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Codified Genomics

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Houston, Texas, US

About Codified Genomics

Codified Genomics provides data from a multitude of sources on the variant, gene, pathway and local genomic levels and helps hone in on causative variants quickly and accurately; Codified puts a world of knowledge at the clinician's fingertips. Automated processes enable the clinical report to be fully ACMG... Show more »

Codified Genomics provides data from a multitude of sources on the variant, gene, pathway and local genomic levels and helps hone in on causative variants quickly and accurately; Codified puts a world of knowledge at the clinician's fingertips. Automated processes enable the clinical report to be fully ACMG compliant without requiring the reviewer to tediously classify every variant, freeing them to do what's most important: saving lives.

With over 24,000 exomes analyzed, the Codified Genomics process has experience at the heart of its development. Our software has enabled hundreds of clinical diagnoses, the discovery of dozens of new disease mutations and the description of entirely novel diseases.

The most expensive component of clinical genome sequencing is the time that healthcare professionals spend poring over data. The Codified Genomics process streamlines and standardizes tertiary analysis enabling the clinician to make the most of her time.

Codified Genomics provides data from a multitude of sources on the variant, gene, pathway and local genomic levels and helps hone in on causative variants quickly and accurately; Codified Genomics puts a world of knowledge at the clinician's fingertips. Automated processes enable the clinical report to be fully ACMG compliant without requiring the reviewer to tediously classify every variant, freeing them to do what's most important: saving lives.

Codified Genomics enables intelligent filtering and prioritization by gathering all salient information for the genomic coordinate, variant, gene model, protein, function, expression, disease, population and system-interactions. This data is compiled together with assay metrics to allow automatic filtering and prioritization of variants for a patient. The data is displayed simply and cleanly to let the clinician make the final choice about which variants are and are not important. Finally, this information is captured and used the next time a patient is reviewed to help make even more accurate diagnoses.


Relevant publications:
- Bainbridge MN, Hu H, Muzny DM, Musante L, Lupski JR, Graham BH, Chen W, Gripp KW, Jenny K, Wienker TF, et al.: De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome.
Genome Med 2013, 5(2):11.

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Our Services (7)


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Whole Exome Sequencing Data Analysis

Starting at $150.00 per sample

Whole exome sequencing data annotation for interpretation

The codified variant analysis tool extensively annotates data using >40 public and private sources and ranks variants based on their likelihood to cause a patient’s phenotype, the rarity of the variant and the likelihood of being deleterious.

INPUT: Variant Call... Show more »

Whole exome sequencing data annotation for interpretation

The codified variant analysis tool extensively annotates data using >40 public and private sources and ranks variants based on their likelihood to cause a patient’s phenotype, the rarity of the variant and the likelihood of being deleterious.

INPUT: Variant Call Format (VCF) file(s) from a single case or family (trio or multiple affecteds). Additionally, we provide an interface for entering patient phenotype terms.

OUTPUT:
User friendly web-interface where the alleles are ranked and annotated with a wide variety of data including:
- Allele frequency data from Thousand Genomes and ESP
- Allele frequency data from a cohort of 11K unaffected individuals
- Disease information from OMIM
- Functional data from SwissProt
- Human Phenotype Ontology data
- Disease inheritance model for each gene
- Zygosity of the mutation
- Mutation type (synonymous, etc)
- Historical data on appearance of variants in your other samples and sequence batches
- Clinvar disease association database
- COSMIC
- ZFIN (zebrafish model) and MGI (mouse model) data.
- Pathogenic mutation profile data which shows the type of mutation tend to cause disease in a given gene
- Allele fraction
- Sequencing quality
- Pileup features (if a BAM is provided)
- Predicted functional impact using Polyphen2, LRT Omega, FathMM, Mutation Taster, GERP, Mutation Assessor, 29 way and Codified’s own proprietary algorithm.
- Loss of homozygosity data

Additionally, we provide a number of tools that allow you to look for trends across patients, including:
- Patients with mutations in the same gene
- Variants shared in a cohort patients
- Variants unique to a patient in a cohort
- Ideograms for absence of heterozygosity

The variant analysis tool also allows reviewers to score and comment on individual variants. We will work with you to produce an exported report in the format you need.

PRICE: $150 per sample for exome analysis, $200 per sample for trios. We offer discounts for bulk orders and research groups.

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Biology

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Nucleic Acid Analysis

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Nucleic Acid Services

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Biochemistry & Molecular Biology

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Sequencing Data Analysis and Management

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Nucleic Acid Data Analysis

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