Cancer Genetics

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.

Most tumors are heterogenous and are composed of distinct molecular clones. Subclonal mutations are defined as mutations not present in the entire proportion of malignant cells and can be difficult to detect.

Variant Detection

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.

 

Variant Annotation

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.

Quality Validation of Sequencing Panel

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

Why choose Onco LifePipe®?

Compliant

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.

Complete

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.

Quality

Our developments follow a strict quality process in accordance with ISO 62304 recommendations. Onco LifePipe® is CE Marked for use as an aid for diagnosis and screening

Supported

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.

Validation Study

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%.

Latest News

SFH 2018

SFH 2018

28th
March , 2018

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®.

9èmes Assises de Génétique Humaine et Médicale

9th Assises de Génétique Humaine et Médicale

24th
January , 2018

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.

SFH 2018

Onco LifePipe® CE Marked!

4th
January , 2018

Onco LifePipe®, our software dedicated to cancer genetics, is now CE Marked for use as an aid for diagnosis and screening.

ESHG

ESHG 2017

27
May , 2017

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.

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