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公开(公告)号：US08725422B2
公开(公告)日：2014-05-13
申请号：US13270989
申请日：2011-10-11
Applicant: Aaron Halpern , Krishna Pant
Inventor： Aaron Halpern , Krishna Pant
CPC classification number: G06F19/18 , C12Q1/6809 , C12Q1/6827 , G06F19/20 , G06F19/22 , G06F19/24 , C12Q2537/16 , C12Q2537/165
Abstract: Methods for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. Genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.
Abstract translation: 公开了用于确定样品中靶序列的检测位置处的基因组区域的拷贝数的方法。 对样品中靶序列的基因组区域进行测序，并获得序列覆盖度的测量数据。 校正序列覆盖偏差并且可以相对于基线样本进行归一化。 执行隐马尔科夫模型（HMM）分割，评分和输出，并且在一些实施例中，也可以执行基于群体的无呼叫和低置信区域的识别。 然后估计多个区域的总拷贝数值和区域特定拷贝数值。
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公开(公告)号：US20070092889A1
公开(公告)日：2007-04-26
申请号：US11446599
申请日：2006-06-02
Applicant: David Cox , Demetrius Maraganore , Dennis Ballinger , Krishna Pant , Timothy Lesnick
Inventor： David Cox , Demetrius Maraganore , Dennis Ballinger , Krishna Pant , Timothy Lesnick
CPC classification number: C12Q1/6883 , C12Q2600/106 , C12Q2600/136 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , C12Q2600/172
Abstract: Compositions and methods for use in the therapeutic and preventative treatment, study, diagnosis and prognosis of PD-related disease are disclosed. Also provided are kits and reagents for prognosis and diagnosis of PD-related disease and related conditions.
Abstract translation: 公开了用于PD相关疾病的治疗和预防性治疗，研究，诊断和预后的组合物和方法。 还提供了用于PD相关疾病和相关病症的预后和诊断的试剂盒和试剂。
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公开(公告)号：US20050003410A1
公开(公告)日：2005-01-06
申请号：US10845316
申请日：2004-05-12
Applicant: Kelly Frazer , David Cox , Heng Tao , Krishna Pant , Geoffrey Nilson
Inventor： Kelly Frazer , David Cox , Heng Tao , Krishna Pant , Geoffrey Nilson
IPC: C12Q1/68
CPC classification number: C12Q1/6809 , C12Q1/6827 , C12Q2531/113 , C12Q2565/501
Abstract: The invention provides methods of analyzing genes for differential relative allelic expression patterns. Haplotype blocks throughout the genomes of individuals are analyzed to identify haplotype patterns that are associated with specific differential relative allelic expression patterns. Haplotype blocks that contain associated haplotype patterns may be further investigated to identify genes or variants of genes involved in differential relative allelic expression patterns.
Abstract translation: 本发明提供了分析差异相对等位基因表达模式的基因的方法。 分析个体基因组中的单倍型区域，以鉴定与特异性差异相对等位基因表达模式相关联的单倍型模式。 可以进一步研究包含相关单体型模式的单倍型区域，以鉴定参与差异相对等位基因表达模式的基因的基因或变体。
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公开(公告)号：US09811552B1
公开(公告)日：2017-11-07
申请号：US15133089
申请日：2016-04-19
Applicant: Katsuya Noguchi , Krishna Pant , Ryan Barrett , Elad Gil , Othman Laraki
Inventor： Katsuya Noguchi , Krishna Pant , Ryan Barrett , Elad Gil , Othman Laraki
CPC classification number: G06F17/30371 , G06F17/30327 , G06F17/30598 , G06F17/30867
Abstract: Techniques, systems, and products for analyzing sparse indicators and generating communications based on bucketing of sparse indicators are disclosed.
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公开(公告)号：US09811391B1
公开(公告)日：2017-11-07
申请号：US15449579
申请日：2017-03-03
Applicant: Ryan Barrett , Taylor Sittler , Krishna Pant , Zhenghua Li
Inventor： Ryan Barrett , Taylor Sittler , Krishna Pant , Zhenghua Li
CPC classification number: G06F19/18 , G06F9/5083 , G06F19/22 , G06F19/24
Abstract: Embodiments in the disclosure are directed to the use of distributed computing to align reads against multiple portions of a reference dataset. Aligned portions of the reference dataset that correspond with an above-threshold alignment score can be assessed for the presence of sparse indicators that can be categorized and used to influence a determination of a state transition likelihood. Various tasks associated with the processing of reads (e.g., alignment, sparse indicator detection, and/or determination of a state transition likelihood) may be able to take advantage of parallel processing and can be distributed among the machines while considering the resource utilization of those machines. Different load-balancing mechanisms can be employed in order to achieve even resource utilization across the machines, and in some cases may involve assessing various processing characteristics that reflect a predicted resource expenditure and/or time profile for each task to be processed by a machine.
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公开(公告)号：US20070148664A1
公开(公告)日：2007-06-28
申请号：US11515497
申请日：2006-09-01
Applicant: Krishna Pant , Renee Stokowski , David Cox , Martin Green , Franciscus Van Der Ouderaa , Rebecca Ginger , Amelia Fereday , Wendy Filsell , Carl Jarman , Anthony Dadd
Inventor： Krishna Pant , Renee Stokowski , David Cox , Martin Green , Franciscus Van Der Ouderaa , Rebecca Ginger , Amelia Fereday , Wendy Filsell , Carl Jarman , Anthony Dadd
CPC classification number: G01N33/68 , C12Q1/6876 , C12Q2600/158 , G01N33/5008 , G01N33/5011 , G01N33/502 , G01N33/5088
Abstract: The invention provides a collection of polymorphic sites associated with variations in human skin color, and genes containing or proximal to the sites.
Abstract translation: 本发明提供了与人皮肤颜色变化相关的多态性位点以及含有或靠近该位点的基因的集合。
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公开(公告)号：US09773031B1
公开(公告)日：2017-09-26
申请号：US15489473
申请日：2017-04-17
Applicant: Krishna Pant , Taylor Sittler , Ryan Barrett
Inventor： Krishna Pant , Taylor Sittler , Ryan Barrett
IPC: G06F17/30
CPC classification number: G06F17/30303 , G06F17/30312 , G06F17/30569 , G06K9/00483 , G06K9/6249
Abstract: Techniques for accurately identifying duplications and deletions using depth vectors. A depth vector is generated for each of multiple clients based on a set of reads that is received and aligned to a reference data set. A transformation processing of the depth vectors is performed to produce multiple components. Each of the components is assigned an order based on the extent to which it accounts for cross-client differences in the depth vectors. Each of the components includes an intensity, multiple values, and multiple client weights. A subset of the components is identified based on the order. A sparse indicator and positional data for the sparse indicator can be determined from the components in the subset, and one or more clients can be identified as being associated with the components.
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公开(公告)号：US09813467B1
公开(公告)日：2017-11-07
申请号：US15452241
申请日：2017-03-07
Applicant: Ryan Barrett , Taylor Sittler , Krishna Pant , Zhenghua Li , Katsuya Noguchi , Nishant Bhat
Inventor： Ryan Barrett , Taylor Sittler , Krishna Pant , Zhenghua Li , Katsuya Noguchi , Nishant Bhat
CPC classification number: G06F17/30 , G06F17/30516
Abstract: Techniques are disclosed for processing and aligning incomplete data. A stream of data is received from a data source including a plurality of reads. While receiving the stream of data and prior to having received all of the plurality of reads, a set of reads is extracted from the plurality of reads. Each of the set of reads is aligned to a corresponding portion of a reference data set. For each particular position of a plurality of particular positions of the reference data set, a subset of reads of the aligned set of reads is identified. A value of a client data set is generated based on the subset of reads. A variable is generated based on the client data set. Data is routed when a condition, based on the variable, is satisfied.
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公开(公告)号：US09811439B1
公开(公告)日：2017-11-07
申请号：US15489492
申请日：2017-04-17
Applicant: Ryan Barrett , Krishna Pant
Inventor： Ryan Barrett , Krishna Pant
CPC classification number: G06F11/3612 , G06F11/26
Abstract: Techniques for using functional testing to detect run-time impacts of code modifications. A method includes accessing a workflow including a plurality of stages for processing reads. The stages are defined based on modifiable code and include a first stage for aligning reads with a corresponding portion of a reference data set and a second stage for collectively analyzing data corresponding to the aligned reads. The method includes identifying functional testing specifications to correspond with the workflow, including a definition of which stages are to be performed during functional testing, a reduced reference data set, and a set of reads. The method includes performing the functional testing using the reduced reference data set and the set of reads, detecting a result generated via the performance, and outputting the result.
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10.发明申请METHODS FOR DETERMINING ABSOLUTE GENOME-WIDE COPY NUMBER VARIATIONS OF COMPLEX TUMORS 审中-公开确定复杂肿瘤的绝对基因组复制数变异的方法
公开(公告)号：US20130316915A1
公开(公告)日：2013-11-28
申请号：US13888146
申请日：2013-05-06
Applicant: Aaron HALPERN , Krishna Pant
Inventor： Aaron HALPERN , Krishna Pant
IPC: C12Q1/68
CPC classification number: G16B30/00 , C12Q1/6827 , G16B20/00 , G16B35/00 , G16B40/00 , G16B45/00 , G16B50/00 , G16C20/60 , C12Q2537/16 , C12Q2537/165
Abstract: Methods for interpreting absolute copy number of complex tumors and for determining the copy number of a genomic region at a detection position of a target sequence in a sample are disclosed. In certain aspects, genomic regions of a target sequence in a sample are sequenced and measurement data for sequence coverage is obtained. Sequence coverage bias is corrected and may be normalized against a baseline sample. Hidden Markov Model (HMM) segmentation, scoring, and output are performed, and in some embodiments population-based no-calling and identification of low-confidence regions may also be performed. A total copy number value and region-specific copy number value for a plurality of regions are then estimated.
Abstract translation: 公开了用于解释复合肿瘤的绝对拷贝数和用于确定样品中靶序列的检测位置的基因组区域的拷贝数的方法。 在某些方面，对样品中靶序列的基因组区域进行测序，并获得序列覆盖率的测量数据。 校正序列覆盖偏差并且可以相对于基线样本进行归一化。 执行隐马尔科夫模型（HMM）分割，评分和输出，并且在一些实施例中，也可以执行基于群体的无呼叫和低置信区域的识别。 然后估计多个区域的总拷贝数值和区域特定拷贝数值。
