email: contact@intelliseq.com

Workflows

Software solutions for precision medicine and consumer genomics.

Technology Overview

Workflows are fundaments of the IntelliseqFlow platform, and their development is the core activity of the Intelliseq company. We are focused on providing solutions based on the latest standards and recommendations.

The list of already developed extends 100 workflows, including pipelines, modules, and tasks. The number is continuously growing, thanks to our R&D activities. Below are selected information about the technology we use:

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Core
  • Short path from idea to results
  • 100+ workflows available
  • One platform any test
  • Quality and reproducibility
  • From raw reads to report
  • Bioinformaticiansless
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Features
  • Organization management
  • Project management
  • Analysis management
  • Sample control and management
  • Register of activity
  • Full automatic reports
  • Cost control
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Technology
  • WDL
  • Cromwell
  • Docker containers
  • Amazon Web Services
  • Biocompute objects
  • Microservices architecture

Analysis Areas

  • Alignment (bwa-mem, bowtie, STAR)
  • SNV and short indel variant calling (GATK Best Practices implemented, Mutect, DeepVariant)
  • Variant level annotation (precise versioning of data sources)
  • Variant level filtration
  • Gene level annotation
  • Gene level filtration (fixed and phenotype-based panels)
  • Phenotype-based gene prioritisation
  • ACMG recommendations
  • Annotation of unaligned reads
  • Cancer focused annotation (Civic based)
  • IGV images for filtered variants
  • CNV  Calling, Regions of autozygosity (GATK, Lumpy, Delly)
  • CNV Annotation and Filtration
  • Fastq, bam and vcf quality check
  • Automated reporting (docx, odt. html, pdf)
  • Variant imputation
  • Polygenic scores (PGS Catalog)
  • Ancestry and sex determination 
  • Short read based pharmacogenes genotyping (including CNV proprietary AI algorithms)
  • Pharmacogenomic reporting (Pharmcat based)
  • RNA-seq quantification (Cuffquant)

Traits and Diesases

Clinical Application | Germline testing

Created with GATK best practices and ACMG recommendations target-seq workflows for phenotype-based custom panels or 237 fixed panels grouped in 16 areas:
Hematological diseases | Neurodevelopmental diseases | Kidney diseases | Neuromuscular diseases | Cardiovascular diseases | Genetic ear diseases | Liver diseases | Hereditary cancers | Bone diseases | Cliliopathy | Hearing disorders and deafness | Mitochondriopathie | Skin diseases | Connective tissue diseases | Neurodegenerative diseases | Immunological diseases

Clinical Application | Pharmacogenomics

Created with Clinical Pharmacogenetics Implementation Consortium (CPIC) recommendations target-seq workflows for organism response to 28 drugs:
Amitriptyline | Capecitabine | Desipramine | Imipramine | Ondansetron | Sertraline | Trimipramine | Atazanavir | Escitalopram | Doxepin | Ivacaftor | Paroxetine | Simvastatin | Tropisetron | Azathioprine | Clomipramine | Fluorouracil | Mercaptopurine | Phenytoin | Tacrolimus | Voriconazole | Codeine | Clopidogrel | Fluvoxamine | Nortriptyline | Ribavirin | Thioguanine | Warfarin

Consumer Genetics | Custom developed

Ready to use, custom developed, computational models for below listed polygenic scores:
Nutrition: Magnesium level | Lactose intolerance | BMI | Vitamin E level | Fasting glucose homeostasis | Vitamin B12 level | Vitamin D level | Caffeine sensitivity | Folate level | Vitamin B6 level | Cardio: Iron overload | Heart Attack | Heart rate increase in response to exercise | Circadian rhythms | Blood pressure | High - density lipoprotein cholesterol HDL | Low-density lipoprotein cholesterol LDL | Metabolic syndrome | Cancer: Breast cancer | Prostate Cancer | Lung Cancer | Melanoma | Other: Alzheimer | Depression | CRP Level | Alcohol-related life cirrhosis | Bone Density | Type 2 diabetes | Telomere length | Parkinson | Alcohol dependence

Consumer Genetics | Polygenic Scores Catalog

Ready to use traits implemented from The Polygenic Scores Catalog:
BMI | Coronary heart disease | Coronary artery disease | Breast cancer | ER-positive Breast Cancer | ER-negative Breast Cancer | Type 2 diabetes | Atrial fibrillation | Inflammatory bowel disease | Type 1 diabetes | Alzheimer’s Disease Type 2 diabetes (based on SNPs involved in ß-cell function) | Type 2 diabetes (based on SNPs involved in insulin resistance)

Contact us to hear more!

Intelliseq is a team of experienced scientist, geneticists, bioinformaticians and software engineers. We have already solved many problems for our clients globally. 

Let us help you with yours. 

Allele frequencies

1000 Genomes Project phase 3 data, UK10K cohorts data, ExAC consortium data, gnomAD v2.1.1 and v3 data, NHLBI Exome Sequencing Project ESP6500 data, MITOMAP: a human mitochondrial genome database.

Reference Genome

Grch38.p2 with a decoy and random contigs, without ALTs and with a pseudoautosomal region on Y chromosome masked is used during the alignment process. Decoy and random contigs are excluded during the downstream analysis.

Gene annotations

Human Phenotype Ontology (HPO) with 12,111 different phenotypes and ready to use disease panels eg. Marfan Syndrome (4 genes), Iron deficiency anemia (31 genes), Cardiomyopathy (70 genes), Osteoporosis (414 genes). Online Mendelian Inheritance in Man (OMIM) with all known mendelian disorders and over 15,000 genes.

Pathogenicity prediction algorithms:

SIFT, SIFT4G Polyphen2-HDIV, Polyphen2-HVAR, LRT, MutationTaster2, MutationAssessor, FATHMM, MetaSVM, MetaLR, CADD, VEST4, PROVEAN, FATHMM-MKL coding, FATHMM-XF coding, fitCons, LINSIGHT, DANN, GenoCanyon, Eigen, Eigen-PC, M-CAP, REVEL, MutPred, MVP, MPC, PrimateAI, GEOGEN2, ALoFT.

Conservation

PhyloP, phastCons, GERP++, SiPhy, bStatistic

Effect on protein

VEP, SnpEff

Known variant database

ClinVar, HGMD public.