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Kokotas H.,Sophia Genetics | Petersen M.B.,Sophia Genetics
Clinical Genetics | Year: 2010

Aniridia is a severe, congenital ocular malformation inherited in an autosomal-dominant fashion with high penetrance and variable expression. Eye morphogenesis in humans involves a molecular genetic cascade in which a number of developmental genes interact in a highly organized process during the embryonic period to produce functional ocular structures. Among these genes, paired box gene 6 (PAX6) has an essential role as it encodes a phylogenetically conserved transcription factor almost universally employed for eye formation in animals with bilateral symmetry, despite widely different embryological origins. To direct eye development, PAX6 regulates the tissue-specific expression of diverse molecules, hormones, and structural proteins. In humans, PAX6 is located in chromosome 11p13, and its mutations lead to a variety of hereditary ocular malformations of the anterior and posterior segment, among which aniridia and most probably foveal hypoplasia are the major signs. Aniridia occurs due to decreased dosage of the PAX6 gene and exists in both sporadic and familial forms. The mutations are scattered throughout the gene and the vast majority of those reported so far are nonsense mutations, frameshift mutations, or splicing errors that are predicted to cause pre-mature truncation of the PAX6 protein, causing haploinsufficiency. Here we review the data regarding the mechanisms and the mutations that relate to aniridia. © 2010 John Wiley & Sons A/S.


Douzgou S.,Sophia Genetics | Petersen M.B.,Sophia Genetics
Clinical Genetics | Year: 2011

Cohen syndrome (CS) (OMIM#216550) is an uncommon autosomal recessive developmental disorder that has been attributed to mutations in the COH1 gene in at least 200 patients of diverse ethnic background so far. The clinical heterogeneity of CS is evident when comparing patients of different ethnic backgrounds, especially when evaluating specific system phenotypes separately, such as the ophthalmic and central nervous systems. We reviewed the available clinical data on CS cohorts of patients who share a founder effect and demonstrated that most features associated so far with CS are less than those always present in the patients who share a founder mutation thus representing clinical heterogeneity. Furthermore, there is a wide clinical variability of CS in the distinct founder mutation cohorts, the Finnish, Greek/Mediterranean, Amish and Irish travelers. The Greek/Mediterranean founder mutation is correlated to a CS phenotype characterized by specific and persistent skeletal features, corneal changes, periodontal disease, a distinct neurocognitive phenotype for the high recurrence of autism and non-verbal communication and inconstant microcephaly. © 2011 John Wiley & Sons A/S.


A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads positions, the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank. The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.


A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads positions, the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank. The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.


Trademark
Sophia Genetics | Date: 2016-03-17

Data processing and computer equipment; data banks (software); software (recorded programs); computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; recorded or downloaded sounds, images or data. Business management; commercial administration; office functions; collection of information into computer databases; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; systematization of data in a central file; professional consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization. Project studies, expert reports and research of a technical nature; writing, design, development and updating of software; technical support concerning the use of software; hosting of online platforms; provision of online non-downloadable software; provision of software on platforms enabling users to access software, computer networks, computer servers and computer and data storage systems and to use them; provision of scientific information via web-based platforms; data storage and cloud computing for bioinformatic analysis; bioinformatic analysis services, development of software and pipeline architectures; provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management software, database construction; development of genomic and bioinformatic applications; storage of data by computer; provision of advice and information for the aforesaid services or those relating thereto. Medical services; health services; medical analysis services related to the treatment of individuals; medical diagnostics, diagnostics in the field of medicine.


Trademark
Sophia Genetics | Date: 2016-05-12

Data processing and computer equipment; data processing systems; software (recorded programs); data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; recorded or downloaded sounds, images or data. Business management; business administration; office functions; compilation of information into computer databases; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; systematization of data in a central file; professional consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization. Medical services; health care services; medical analysis services related to the treatment of individuals; medical diagnostics, diagnostics in the field of medicine.


News Article | July 8, 2014
Site: www.finsmes.com

The round was led by Dr Mike Lynch’s Invoke Capital, Swisscom and Endeavour Vision. Led by Jurgi Camblong, CEO, Sophia Genetics is a pioneer in Data-Driven Medicine, a crossover field that requires deep expertise in Next Generation Sequencing (NGS), combined with accurate and scalable predictive algorithms to diagnose genetic diseases. With this investment, the company gains access to Invoke’s portfolio company Genalys, whose Cambridge-based mathematicians apply big data approaches to genomic information. In three years, Sophia Genetics has developed bioinformatics pipelines and visualization tools for more than 70 commercial panels, proprietary custom panels and is extending that capability to whole exomes and genomes. The company obtains CE-IVD marking for each supported pipeline and has received ISO 13485 certification.


News Article | February 28, 2017
Site: www.techrepublic.com

Over 14 million new cancer cases worldwide were reported in 2012, with the rate of occurrence expected to jump by approximately 70% over the next two decades, according to the World Health Organization. Cancer patients are often treated with chemotherapy and various types of drugs, but the results of these treatments aren't uniform in effectiveness, which is why it's imperative for hospitals, clinics, and doctors to make the best drug treatment choices for each individual patient. Getting drug therapies right is an area where digitalized genomics data can help. "The technique that we use for this is genomic sequencing," explained Dr. Jurgi Camblong, cofounder of Sophia Genetics, a provider of artificial intelligence that pinpoints the genomic code mutations behind cancers and rare disorders to assist physicians and healthcare institutions in prescribing optimal drug treatments for their patients. Today, 240 hospitals in 39 countries use the Sophia platform. "What the technology does is spot variations in different genetic codes so we can use historical data that aids in prescribing the best combination of drugs to treat a particular cancer or condition in an individual patient," said Camblong. "This is next-generation genomic sequencing, and it is used in two different areas: chronic hereditary disorders and oncology. By using the algorithms that are part of our artificial intelligence, we can spot the origin of a genetic mutation causing a cancer or a particular condition and then give an idea of what the best drug treatment would be to the attending physician." An example is lung cancer, where treatment in the past was prescribed based upon the patient's tissue type instead of on a particular genetic mutation. By using genetic sequencing and mutation detection instead of tissue analysis, physicians can now identify the genetic events that caused the condition in the first place, and not just treat symptoms. "The more we understand the molecular events at the origin of the disease or disorder, the better we can understand the effects of what certain combinations of drugs are likely to be," said Camblong. "The process begins with the extraction of the patient's DNA via a blood draw or biopsy, said Camblong. "The hospital then uses molecular biology processes to prepare the samples and subsequently digitizes them using a DNA sequencer. The resulting genomic data is then submitted to the company AI on the Sophia DDM Software as a Service (SaaS) platform, which digs around to identify the patient's genomic mutations. The more hospitals use the analytics platform, the more patients' genomic profiles are accumulated, and the smarter the AI gets." "Without this technology, the process of determining a drug treatment takes about two days work, and in some cases can take several months when using old technologies," said Camblong. In contrast, healthcare professionals who use Sophia for genetic sequencing and analysis can get drug treatment regime recommendations for individual patients in one day. When developing the solution, one challenge Sophia and its healthcare customers faced was guaranteeing patient privacy. To ensure privacy, references to individual patients are stripped off of all treatment records so that the data is fully anonymized before it is ever admitted to Sophia's data repository. One benefit to the Sophia system being a SaaS-based solution is that even smaller hospitals and clinics can afford the technology, which on average costs $50-$200 per genetic evaluation. A second advantage that a SaaS-based platform brings is democratization of information, because drug outcomes for different cancers and conditions can be shared globally. "This democratization of the data is extremely important," said Camblong, "because not every hospital has the clinical expertise to prescribe the optimal treatments for different conditions. Because we can share data and encourage collaboration through the platform, these clinics now have access to experts and results from around the world."


LAUSANNE, Switzerland, Nov. 10, 2016 /PRNewswire/ -- Today, at the AMP 2016 Annual Meeting, Sophia Genetics, global leader in Data-Driven Medicine, and world-class Next-Generation Sequencing (NGS) assay developer ArcherDX, announced the signing of a new partnership to combine their...

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