In rare disease genetic testing whole genome sequencing is a comprehensive technology to address the limitations of gene panels and exome analysis. The latter use selective capturing of target regions. Only WGS is able to provide sufficient coverage of the coding region of the genome especially for GC-rich regions.In this context it becomes evident that in order to find rare but valuable variants related to genetic disorders, the use of the full genome sequence as starting input is clinically essential.The Foundation of People with Rare Diseases is constantly on the outlook to improve the performance of their whole genome analysis process. Dealing with large-scale whole genome sequencing requires read mapping and variant calling solutions which deliver fast turn around times, manageable output file size and high variant calling accuracy. Their most recent study in which 4 analysis pipelines were compared has been published on line in PNAS at http://www.pnas.org/content/early/2017/09/14/1713830114.short?rss=1The four pipelines include BWA/ GATK, GENALICE MAP, PEMapper/PECaller and Isaac. The experiment assessed sensitivy/recall, precision, computation time and disk footprint. It is concluded that in the field of accurate whole-genome data analysis GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac.For further details feel free to contact us at firstname.lastname@example.org
PNAS Publication: Demonstrating great GENALICE MAP performance of whole genome analysis in rare disease genetic testing
Monday 18 September 2017
Friday 8 September 2017
Generate, Process, and Apply. Solutions for Agrigenomic big data challenges
The Agri & Food industry has to solve the big data challenges brought by the next generation sequencing revolution. More data is better as it provides more insights for better breeding strategies. The enormous amount of generated data however has to be processed and applied in such a way that it creates added value rather than headaches over heavy, lengthy and costly computing time.
This symposium, organized by KeyGene and GENALICE, will focus on the genomic big data challenges i.e. processing and application, by highlighting techniques and solutions. Cases from industry are included
After the seminar you will know more about how to process and apply big data in a faster, better and easier way. You will have more clarity on how the continuously growing flow of big data can add value for your business.
You are most welcome to attend this FREE seminar which will be held at KeyGene in Wageningen, the Netherlands. Joining online is possible. Feel invited to register on Eventbrite:» Continue reading
PRESS RELEASE: Swiss Foundation for People with Rare Diseases and GENALICE collaborate on the study of genetic rare diseases
Monday 4 September 2017
Foundation for People with Rare Diseases (Schlieren-Zurich, Switzerland) and GENALICE collaborate on the study of genetic rare diseases
September 4, 2017 – Harderwijk, the Netherlands –
The Foundation for People with Rare Diseases (FPRD) and genomic big data solutions company GENALICE announce their collaboration and the closing of a new 3 year GENALICE MAP license agreement. This allows FPRD ultra-fast and accurate analysis of complex whole genomes from rare disease patients.
Implementation and further development of GENALICE solutions enable FPRD to support patients with rare diseases by investigating genetic variants and their clinical consequences.
Caroline Henggeler, specialist in medical genetics at FPRD explains: “Fast and accurate analysis of genome-scale sequencing data constitutes a computational bottleneck in the current genomics era.” “In our recent PNAS benchmarking study, GENALICE MAP achieved superior speed and lowest disk footprint with BWA/GATK-like sensitivity”, completes Dr. Janine Meienberg, human biologist at FPRD. The full study has recently been accepted for publication.
Dr. Anna Kopps, molecular biologist at FRPD and co-first author of the pipeline benchmarking study, states: “We really like the use of the Population Calling Module to investigate the variants of individuals in the context of the population. Because of its high processing speed we can easily optimize the best accuracy for rare disease testing for which we need to get false negative results reduced to zero.”
Dr. Michelle Meijer, Commercial Director at GENALICE comments: “Indeed the ultra-fast iteration options of the GENALICE MAP Population Calling module are highly critical for genetic testing in clinical rare disease applications. We can process a human whole genome 30x sample, delivering a complete VCF file in less than 30 minutes, where existing tools easily require up to 80 hours. Our balanced solution providing maximum sensitivity combined with fast delivery is an easy and natural fit for any scale genetic rare disease testing.”
About the Foundation for People with Rare Diseases
The Swiss Foundation for People with Rare Diseases conducts nationally and internationally recognized research in the field of human genetics and creates the basis for the diagnosis and treatment of rare diseases, as well as for the counselling of patients and their relatives, through genetic investigations. The Foundation performs teaching at university level as well as promotes the expansion and deepening of the knowledge of rare diseases. www.stiftung-seltene-krankheiten.ch
GENALICE is a highly innovative genomics big data company, based in in the Netherlands. GENALICE designs and builds ground-breaking software solutions for ultra-fast, highly accurate and cost-effective DNA data processing and analysis on general-purpose hardware. With GENALICE MAP, it introduced the first NGS data processing pipeline with true population power. 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.
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.
OUR NEWEST RELEASE BRINGS:
- 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.» Continue reading
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.
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.
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