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Patent
Counsyl Inc. | Date: 2017-07-26

Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same. I some embodiments, a high throughput sample processing system comprises a sample dispensing device, a plurality of contactless liquid level sensors, a plurality of aspirators, a plurality of contactless treatment stations, a waste management system, and a control system.


Patent
Counsyl Inc. | Date: 2016-08-06

Integrated modular liquid handling systems are described. The modular liquid handling systems may be customized for use in a variety of applications, including sample processing, assays, diagnostic analyses, and separation of biomolecules. The liquid handling systems may include a variety of integrated modules that provide functions including dispensing of liquids, aspiration of liquids, sensing of liquid parameters, and detection of signals.


Patent
Counsyl Inc. | Date: 2016-04-09

Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same.


Patent
Counsyl Inc. | Date: 2015-12-16

Provided herein are methods, systems, and devices for genetic screening. The genetic screening of two or more individuals can be utilized to predict the phenotype of a child from the group of individuals. Also disclosed is prediction of a phenotype of a child from a subset of biological relatives, such as a potential mother and father, before conception. In many instances, the methods, systems and devices herein are utilized to predict the probability of a child developing a rare genetic disease.


Recent developments in cost-effective DNA sequencing allows for individualized genomic screening of a subject for genetic sequence variants. Training a pathogenicity prediction model using semi-supervised training methods produces a better model for predicting the pathogenicity of a test genetic sequence variant. Provided herein are methods for predicting the pathogenicity of a test genetic sequence variant by utilizing a training data set comprising labeled benign genetic sequence variants unlabeled genetic sequence variants, the unlabeled genetic sequence variants comprising a mixture of benign genetic sequence variants and pathogenic genetic sequence variants. The genetic sequences are annotated with one or more features and a machine learning model is trained in a semi-supervised process based on the training data. The test genetic sequence is then annotated using the one or more features and the probability that the test genetic sequence variant is pathogenic is predicted based on the trained machine learning model.


Patent
Counsyl Inc. | Date: 2015-06-02

Disclosed herein are high-throughput sample processing systems and waste management systems, and methods of using the same.


Patent
Counsyl Inc. | Date: 2014-03-12

The present disclosure provides for compositions and methods for the testing and analysis of genetic alterations of a sample comprising maternal and fetal polynucleotides. Generally, the composition and methods of this disclosure provide for the isolation of a mixture of maternal and fetal polynucleotides from a sample, generally from the mother. Polynucleotides are isolated and purified and further tested to determine the presence or absence of genetic alterations, such as copy number variation, or causal variants at one or more loci in the sample.


Patent
Counsyl Inc. | Date: 2014-11-13

The present disclosure relates to processes for determining the number of nucleic acid repeats in a DNA fragment comprising a nucleic acid repeat region. One example method may include receiving DNA size and abundance data generated by resolving DNA amplification products. A set of low-pass data may be generated by applying a low-pass filter to the DNA size and abundance data and a set of band-pass data may be generated by applying a band-pass filter to the DNA size and abundance data. A peak of the DNA size and abundance data representative of a number of nucleic acid repeats in the DNA may be identified based on peaks identified from the low-pass data and the band-pass data.


Patent
Counsyl Inc. | Date: 2015-10-15

Processes and systems for reading variants from a genome sample relative to a reference genomic sequence are provided. An exemplary process includes collecting a set reads and generating a k-mer graph from the reads. For example, the k-mer graph can be constructed to represent all possible substrings of the collected reads. The k-mer graph may be reduced to a contiguous graph, and a set of possible haplotypes generated from the contiguous graph. The process may further generate, the error table providing a filter for common sequencer errors. The process may then generate a set of diplotypes based on the set of haplotypes and the generated error table and score the set of diplotypes to identify variants from the reference genome. Scoring the diplotypes may include determining a posterior probability for each of the diplotypes, with the highest scoring diplotype(s) reported as the result.


Patent
Counsyl Inc. | Date: 2015-12-28

Described herein are methods directed to determining the carrier status or genotype of a subject. Described herein is a method that combines experimental and computational approaches to resolve the structure of genomic loci (i.e., the genotype) whose sequences are highly homologous to other sequences in the genome. In particular, the determination of carrier status and/or copy number of a gene in a subject, wherein the gene has a corresponding highly homologous homolog, e.g., gene or pseudogene, utilizes Next Generation Sequencing. Also described herein is a computer-assisted method for such determinations.

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