Massive parallel sequencing of nucleic acids enables large scale DNA analysis. The most prevalent implementation of these next generation sequencing technologies for oncology is mutation detection via targeted panels. Onco LifePipe® detects and annotates variants in tumoral samples using several bioinformatics tools in order to identify clinically relevant mutations.
Sequencing data is processed to allow highly accurate detection
of mutations. This is performed by combining the results of
several variant callers after local realignments of reads around
insertions or deletions. Each variant caller has been chosen
after the evaluation of its specific quality regarding subclonal
punctual mutations as well as insertions and deletions.
Quality annotation added for each variant provides indications
to distinguish somatic mutations from sequencing errors.
Each variant is traced back to the gene, coding exon and
functional domain level. Its functional impact prediction is
also computed using several methods.
The frequency of each variant in the current analyzed run or all
previous runs is computed to distinguish sequencing errors from
real mutations. Finally, all variants are annotated using
different pathogenic and nonpathogenic catalogs of variants, to
highlight mutations having higher clinical significance
probability.
Each run quality is determined to validate that variant results
can be interpreted:
•General alignment and panel coverage
•Basic quality of
all detected variants per samples
You can analyze your sequencing results obtained by different sequencing technologies and all analysis platforms. The tool can be adapted for all your targeted panels.
Our tool provides comprehensive annotations for each variant to
facilitate distinction between germinal and somatic mutations.
Ranking rules are also used to classify variants and easily
interpret the results.
Onco LifePipe® is also able to detect clonal as well as
subclonal mutations with high accuracy to enable clonal dynamic
tracking of tumors.
Regular updates are released by our team to always benefit from the most up-to-date algorithms. We also provide support and training for users to familiarize them with the tool and help them in the interpretation of their data.
We have validated Onco LifePipe® by analyzing two dataset with
different mutations.
The first dataset was InSilico data containing 15 mutations
among the most common mutated genes in myelodisplasic syndromes.
Each mutation was insertedwith variable allele frequencies. The
second dataset corresponds to Illumina shared data, sequenced
with Cancer Hotspot panel on MiSeq system. These samples have 12
to 44 variants with median allele frequency of 8%.
Firstly, on in silico data, we showed that the association of
complementary variant callers improves the detection of all
variant types (SNP, insertion or deletion). Moreover, we
observed that sequencing conditions (depth and error rate) can
have a limited impact on variant detection, depending on the
variant calling tool. On Illumina public data, we confirmed Onco
LifePipe® robustness for somatic driver variants detection
including subclonal variants until an allele frequency of 1%.
Life and Soft was present at the 38th congress of the French Society of Hematology in Paris with a poster selected by the SFH scientific committee and introducing Onco LifePipe®.
Life & Soft will participate to the Assises de Génétique Humaine et Médicale in Nantes, from January 24th to 26th. Our team will be present at booth #41 and at the poster area for a presentation of our work on quantification of micro-organisms from WGS data. Please contact us to plan a meeting during the event.
Onco LifePipe®, our software dedicated to cancer genetics, is now CE Marked for use as an aid for diagnosis and screening.
Life and Soft will be attending the next European Society of Human Genetics conference, May 27-30, Copenhagen. Don’t miss the opportunity to learn more about the latest advances in our range of LifePipe® products, which focus on the exploitation of NGS data and nucleotide sequence design for CRISPR experiments.
Ask about our offer, find answers to your questions and get in touch.