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1. 发明申请

WO2018160907A1 EXTRACTION OF NUCLEIC ACIDS FOR REDUCED PROBE COUNT VARIABILITY 审中-公开
公开(公告)号：WO2018160907A1
公开(公告)日：2018-09-07
申请号：PCT/US2018/020553
申请日：2018-03-02
申请人： COUNSYL, INC.
发明人： CREGG, James F. , WONG, Karina Liang , COPELAND, Nathan Daniel
IPC分类号： C12M1/34 , C12N15/09 , C12Q1/68 , G06F19/18 , G06F19/22
CPC分类号： C12Q1/6806 , C12Q2527/125 , C12Q2535/122 , C12Q2537/159
摘要： Provided herein are methods and compositions for reducing probe count variability of a biological sample. After obtaining a biological sample, such as a saliva sample, the sample is pretreated with a lysis buffer that includes a detergent to form an extraction solution. Nucleic acids are isolated from the extraction solution and fragmented into polynucleotide fragments, which are then mixed with homologous capture probes, which, for example, are bound to a flow cell of a direct targeted sequencing system. The capture probes bind to targeted sequences of the polynucleotide fragments, thereby capturing the targeted polynucleotide fragments. Based on binding of polynucleotides fragments to the homologous capture probes, a probe count is determined for the homologous probes. By mixing the lysis buffer with the biological sample to form the extraction solution, variability of the determined probe count is substantially reduced.

2. 发明申请

WO2018144365A1 CUSTOMIZED REAGENT PLATES 审中-公开
公开(公告)号：WO2018144365A1
公开(公告)日：2018-08-09
申请号：PCT/US2018/015652
申请日：2018-01-29
申请人： COUNSYL, INC.
发明人： LAI, Henry H. , CHU, Clement S.
IPC分类号： C12N15/09 , C12N15/10 , C12N9/10
CPC分类号： B01J19/0046 , B01J19/0033 , B01J19/0093 , B01J2219/00317 , B01J2219/00351 , B01L3/50 , C12Q1/00 , C40B40/06 , C40B50/14
摘要： Disclosed are high concentration reagents for use in preparing DNA samples in low volume reactions. Such reagents include, for example, DNA end repair buffers for use in low volume DNA blunting and phosphorylating reactions, DNA adenylating buffers for use in a low volume DNA adenylating reaction, and DNA ligation buffers for use in low volume DNA adaptor ligation reactions with adaptors. Also disclosed are customized reagent plates and kits containing one or more of these low volume buffers for use in low volume DNA blunting, phosphorylating, adenylating, and ligation reactions. Methods of using the high concentration reagents (low volume buffers) and the customized reagent plates for preparing DNA sequencing libraries in low volume reactions are also disclosed.

3. 发明申请

WO2018085779A1 METHODS FOR ASSESSING GENETIC VARIANT SCREEN PERFORMANCE 审中-公开
标题翻译：评估遗传变异筛选表现的方法
公开(公告)号：WO2018085779A1
公开(公告)日：2018-05-11
申请号：PCT/US2017/060222
申请日：2017-11-06
申请人： COUNSYL, INC.
发明人： GOULD, Genevieve, M. , WANG, Xin , GRAUMAN, Peter, V. , HOGAN, Gregory, John , ROBERTSON, Alexander, De Jong , MAGUIRE, Jared, Robert , KANG, Hyunseok , HAQUE, Imran, Saeedul , EVANS, Eric, Andrew , HAAS, Kevin, R.
IPC分类号： G06F19/22 , C40B30/02 , G06F17/30 , G06F19/28
CPC分类号： G16B40/00 , G06F16/00 , G16B20/00 , G16B35/00 , G16C20/60
摘要： Described herein are methods of assessing the performance of a genetic variant screen. A summary statistic can be determined to assess the performance of the genetic variant screen. In some embodiments, the summary statistic is determined using synthetic copy number variants. In some embodiments, the summary statistic is determined using a reference sequence having a synthetic variant.
摘要翻译：本文描述了评估遗传变体筛选的表现的方法。可以确定总结统计以评估基因变体筛选的表现。在一些实施例中，使用合成拷贝数变体来确定汇总统计量。在一些实施方案中，使用具有合成变体的参考序列来确定概要统计。

4. 发明申请

WO2017116997A3 ROBOTIC SYSTEM FOR SORTING SAMPLE TUBES 审中-公开
公开(公告)号：WO2017116997A3
公开(公告)日：2017-07-06
申请号：PCT/US2016/068337
申请日：2016-12-22
申请人： COUNSYL, INC.
发明人： LAPHAM, Kyle , NASH, Ethan , TURNER, Peter , HAAS, Kevin , WONG, Christopher
IPC分类号： B07C5/00
摘要： A device and method for sorting sample tubes, having a robotic assembly with a horizontal robotic arm which is configured to pivot around the base. The end of tooling arm is configured to pick up and hold a sample tube when a vacuum is applied and to deposit the sample tube into a designated slot in a tube rack when the vacuum is removed. The device includes a vacuum source to pull a vacuum through the tooling; an air source to expel air through the tooling; a horizontal stage underneath the robotic arm to hold a plurality of tube racks in a position; a vision system configured to record coded information on sample tubes and on the sides of tube racks in the device and to convey the coded information to a control system; and tube racks to store the sample tubes.

5. 发明申请

WO2017027425A1 MODULAR LIQUID HANDLING SYSTEM 审中-公开
标题翻译：模块化液体处理系统
公开(公告)号：WO2017027425A1
公开(公告)日：2017-02-16
申请号：PCT/US2016/045924
申请日：2016-08-06
申请人： COUNSYL, INC.
发明人： LAPHAM, Kyle , KIM, Tony Hyun , BREMNER, Christopher
IPC分类号： G01N35/10 , G01N1/00 , G01N1/28 , G01N35/00 , G01N35/02 , G01N35/04
CPC分类号： G01N35/026 , G01N35/00584 , G01N35/0099 , G01N35/10 , G01N35/1065 , G01N2035/0418
摘要： 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.
摘要翻译：描述了集成的模块化液体处理系统。模块化液体处理系统可以定制用于各种应用，包括样品处理，测定，诊断分析和分离生物分子。液体处理系统可以包括提供包括液体分配，液体抽吸，液体参数检测以及信号检测功能的各种集成模块。

6. 发明申请

WO2015073650A3 AUTOMATED NUCLEIC ACID REPEAT COUNT CALLING METHODS 审中-公开
标题翻译：自动核酸重复计数调用方法
公开(公告)号：WO2015073650A3
公开(公告)日：2015-12-03
申请号：PCT/US2014065419
申请日：2014-11-13
申请人： COUNSYL INC
发明人： PATTERSON A SCOTT , HAQUE IMRAN S , EVANS ERIC A , CHU CLEMENT
IPC分类号： A61K31/56 , A61K31/12 , C12Q1/68
CPC分类号： G06F19/22 , G06F19/18
摘要： 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.
摘要翻译：本公开涉及用于确定包含核酸重复区域的DNA片段中的核酸重复数目的方法。一个示例性方法可以包括接收通过解析DNA扩增产物产生的DNA大小和丰度数据。可以通过对DNA大小和丰度数据应用低通滤波器来生成一组低通数据，并且可以通过对DNA大小和丰度数据应用带通滤波器来生成一组带通数据。代表DNA中大量核酸重复的DNA大小和丰度数据的峰可以基于从低通数据和带通数据中识别出的峰来识别。

7. 发明申请

WO2014165267A2 SYSTEMS AND METHODS FOR PRENATAL GENETIC ANALYSIS 审中-公开
标题翻译：用于初步遗传分析的系统和方法
公开(公告)号：WO2014165267A2
公开(公告)日：2014-10-09
申请号：PCT/US2014/025031
申请日：2014-03-12
申请人： COUNSYL, INC.
发明人： EVANS, Eric , CHU, Clement , DAVISON, Daniel , RICHARDS, Hunter
IPC分类号： C12Q1/68
CPC分类号： C12Q1/6827 , C12Q2521/501 , C12Q2525/307 , C12Q2531/125 , C12Q2537/143
摘要： 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.
摘要翻译：本公开提供了用于测试和分析包含母体和胎儿多核苷酸的样品的遗传改变的组合物和方法。通常，本公开的组合物和方法提供从样品（通常来自母体）分离母体和胎儿多核苷酸的混合物。分离和纯化多核苷酸并进一步测试以确定在样品中的一个或多个基因座处存在或不存在遗传改变，例如拷贝数变异或因变量。

8. 发明申请

WO2008134588A1 METHODS AND SYSTEMS OF AUTOMATIC ONTOLOGY POPULATION 审中-公开
标题翻译：自动人口学方法与系统
公开(公告)号：WO2008134588A1
公开(公告)日：2008-11-06
申请号：PCT/US2008/061681
申请日：2008-04-25
申请人： COUNSYL, INC. , SRINIVASAN, Balaji, S. , SNOW, Rion, L.
发明人： SRINIVASAN, Balaji, S. , SNOW, Rion, L.
IPC分类号： G06Q50/00
CPC分类号： G06F17/2785 , G06F17/30684
摘要： Methods and systems for creating a knowledge graph that relates terms in a corpus of literature in the form of an assertion and provides a probability of the veracity of the assertion are disclosed herein. Various aspects of the invention are directed to and/or involve knowledge graphs and structured digital abstracts (SDAs) offering a machine readable representation of statements in a corpus of literature. Various methods and systems of the invention can automatically extract, structure, and visualize the statements. Such graphs and abstracts can be useful for a variety of applications including, but not necessarily limited to, semantic-based search tools for search of electronic medical records, specific content verticals (e.g. newswire, finance, history) and general internet searches.
摘要翻译：用于创建知识图的方法和系统，其以断言的形式关联文献语料库中的术语并且提供断言的真实性的概率。本发明的各个方面涉及和/或涉及知识图和结构化数字抽象（SDA），其提供文献语料库中的语言的机器可读表示。本发明的各种方法和系统可以自动提取，构造和可视化语句。这些图形和摘要可用于各种应用，包括但不一定限于用于搜索电子医疗记录的基于语义的搜索工具，特定的内容垂直（例如新闻稿，财务，历史）和一般互联网搜索。

9. 发明申请

WO2018161019A1 METHODS FOR OPTIMIZING DIRECT TARGETED SEQUENCING 审中-公开
公开(公告)号：WO2018161019A1
公开(公告)日：2018-09-07
申请号：PCT/US2018/020744
申请日：2018-03-02
申请人： COUNSYL, INC.
发明人： LAI, Henry , CHU, Clement
IPC分类号： C12P19/34 , C12Q1/68 , C12Q1/6869 , C40B20/00 , C40B30/04
摘要： Described are methods for selecting an amount of a critical parameter (such as an amount of a sequencing library, amount of a capture probe library, or a number of amplification cycles) for direct targeted sequencing. The methods include hybridizing capture probes in a capture probe library to surface-bound oligonucleotides; extending the surface-bound oligonucleotides using the hybridized capture probes as a template; hybridizing nucleic acid molecules from a sequencing library to the surface-bound capture probes; extending the surface-bound capture probes using the hybridized nucleic acid molecules as a template; amplifying the surface-bound complements of the nucleic acid molecules by bridge amplification for a number of amplification cycles; sequencing the amplified surface-bound complements of the nucleic acid molecules to determine an average cluster density after a predetermined number of sequencing cycles; repeating these steps at a plurality of different amounts of the critical parameter; and selecting an amount of the critical parameter.

10. 发明申请

WO2018144363A1 SEQUENCING LIBRARY PREPARATION IN SMALL WELL FORMAT 审中-公开
公开(公告)号：WO2018144363A1
公开(公告)日：2018-08-09
申请号：PCT/US2018/015648
申请日：2018-01-29
申请人： COUNSYL, INC.
发明人： LAI, Henry H. , CHU, Clement S.
IPC分类号： C12N15/10 , C12Q1/68
CPC分类号： C40B50/06 , B01J19/0046 , B01J2219/00315 , C12N15/1093 , C12Q1/6806 , C12Q1/6869 , C12Q1/6876 , C40B40/06 , C40B50/14 , C12Q2527/125 , C12Q2527/137 , C12Q2535/122 , C12Q2563/159
摘要： Disclosed are high concentration reagents for use in preparing DNA samples in low volume reactions. Such reagents include, for example, DNA end repair buffers for use in low volume DNA blunting and phosphorylating reactions, DNA adenylating buffers for use in a low volume DNA adenylating reaction, and DNA ligation buffers for use in low volume DNA adaptor ligation reactions with adaptors. Also disclosed are customized reagent plates and kits containing one or more of these low volume buffers for use in low volume DNA blunting, phosphorylating, adenylating, and ligation reactions. Methods of using the high concentration reagents (low volume buffers) and the customized reagent plates for preparing DNA sequencing libraries in low volume reactions are also disclosed.

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