• GENALICE MAP V2.5 New Release

    Monday 3 April 2017

    GENALICE 2.5 marks another important milestone on performance, quality and functionality. All modules in the suite work well with WGS, WES or panel data and is reference independent. NGS input data from Illumina devices have been validated.


    • Mapping performance has been increased and the time to write a GAR file (WGS 5GB) has been reduced with >80%;
    • Improved INDEL calling;
    • Embedded trio-analysis in the population caller;
    • Improved somatic calling;
    • Improved CNV calling;
    • Support for GRCh38 with ‘alt’ sections enabling users to find new variants in this richer and more accurate reference.

    With this release, the GENALICE MAP production suite consists of the following modules:

    • MAP is a simple one step operation to align short NGS reads from FASTQ, BAM or GAR to a reference. The reference can range from very small to extremely large. We support many sections in a FASTA, which allows you e.g. to use an assembly output or a library with many sections to map against. Mapping a human WGS (30x) takes about 25 minutes on a single node with a commodity Intel E5 processor.
    • Variant Calling provides a robust and repeatable method for single sample variant calling. It is a monolithic tool that takes a GAR file input and produces a VCF. The implementation is scalable. On a small Intel node this takes 5 minutes. On a quad E7, it takes a bit over 1 minute. Note that GENALICE variant calling uses a pure observation approach. This means that there is no bias towards known mutations, making the tool extremely useful in cases where the Caucasian reference is not the norm. For clinical labs, we support profiles that can be setup to enhance the sensitivity to variants that are of special interest.

    The combination of MAP and Variant allows the full process from FASTQ to VCF to complete in less than 30 minutes.

    • Population Calling is a unique tool implementing a well known concept of using the intrinsic population observations to improve variant calling. This inContext calling, or Consensus based Call Enhancement, improves both sensitivity and precision. The implementation scales linear from a few to many samples and from one to many nodes. The storage system is designed and tested to run with eventually consistent file systems such as S3 from Amazon. The Population Caller has embedded trio support, resulting in consistent Mendelian error detection to assist finding mutations related to rare diseases. Population Calling takes about 6 minutes per sample. This replaces the time it takes to run Variant Calling. Just as with Variant Calling, Population Calling is done on the GAR file. The variants for a population (cohort) are stored in a GVM (GENALICE Variant Map). This is a repository that can be used to manage the samples and to search for patterns in the genetic profile. The use of GVM allows you to play with the data. You can take different groups of samples out of a large GVM into a separate GVM to further enhance the quality of the calls in e.g. a phenotype related cohort. The speed and ease of use frees up time to really focus on the meaning of the data instead of dealing with the data (Population Calling Module Infographic). The population has been build to deal with very large cohorts that can be stored and analyzed quickly while stored in the GVM. Population management scales linear with expanded compute and storage requirements due to the unique format and parallel processing design.
    • Somatic Calling takes two samples from the same subject and does an in depth comparison to find variants that are different for each sample. In general this technique is used for tumor/normal analysis when looking for somatic mutations. The GENALICE Somatic Caller uses two GAR files as input. This provides a detailed background for high quality variant detection. The difficulty with Somatic Calling is that tumor samples are impure. GENALICE implements dynamic tumor purity detection to be able to find the correct balance between sensitivity and precision. This auto tuning facility allows the caller to cover a wide range of signals in the tumor to be correctly detected. Comparison done against a merge of the four different somatic callers all covering part of the signal spectrum shows that the processing time of 6 minutes per sample does not reduce the quality or consistency of the result (Somatic Calling Infographic).
    • Copy Number Variation (CNV) uses the coverage of two samples, or a sample and a group-coverage (GCO – Genalice COverage), and computes a normalized differential between the two inputs. The sample input is obtained from the GAR file. This file has a separate section with coverage data. This facility allows CNV to be completed in seconds instead of hours or days with other tools. The group coverage can be compiled from a set of GAR files, and uses the average and standard deviation of the group to make a call for gain, loss, normal or skip for a segment of the genome (Copy Number Variation Infographic).
    • GAR toolkit combines a convert tool that can convert the GAR file to BAM, SAM or FASTQ and an API (Java and C), that allows tools to access the GAR file content as if it was a BAM file. The aligned reads, the quality and the cigar strings are presented as BAM records through the interface. Position access is provided, such that tools like IGV can browse through the GAR file without noticing the difference in content. The only difference is the ease of use and the speed of accessing the data.


    Somatic Calling is the art of finding the differences between two samples. In a tumor/normal context this is complicated by the fact that the tumor sample is not ‘pure’. This means that standard Variant Calling (including haplotype-calling) is defeated by having a mix of DNA profiles in the same ‘sample’.

    To deal with this, we developed a dynamic purity detection method. It detects and separates tumor signal from normal and noise. This gives a clear signal covering a wide signal range. In addition it allows for proper LOH (Loss Of Heterozygosity) detection in case of HETHOM promotion and total loss of signal.

    The Somatic Caller uses two GAR files as input. The GAR files provide detailed input and the complete context to be able to make a proper call.

    The Caller operates at similar speed as the single sample Variant Caller. It takes ±6 minutes per 30x WGS sample to detect Somatic Calls.

    The Somatic Caller output is a VCF file containing the somatic calls. The output can also be stored directly in the GVM. This allows you to collect a series of somatic outputs (cohort), and apply Consensus based Call Enhancement to further improve the signal. This also provides a repository in which genetic profiles can be detected.

    Because of the speed, the quality and adaptive nature of the caller, it can be used in different environments, ranging from clinic to support high speed diagnosis, research to support genetic profile mining and clinical studies to support fast and efficient validation.

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  • GENALICE and BioDiscovery partner to empower rapid NGS data interpretation

    Wednesday 29 March 2017

    Harderwijk, the Netherlands and El Segundo, CA, USA – March 29, 2017 – GENALICE and BioDiscovery announce a co-marketing partnership to offer their products together as a turn-key end-to-end solution for the use of next-generation sequencing (NGS) data to interpret genomes. GENALICE provides an ultra-fast and highly accurate secondary analysis suite that seamlessly connects to BioDiscovery’s tertiary informatics and genomics interpretation system, NxClinical.

    “The GENALICE and BioDiscovery co-marketing partnership is a response to the rapidly growing volumes and usage of NGS data, which highlights the urgent need for faster processing and interpretation technologies. Only few solutions are on the market that truly speed up read mapping, variant calling and interpretation. Our partnership offers a new reality in which large volumes can be analyzed close to real time, enabling truly important data interpretation and data mining of genomic variants of interest in a cost-effective manner. This game-changing solution in big data processing will have a significant positive impact in clinics towards the goal of achieving precision medicine in complex DNA disease areas, for instance in oncology” GENALICE’s Commercial Director Michelle Meijer comments.

    “BioDiscovery’s reputation as the gold standard for array-based cytogenomic analysis and interpretation software is based on over a decade of high-quality cutting-edge systems used by hundreds of labs across the globe. With our recent introduction of NxClinical 3.0, we have expanded this capability into molecular genetics with complete management of NGS generated variant analysis and interpretation in combination with CNV – a truly unique feature,” says Dr. Soheil Shams, President of BioDiscovery. “We are very excited about working with GENALICE to offer many of our customers a complete end-to-end solution starting from raw read files straight from the equipment.”

    GENALICE MAP and NxClinical seamlessly work together offering customers, who want the advantage of the combined system, a reduction of NGS big data bottlenecks with unmatched visualizations and integrated interpretation of sequence variants and Copy Number Variations (CNVs). GENALICE MAP is the accelerator that improves the process of aligning and calling genomes, whilst NxClinical focuses on providing an enterprise-wide multi-user database enabling reviewing and reporting combined data of Single Nucleotide Variants (SNVs), INDELs, and CNVs. A single database system is used for NGS and microarray data sets. The two products create a complementary workflow that eliminates many of the frustrations of wrangling NGS data today.

    “We are excited to present our proof of concepts during a joint Industry Workshop, entitled ‘Innovative Approaches for High Quality Somatic Mutation Detection and Interpretation Delivering Fastest Turnarounds’ at the AMP Global conference in Berlin next week. On Wednesday, April 5, our companies will demonstrate customer cases of the combined workflow, somatic calling and CNV pipeline comparisons,” says Michelle.

    About GENALICE

    GENALICE is a highly innovative genomics big data company. GENALICE designs and builds groundbreaking software solutions for ultra-fast, highly accurate and cost-effective DNA data processing and analysis that can operate on general-purpose hardware. GENALICE has introduced the first NGS data processing pipeline with true Population Power and is leading the way in Somatic Variant Calling. By partnering with world-renowned research institutes and healthcare companies, GENALICE is committed to unlocking the potential of whole genome and exome sequencing for biomarker discovery and medical application. More information on GENALICE and GENALICE MAP can be found at www.genalice.com.

    About BioDiscovery

    BioDiscovery, Inc. is dedicated to the development of state-of-the-art software products for life science research as well as clinical applications. The company’s mission is to enable scientists to eliminate disease and suffering through application of computational technologies and translating these findings directly and rapidly to clinical use. From its inception in 1997, BioDiscovery has been an innovative leader in the genomics field having introduced the first dedicated commercial software tool for analyzing microarray images. Since then, innovation has continued to be a top priority. BioDiscovery’s passion to make a difference has further extended the company’s reach into creating the most comprehensive enterprise-wide system enabling research findings to translate into clinical applications and make direct impact on patient care. For more information on BioDiscovery, visit www.biodiscovery.com

    Please note the following: The BioDiscovery software tools referenced are designed to assist clinical researchers and are not intended as primary diagnostic tools. It is each lab’s responsibility to use the software in accordance with internal policies as well as in compliance with applicable regulations.


    For more information, please contact:

    GENALICE B.V.                                            BioDiscovery
    Dr. Michelle Meijer                                        Shalini Verma
    Commercial Director                                     MarCom Manager
    +31 88 1221 000                                           310-414-8100

    michelle.meijer@genalice.com                    MarCom@biodiscovery.com


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  • KeyGene and GENALICE extend their collaboration on big data for crop improvement

    Saturday 14 January 2017

    Harderwijk, Wageningen, the Netherlands – Today, at the first day of the international Plant and Animal Genome XXV Conference in San Diego, the Crop Innovation Company KeyGene and genomic big data solutions company GENALICE, announce the continuation of their strategic partnership. Jointly the companies will stand unmatched in exploiting the tremendous value of genomics related big data analysis in crop innovation.

    The KeyGene Vision – an expert’s perspective on agrigenomics & crop innovation

    KeyGene supports its customers and partners with cutting edge molecular breeding technologies and plant trait platforms. For many important agronomical crops, KeyGene has elucidated their highly complex genomes. With its in-house Genome Analysis Platform for the processing of sequencing data, and its proprietary CropPedia interactive platform for big data integration, interpretation, and application, the company has brought crop genomics to a next level. These two platforms create the perfect view on exploitable genetic variation, enabling more efficient use of germplasm and elite breeding materials, and revealing the genetic basis of commercial traits.

    In the partnership with GENALICE, KeyGene was the first company to benchmark GENALICE MAP on agronomic crops. Back in 2012, Prof. Dr. Roeland van Ham, VP Bioinformatics and Modeling at KeyGene, recognized, as one of the first experts in this field, the amazingly high short read alignment speed of GENALICE MAP. He implemented GENALICE MAP as KeyGene’s main NGS secondary analysis pipeline and added Population Calling functionality, which enables KeyGene to process and analyze large cohorts. The software suite currently enables KeyGene to process massive amounts of sequencing data with unparalleled speed and reliability, which is crucial in optimizing and accelerating the molecular breeding process. In the partnership, KeyGene will continue to jointly develop innovative views on genome variation data, and focus on the downstream exploitation of genome data in trait and crop development.” Arjen van Tunen, CEO of KeyGene, comments: “GENALICE and KeyGene are strategically collaborating in a fruitful and mutually profitable way for several years already. I am very pleased with the extension of our partnership which enables both parties to benefit from the further development and use of multi-genome analysis software for AgroFood applications. This will be instrumental for the development of innovative crop varieties that meet future demands for healthy & high quality agricultural products.”

    The GENALICE Vision – an expert’s perspective on high quality, high speed NGS data analysis solutions

    Hans Karten, CEO / CTO of GENALICE, says in a statement: “GENALICE and KeyGene have been collaborating in the space of NGS secondary analysis over the past three years. GENALICE is proud to have played a vital role in KeyGene’s ability to improve their genomic breeding strategies. The advantages of GENALICE MAP core functionality and its Population Calling module have enabled new business opportunities for KeyGene. We are very pleased that this fruitful collaboration is continued by this strategic partnership for the next three years. Again we join efforts in improving plant genomic data analysis and efficiency. The challenges in the food sector continue to increase with stricter health regulations and a fast growing population. This requires the ability to implement innovative approaches, which is a dominant gene in our two companies’ DNA profiles.”

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  • Rollout of GENALICE MAP V2.4.0. on track

    Monday 5 December 2016

    After the initial announcement at the American Society of Human Genetics, in October this year, the GENALICE team is working hard to rollout the new version of the GENALICE MAP NGS secondary data analysis suite, at all of its customer sites. With this new version (V2.4.0) the suite has greatly improved on various elements and expanded with new functional modules.

    In short, the most important updates contain improvements in the basic toolset (Production Box) for single sample short read alignment and variant calling:

    • Further variant detection accuracy improvements; INDEL call optimization
    • Further footprint reduction of unmapped reads, resulting in even smaller GAR file sizes
    • Full GRCh38 support of alternative section/contigs (e.g. distinct haplotypes, decoys) during read mapping
    • HTTPS IO support to be able to run HIPAA compliant
    • HTTP and S3 compatible logging and error report file handles
    • Download of tutorials for training purposes

    Like in earlier versions, V.2.4.0 will give its users access to the GAR toolbox. This toolbox contains the following functionalities:

    • GAR API – providing access to the GAR through C & Java
    • IGV plugin – to view the GAR directly
    • GAR conversion tool (to BAM, SAM and FASTQ)


    The Analysis Suite has been expanded with new functional modules. These modules are considered upgrades; hence they could be added to a standard license for single-sample alignment and variant calling.

    POPULATION CALLING MODULE (already available as an upgrade option within V2.3.0, and now further advanced)
    Advances in the unique Population Calling feature:

    • Profile creation, e.g. a profile can be used as a cohort specific or targeted training set, to better detect known variants. While tools like GATK make use of generic training sets, GENALICE MAP offers users the opportunity to create e.g. race, native population or disease specific profiles. Such a profile allows for target call amplification and suppression, and results in better detection of known variants in the chosen population.
    • Read pileup – The new pileup functionality is a GVM fed read mapping inspection tool. It quantifies coverage depths and variant counts directly from a GAR file.

    A method to distinct variants found in normal tissue from variants in a tumor sample, in order to identify tumor specific DNA mutations. In the Agbio industry, Somatic Calling can also be applied for the identification of new mutations to enhance breeding strategies while finding differentials between a target and base line.

    This newly released Copy Number Variation detection functionality uses a differential approach targeting tumor/normal pairs. Several filters can be applied to surface these areas that have a significant deviation from the expected coverage levels.


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    In case you would like to receive more information about and pricing of our GENALICE MAP NGS secondary data Analysis Suite, please let us know. Just give us a call or send an email us a call or send an email to sales@genalice.com. We are happy to answer all of your questions.

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  • GENALICE expands its NGS secondary analysis suite with important functionality for better diagnosis of oncology patients

    Tuesday 18 October 2016

    Today, at the opening of the Annual Meeting of the American Society of Human Genetics, GENALICE announced the release of a new version (V2.4.0) of its Next-Generation Sequencing (NGS) secondary data analysis suite, GENALICE MAP. The key component of this release is the Somatic Calling module, with impressive performance and best-in-class quality results. Somatic Calling is used for molecular diagnosis of oncology patients. It concerns a technology to distinct variants found in normal tissue from variants in a tumor sample, in order to identify tumor specific DNA mutations.

    In a head-to-head comparison the GENALICE MAP Somatic Calling module outperforms the combination of four commonly used pipelines (MuTect, Strelka, FreeBayes, VarScan), by being 190 times faster and producing better results. None of the individual pipeline results came even close to the results of GENALICE MAP.

    Hans Karten, CEO/CTO, explains: “With the addition of the Somatic Calling module, our NGS secondary analysis solution immediately becomes more relevant for clinical application. The exceptional validation results clearly show our added value in this field. This is an important step forward in realizing the mission of our company to save lives and improve the quality of life of patients with complex DNA diseases, such as cancer.”

    Other important additions to this new software version are:

    1. Profiles: While other tools rely on generic training sets to improve the outcome of known variants in a patient sample, MAP allows for the creation of specific profiles for any defined cohort from no matter what species. Such a profile allows for very targeted call amplification and suppression and thus boosts accuracy of detecting known variants.
    2. Copy Number Variation (CNV): CNV detection, as a first and important element of Structural Variant detection, is now available in GENALICE MAP.
    3. HIPAA compliance: To be able to run HIPAA compliant, hooks to encrypt data in transit and data at rest are provided.
    4. GRCh38 support: Specific support of the ‘alternative sections’ as used in GRCh38 has been added.

    “Another important milestone for our company,” Hans continues, “is the announcement of the first version of our workflow manager. With growing data sets and increasing functionality the need for an excellent system to support smooth big data processing and management in complex environments is clear. The workflow manager delivers full version control and provides a unified view of all samples stored anywhere. The scheduler can work in flex-compute environments and all functionality is accessible through API or Graphical User Interface. We expect this to be an important addition to our product to further reduce the complexity of NGS data processing.”

    For more information on the new Somatic Calling module, please follow this link.


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