis due to the user-friendly application interface; quick solution of problems — in this case, client support will help.

More about the assay, mutations included and features on product page.

Parseq Lab and PreMed: custom assay for thyroid cancer diagnostics

Parseq Lab and St. Petersburg State University will find the genetic causes of diabetes and obesity

Parseq Lab will take part in St. Petersburg State University's project, aimed at the search for genetic causes of some forms of diabetes and endocrine disorders leading to obesity. As a result there will be proposed a method to detect genetic disorders, associated with these diseases, and a method of risk assessment of their development.

The project is designed for two years and will begin with groups formation of the patients, suffering from hereditary diseases of the endocrine system, medical anamnesis collection and samples collection. A control group of healthy people will be formed as well. The biological samples will be stored in the "Biobank" cryostorage of St. Petersburg State University resource center.

The samples will be analyzed by high-throughput sequencing method and then bioinformatics will process the data. This will allow to study the genetic variations in samples.

A database of diseases genetic markers will be based on the research results. Scientists will select markers that are the most informative and valid for the diagnosis of pathological states or risk assessment of their development.

The project employs molecular biologists, medical geneticists, bioinformatics and software developers.

Parseq Lab: CONVector in BMC Bioinformatics

Publication in the BMC Bioinformatics

We are happy to announce that on 22nd October our article "A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data" was published in the BMC Bioinformatics.

The article describes a new method of determining the copy number variations (CNV), which allows to search for deletions and insertions in the targeted sequencing data obtained using multiplex PCR-based library preparation techniques. The article is written by German Demidov (Centre for Genomic Regulation (CRG), formerly Parseq Lab), Tamara Simakova, Julia Vnuchkova and Anton Bragin (Parseq Lab). First results were presented at the Moscow international conference on computational molecular biology (MCCMB2015) in 2015.

Multiplex PCR is a commonly used technique for sample preparation in carrying out targeted high-throughput sequencing (Massively parallel sequencing, MPS) that are widely used in biomedical research and clinical diagnostics as a quick, accurate and inexpensive comparing to whole genome sequencing method of genetic variants (e.g. single nucleotide polymorphisms – SNP) search. However, the detection of large-scale changes in the genome, such as, for example, deletions of several hundred or thousand nucleotides, or copy number variations of sequences (CNV) is a difficult task for targeted sequencing due to the complex mechanism of the influence of sample preparation on the sequencing results.

Taking into account the fact that such variants can play a crucial role in the development and progression of diseases, it's required to enable discovery of large-scale changes in the genome. Now it's possible applying the algorithm and the corresponding open source software, CONVector, developed by the Parseq Lab team.

CONVector is currently being verified for inclusion in the diagnostic test system VariFind, developed by the Parseq Lab team and designed to work with targeted panels.

While preparing the articles, the authors compared CONVector with the similar tools and showed its superiority over competitors; also the analytic sensitivity and specificity were determined, which is 84,62 % and of 100 % respectively.

The article is in open access on the website of the BMC Bioinformatics.

Parseq Lab at ISNS conference

ISNS2016 summary

9th ISNS International Meeting jointly with the 10th ISNS European Regional Meeting (Hague), in which we participated, ended on 14 September.

We are pleased that we met representatives of the largest screening laboratories and molecular genetic centers at university hospitals of such countries as Taiwan, Poland, Portugal, Costa Rica, Mexico, USA.

Pleased to note that one of the areas in which we are engaged: targeted diagnostic panels based on high-throughput sequencing (in particular, used for the diagnostics of cystic fibrosis), are in demand, and we're planning to develop the product, adapt it to the needs of a specific user, focusing on diseases that are specific to particular countries or ethnic groups.

For example, among Ashkenazi Jews high frequency of mutations of the GBA gene, leading to the development of Gaucher's disease, makes this diagnostic panel in this ethnic group in-demand.

The conference became a platform not only to acquire new and strengthen existing contacts, but also allowed us to collect information about current trends in neonatal screening in various countries. The information obtained will be used to promote company products taking into account specifics of the regional markets.

Molecular-genetic diagnostic panel for thyroid cancer
Project for molecular-genetic diagnostic panel for thyroid cancer design in cooperation with scientific clinical centre Premed — European Technology and Research Centre of Medical Genetics.

Project news: molecular-genetic diagnostic panel for thyroid cancer

Scientific clinical centre Premed — European Technology started experimental verification of molecular-genetic diagnostic panel for thyroid cancer: a trial conducted experiments on clinical samples and selected cell lines with mutations typical of thyroid cancer. The results will define the optimal test parameters, and if necessary panel design will be adjusted, data about the test sensitivity and specificity will be received. In the end of this stage it will be possible to begin clinical trials to evaluate clinical accuracy of the test (ability to accurately determine the malignant forms of the thyroid gland in real conditions).

PreMed in cooperation with Research Centre of Medical Genetics (RCMG) and Parseq Lab is developing a method for molecular-genetic diagnosis of thyroid cancer. For a moment a design of a diagnostic panel for determent of the 456 somatic mutations in 25 genes is developed. That will allow not only to distinguish thyroid cancer from thyroid adenoma, but also to determine the subtype of cancer, which is important for the effective treatment and prognosis.

Research Centre of Medical Genetics (RCMG) (Moscow) is a leading Russian center in field of medical genetics and human genetics, the largest center in Russia, providing services for genetic counselling. The center conducts research for the diagnosis of hereditary and malignant diseases. Medical genetic research center constantly develops and implementing new methods of diagnostics.

Parseq Lab is a private research company that works with high-performance sequencing technology and its applications. Main directions of activity are: development and introduction of diagnostics test systems, solutions for human identification; genome data analysis. The company's products are used in scientific and clinical research in Russia, Europe, the Middle East and Latin America.

Parseq Lab at ISNS 2016 conference
ISNS 2016

Participation in ISNS 2016, Hague

From 11 to 14 September 2016 Parseq Lab participates in the annual meeting of the International Community of Neonatal Screening — ISNS 2016. The exhibition will take place during the meeting, where Parseq Lab will present the test-system VariFind™ Neoscreen assay designed for detecting hereditary diseases (cystic fibrosis, phenylketonuria and galactosemia). This validated test-system is used for confirming diagnostics of the abovementioned diseases in newborn screening, and based on the high-throughput sequencing.

Product presentation at such kind of meetings for professionals in the field of neonatal screening (for example for heads of national reference laboratories in Europe, South America, Australia and Asia, which has already scheduled meetings) is an opportunity to expand the market and find new partners.

Everyone is welcome at booth number 21 in Amazon Foyer hall, where you can get detailed information about all our products and services.

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