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公开(公告)号：US20200089842A1
公开(公告)日：2020-03-19
申请号：US16134222
申请日：2018-09-18
发明人： Raphael Polig , Mitra Purandare
摘要： A random sequence generation of defined values may be provided. A method comprises pre-loading a RAM block with an initial list comprising the defined values of a sequence of values to be updated, and shuffling the defined values of the sequence using a counter and a random offset for indices in the list.
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公开(公告)号：US20190388862A1
公开(公告)日：2019-12-26
申请号：US16017682
申请日：2018-06-25
发明人： Karin STRAUSS , Weida CHEN , Robert GRASS , Alexander Xavier Christof KOHLL , Bichlien Hoang NGUYEN
摘要： A data storage medium is disclosed comprising a substrate covered with alternating layers of a polycationic molecule and artificially synthesized DNA molecules encoding digital information. The magnetic substrate may be a metallic nanoparticle formed from a metal such as iron or cobalt. The polycationic molecule may be polyethyleneimine (PEI). The DNA is protected from degradation by encapsulation in silica. A process for stably storing DNA is also disclosed. Stored DNA may be freed from the silica for sequencing or other analysis by washing the silica-coated DNA with a buffered hydrogen fluoride solution. Storage densities of more than 7% DNA by weight are achieved on nanoparticles.
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公开(公告)号：US10451536B2
公开(公告)日：2019-10-22
申请号：US13265439
申请日：2010-04-23
申请人： Nicholas Thomas
发明人： Nicholas Thomas
摘要： In one aspect, the present invention relates to a method 200 for identifying one or more phenotypes from a multi-parameter data set. The method 200 comprises measuring 202 correlation between pairs of parameters within the multi-parameter data set, modifying 204 correlated parameter values within a predetermined multi-parameter data analysis set to form an analysis parameter set, and analyzing 206 the multi-parameter data set using the analysis parameter set to identify one or more phenotypes from the multi-parameter data set. Various embodiments of the present invention may, for example, be used in an automated high-content screening (HCS) apparatus 100 for biological cellular analysis.
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公开(公告)号：US10331849B2
公开(公告)日：2019-06-25
申请号：US14709417
申请日：2015-05-11
发明人： John Burke , Stephen Healy Sanders
摘要： Techniques for construction of internal controls for improved accuracy and sensitivity of DNA testing include obtaining first data and determining weights over real numbers for a normalization function in less than a day. The first data indicates a measured amount of reference sequences for nucleic acids from training samples. The reference sequences include a target, for which an abundance is indicative of a condition of interest, and covariates not correlated with the condition of interest. The normalization function involves a sum of abundances of the covariates, as internal controls, each multiplied by a corresponding one of the weights. The weights are determined based on minimizing variance of a Taylor expansion of a ratio of a measured amount of the target divided by a value of the normalization function evaluated with measured amounts of the covariates over a portion of the first data in which the condition is absent.
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公开(公告)号：US10325675B2
公开(公告)日：2019-06-18
申请号：US15906404
申请日：2018-02-27
发明人： Deniz Kural
摘要： The invention provides methods for identifying rare variants near a structural variation in a genetic sequence, for example, in a nucleic acid sample taken from a subject. The invention additionally includes methods for aligning reads (e.g., nucleic acid reads) to a reference sequence construct accounting for the structural variation, methods for building a reference sequence construct accounting for the structural variation or the structural variation and the rare variant, and systems that use the alignment methods to identify rare variants. The method is scalable, and can be used to align millions of reads to a construct thousands of bases long, or longer.
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6.发明申请公开(公告)号：US20190180001A1
公开(公告)日：2019-06-13
申请号：US15834302
申请日：2017-12-07
发明人： Romeo Kienzler , Jenny Li , Stefan Mueck , Stefan Ravizza
摘要： A system and machine-implemented method for sorting Next-Generation Sequencing (NGS) reads in O(n) time and space complexity that makes use low sparsity and nearly uniform distribution of the input array. The genome position field in the input array is used to determine the target position of the output array. Duplicate target positions due to n-fold coverage are handled by assigning either overflow buckets to each position or anterior assigning multiple target slots in the output array for each genome position depending on the distribution of reads over the genome and the resulting probability of hitting an already occupied slot. Once every tuple in the input array has been written to the output array, the output array in read through ascending order and each tuple is appended to the end of a final result array.
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公开(公告)号：US10318706B2
公开(公告)日：2019-06-11
申请号：US15632895
申请日：2017-06-26
IPC分类号： C12Q1/6874 , G06F19/22
摘要： Disclosed herein are compositions, systems and methods related to sequence assembly, such as nucleic acid sequence assembly of single reads and contigs into larger contigs and scaffolds through the use of read pair sequence information, such as read pair information indicative of nucleic acid sequence phase or physical linkage.
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公开(公告)号：US10317392B2
公开(公告)日：2019-06-11
申请号：US15632190
申请日：2017-06-23
发明人： Morgan Mager , John Mannion
IPC分类号： G01N33/487 , C12Q1/6869 , C12Q1/6874 , G01N27/447 , G01N27/327 , G06F19/22 , B82Y5/00 , B82Y15/00 , G01N27/416
摘要： Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.
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公开(公告)号：US10309968B2
公开(公告)日：2019-06-04
申请号：US15599431
申请日：2017-05-18
发明人： Ngoc Hieu Tran , Mohammad Ziaur Rahman , Lin He , Lei Xin , Baozhen Shan , Ming Li
摘要： Methods and systems for determining amino acid sequence of a polypeptide or protein from mass spectrometry data is provided, using a weighted de Bruijn graph. Extracted and purified protein is cleaved into a mixture of peptide and then analyzed using mass spectrometry. A list of peptide sequences is derived from mass spectrometry fragment data by de novo sequencing, and amino acid confidence scores are determined from peak fragment ion intensity. A weighted de Bruijn graph is constructed for the list of peptide sequences having node weights defined by k−1 mer confidence scores. At least one contig is assembled from the de Bruijn graph by identifying node weights having the highest k−1 mer confidence scores.
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公开(公告)号：US10294518B2
公开(公告)日：2019-05-21
申请号：US15268349
申请日：2016-09-16
IPC分类号： G06F19/22 , C12Q1/6827
摘要： The invention discloses methods and apparatuses for the detection and diagnostics of genetic alterations/mutations in a target sample, which may be a solid tissue or a bodily fluid. A reference sample is also acquired, and the target and reference samples are replicated into multiple target and reference replicates. The replicates are sequenced, and the sequence data is analyzed based on a statistical test. The statistical test compares the measurements between the target and reference replicates at respective allelic indices. True positive calls are then made based on the results of the statistical testing, and the desired genetic alterations/mutations are identified at the base-pair level. The invention may be used for diagnostics related to cancer, auto-immune disease, organ transplant rejection, genetic fetal abnormalities and pathogens.
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