公开(公告)号：WO2011114207A2

公开(公告)日：2011-09-22

申请号：PCT/IB2011/000438

申请日：2011-02-28

Applicant: BLUEGNOME LIMITED ,  CRAIG, Andrew ,  BROWN, Anthony ,  HAAN, Nicholas

Inventor： CRAIG, Andrew ,  BROWN, Anthony ,  HAAN, Nicholas

IPC: C12Q1/68 ,  C12N15/11 ,  G01N33/58 ,  C40B40/06 ,  C40B70/00

CPC classification number: G06F19/20 ,  C12Q1/6827 ,  C12Q1/6837 ,  G06F19/18 ,  C12Q2537/16 ,  C12Q2539/115 ,  C12Q2565/515

Abstract: A method for determining the presence of a copy number imbalance in genomic DNA of a test sample is provided. The method can separately measure hybridization of a single test sample to a first hybridization array and hybridization of a plurality of reference samples to a plurality of other, respective test arrays. A determination of copy number can be based on the best fit reference array, relative to the test array. The best fit can be determined based on the closest or most similar signal-to-noise ratio of the measured signals.

Abstract translation: 提供了用于确定测试样品的基因组DNA中拷贝数不平衡的存在的方法。 该方法可以单独测量单个测试样品与第一杂交阵列的杂交和多个参考样品与多个其它相应测试阵列的杂交。 拷贝数的确定可以基于相对于测试数组的最佳拟合参考数组。 可以基于测量信号的最接近或最相似的信噪比来确定最佳拟合。

公开(公告)号：WO2011110751A1

公开(公告)日：2011-09-15

申请号：PCT/FI2011/050216

申请日：2011-03-11

Applicant: MEDISAPIENS OY ,  KILPINEN, Sami ,  OJALA, Kalle ,  AHOPELTO, Timo ,  PISTO, Tommi

Inventor： KILPINEN, Sami ,  OJALA, Kalle ,  AHOPELTO, Timo ,  PISTO, Tommi

IPC: G06F19/20 ,  G06F19/24 ,  C12Q1/68

CPC classification number: G06F17/30598 ,  C12Q1/6886 ,  G06F17/3053 ,  G06F19/18 ,  G06F19/20 ,  G06F19/24 ,  G06F19/28 ,  Y10S707/941

Abstract: An aspect of the present invention is a computer executable method for characterizing, e.g. for diagnostic purposes, utilizing a reference database, a query sample tissue based on the gene expression data of the tissue. The method is characterized in that it comprises the steps of calculating an expression match score (EM-score) indicating the likelihood of having the gene expression level observed in the query sample in each of the tissue categories of the reference database, calculating for the genes of the sample tissue, using e.g. the EM- score, tissue specificity score (TS-score), that expresses how uniquely a gene identifies the query sample as belonging to a certain tissue category, calculating, utilizing e.g. the TS- score, overall similarity of the sample tissue in relation to a tissue category of the reference database, and storing at least some resulting characterization data to a memory device or outputting the data to an output device of a computer. An arrangement and a computer program product are also disclosed.

Abstract translation: 本发明的一个方面是一种计算机可执行方法，用于表征例如 为了诊断目的，利用参考数据库，基于组织的基因表达数据的查询样本组织。 该方法的特征在于，其包括以下步骤：计算表达匹配得分（EM-评分），其指示在参考数据库的每个组织类别中的查询样本中观察到基因表达水平的可能性，计算基因 的样品组织，使用例如 表达基因如何将查询样本识别为属于某一组织类别的EM-分数，组织特异性评分（TS-评分），计算，使用例如 TS-分数，样本组织与参考数据库的组织类别相关的总体相似度，以及将至少一些所得到的表征数据存储到存储器装置或将数据输出到计算机的输出装置。 还公开了一种安排和计算机程序产品。

公开(公告)号：WO2011083312A1

公开(公告)日：2011-07-14

申请号：PCT/GB2011/000012

申请日：2011-01-07

Applicant: OXFORD GENE TECHNOLOGY (OPERATIONS) LTD ,  HURD, Douglas ,  SOUTHERN, Edwin ,  STARK, Richard

Inventor： HURD, Douglas ,  SOUTHERN, Edwin ,  STARK, Richard

IPC: C12Q1/68

CPC classification number: G06F19/20 ,  C12Q1/6837 ,  C12Q1/6883 ,  C12Q1/6886 ,  C12Q2600/156 ,  C12Q2600/172 ,  C12Q2525/151 ,  C12Q2535/131 ,  C12Q2537/16 ,  C12Q2539/115 ,  C12Q2565/513

Abstract: The invention combines the fields of comparative genomic hybridisation (CGH) analysis and SNP array analysis. It relates to methods for detecting and mapping genetic abnormalities associated with various diseases. In particular the invention provides a method for simultaneously performing array CGH and SNP array analysis on a genomic DNA sample comprising contacting a nucleic acid array which comprises a first probe set and a second probe set with a genomic DNA sample, comprising a test and reference sample, under hybridisation conditions, comparing the amount of test sample and reference sample hybridised to the hybridisation probes of the first probe set, comparing the amount of test sample and reference sample hybridised to the hybridisation probes of the second probe set; and using the data obtained to determine the copy number of at least one locus; and at least one SNP in the genomic DNA sample.

Abstract translation: 本发明结合了比较基因组杂交（CGH）分析和SNP阵列分析的领域。 它涉及检测和绘制与各种疾病相关的遗传异常的方法。 特别地，本发明提供了一种用于在基因组DNA样品上同时进行阵列CGH和SNP阵列分析的方法，包括使包含第一探针组和第二探针组的核酸阵列与基因组DNA样品接触，所述核酸阵列包含测试和参考样品 在杂交条件下，比较与第一探针组的杂交探针杂交的测试样品和参考样品的量，比较与第二探针组的杂交探针杂交的测试样品和参考样品的量; 并使用获得的数据来确定至少一个轨迹的拷贝数; 和基因组DNA样品中的至少一个SNP。

公开(公告)号：WO2011073741A1

公开(公告)日：2011-06-23

申请号：PCT/IB2009/056046

申请日：2009-12-18

Applicant: TRANSGENE SA ,  BAIN, Christine ,  GRELLIER, Benoît ,  MARIE BASTIEN, Bérangère ,  VERON, Laure ,  OLIVIER, Delphine

Inventor： BAIN, Christine ,  GRELLIER, Benoît ,  MARIE BASTIEN, Bérangère ,  VERON, Laure ,  OLIVIER, Delphine

IPC: G06F19/00

CPC classification number: G06F19/24 ,  G06F19/20 ,  G06F19/26

Abstract: A method for automatically processing multiple measurements of biological quantifiable parameters to obtain meaningful results comprises the steps of: (a) extracting a set of raw data including measurement values and annotations, said values comprising caliber-dependent values obtained under different caliber conditions and replicate values obtained under the same caliber condition; (b) from said raw data values and annotations and from related reliability range information, performing a correction process on said raw data including value correction and extended annotation generation reflecting abnormal values; (c) performing on each group of caliber-dependent values of the same measurement after correction a best caliber value selection taking into account said extended annotations, thereby retaining sets of replicate values of the same measurements at best calibers; d) performing a mean value determination process on each set of replicate values, said determination process including an abnormal replicate value exclusion process; and e) performing on said mean values a statistical and reporting process. The invention also provides a corresponding system.

Abstract translation: 一种用于自动处理生物可量化参数的多个测量以获得有意义的结果的方法包括以下步骤：（a）提取包括测量值和注释的一组原始数据，所述值包括在不同口径条件下获得的口径相关值和复制值 在相同口径条件下获得; （b）从所述原始数据值和注释以及相关的可靠性范围信息，对包括反映异常值的值校正和扩展注释生成的所述原始数据执行校正处理; （c）在校正之后对相同测量值的每个组的机械尺寸相关值执行考虑所述扩展注释的最佳口径值选择，从而在最佳口径处保留相同测量值的重复值集合; d）对每组复制值执行平均值确定过程，所述确定过程包括异常复制值排除过程; 以及e）对所述平均值执行统计和报告过程。 本发明还提供了相应的系统。

公开(公告)号：WO2011050340A1

公开(公告)日：2011-04-28

申请号：PCT/US2010/053873

申请日：2010-10-22

Applicant: LIFE TECHNOLOGIES CORPORATION ,  SIKORA, Marcin ,  BLANCHARD, Alan

Inventor： SIKORA, Marcin ,  BLANCHARD, Alan

IPC: C12Q1/68

CPC classification number: G06F19/20 ,  C12Q1/6869 ,  C12Q1/6874 ,  G06F19/10 ,  G06F19/22 ,  C12Q2565/102 ,  C12Q2521/501

Abstract: Disclosed are systems and methods for polynucleotide sequencing where detection and correction of base calling errors can be achieved without reliance on a reference sequence. In certain embodiments, redundant information, which may be provided by additional labels, can be introduced during measurement so as to allow such detection of errors. Such redundant information and measurements can be facilitated by encoding of nucleotide sequence being measured. Various examples of such encoding, redundancy introduction, and decoding are provided.

Abstract translation: 公开了用于多核苷酸测序的系统和方法，其中可以在不依赖参考序列的情况下实现基本呼叫错误的检测和校正。 在某些实施例中，可以在测量期间引入可由附加标签提供的冗余信息，以允许这种错误的检测。 可以通过编码被测量的核苷酸序列来促进这种冗余信息和测量。 提供了这种编码，冗余引入和解码的各种示例。

公开(公告)号：WO2006053328A8

公开(公告)日：2011-02-03

申请号：PCT/US2005041442

申请日：2005-11-14

Applicant: HEALTH DISCOVERY CORP ,  GUYON ISABELLE

Inventor： GUYON ISABELLE

IPC: G01N33/48

CPC classification number: G01N33/57434 ,  C12Q1/6886 ,  C12Q2600/112 ,  C12Q2600/158 ,  G01N2800/56 ,  G06F19/18 ,  G06F19/20 ,  G06F19/24

Abstract: Gene expression data are analyzed using learning machines such as support vector machines (SVM) and ridge regression classifiers to rank genes according to their ability to separate prostate cancer from BPH (benign prostatic hyperplasia) and to distinguish cancer volume. Other tests identify biomarker candidates for distinguishing between tumor (Grade 3 and Grade 4 (G3/4)) and normal tissue.

Abstract translation: 使用诸如支持向量机（SVM）和脊回归分类器之类的学习机器来分析基因表达数据，以根据将前列腺癌与BPH（良性前列腺增生）分离的能力来分类基因并区分癌细胞体积。 其他测试鉴定肿瘤（3级和4级（G3 / 4））和正常组织之间的生物标志物候选。

公开(公告)号：WO2010075009A3

公开(公告)日：2010-12-16

申请号：PCT/US2009067765

申请日：2009-12-11

Applicant: DODDS W JEAN ,  STEFANON BRUNO

Inventor： DODDS W JEAN ,  STEFANON BRUNO

IPC: C12Q1/68 ,  G06F19/00

CPC classification number: G01N33/6803 ,  G06F19/18 ,  G06F19/20

Abstract: An analysis of the profile of a non-human animal comprises: a) providing a genotypic database to the species of the non-human animal subject or a selected group of the species; b) obtaining animal data; c) correlating the database of a) with the data of b) to determine a relationship between the database of a) and the data of b); c) determining the profile of the animal based on the correlating step; and d) determining a genetic profile based on the molecular dietary signature, the molecular dietary signature being a variation of expression of a set of genes which may differ for the genotype of each animal or a group of animals Nutrition and pharmalogical assessments are made. Reporting the determination is by the Internet, and payment for the report is obtained through the Internet.

Abstract translation: 对非人类动物的概况的分析包括：a）为非人类动物对象的物种或选定的物种组提供基因型数据库; b）获得动物数据; c）将a）的数据库与b）的数据相关联以确定a）的数据库与b）的数据之间的关系; c）基于关联步骤确定动物的轮廓; 和d）基于分子饮食标记确定基因概况，分子饮食标记是一组基因的表达变化的变化，其可能对于每只动物或一组动物的基因型而言不同。进行营养和药理学评估。 报告决定是通过互联网进行的，报告的付款是通过互联网获得的。

公开(公告)号：WO2010138460A1

公开(公告)日：2010-12-02

申请号：PCT/US2010/035974

申请日：2010-05-24

Applicant: QUEST DIAGNOSTICS INVESTMENTS INCORPORATED ,  SANDERS, Heather R. ,  ALBITAR, Maher ,  MELONI-EHRIG, Aurelia

Inventor： SANDERS, Heather R. ,  ALBITAR, Maher ,  MELONI-EHRIG, Aurelia

IPC: C12Q1/68

CPC classification number: C12Q1/6886 ,  C12Q1/6809 ,  C12Q1/6827 ,  C12Q1/6851 ,  C12Q1/6858 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  G06F19/20 ,  C12Q2545/101 ,  C12Q2537/143

Abstract: Described herein are methods, compositions and kits directed to the detection of gene fusions and/or chromosomal abnormalities, e.g., translocations, insertions, inversions and deletions. Samples containing fusions or genetic abnormalities in a gene of interest may show independent expression patterns for the 5' and 3' regions of the gene. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5' portion of a target gene relative to the 3' region of the target gene.

Abstract translation: 本文描述了用于检测基因融合体和/或染色体异常的方法，组合物和试剂盒，例如易位，插入，逆转和缺失。 含有基因的融合物或遗传异常的样品可能显示基因的5'和3'区域的独立表达模式。 方法，组合物和试剂盒可用于检测导致靶基因相对于靶基因3'区的5'部分的差异表达的突变。

公开(公告)号：WO2010132813A2

公开(公告)日：2010-11-18

申请号：PCT/US2010034969

申请日：2010-05-14

Applicant: IDAHO TECHNOLOGY INC ,  UNIV UTAH RES FOUND ,  ROBBINS THOMAS CHARLES ,  PALAIS ROBERT ANDREW ,  WITTWER CARL THOMAS

Inventor： ROBBINS THOMAS CHARLES ,  PALAIS ROBERT ANDREW ,  WITTWER CARL THOMAS

IPC: G06F17/00 ,  G06F9/00

CPC classification number: G06F19/24 ,  C12Q1/6816 ,  G06F19/18 ,  G06F19/20 ,  C12Q2527/107 ,  C12Q2537/165 ,  C12Q2539/101

Abstract: An experimental melting curve is modeled as a sum of a true melting curve and background fluorescence. A deviation function may be generated based upon the experimental melting curve data and a model of a background signal. The deviation function may be generated by segmenting a range of the experimental curve into a plurality of windows. Within each window, a fit between the model of the background signal and the experimental melting curve data may be calculated. The deviation function may be formed from the resulting fit parameters. The deviation function may include background signal compensation and, as such, may be used in various melting curve analysis operations, such as data visualization, clustering, genotyping, scanning, negative sample removal, and the like. The deviation function may be used to seed an automated background correction process. A background-corrected melting curve may be further processed to remove an aggregation signal.

Abstract translation: 实验熔解曲线被建模为真正的熔解曲线和背景荧光的总和。 可以基于实验熔解曲线数据和背景信号的模型来生成偏差函数。 可以通过将实验曲线的范围分割成多个窗口来产生偏差函数。 在每个窗口内，可以计算背景信号的模型与实验解链曲线数据之间的拟合。 偏差函数可以由所得的拟合参数形成。 偏差函数可以包括背景信号补偿，并且因此可用于各种熔解曲线分析操作，例如数据可视化，聚类，基因分型，扫描，负样本去除等。 偏差函数可用于种子自动背景校正过程。 可以进一步处理背景校正的熔解曲线以除去聚集信号。

公开(公告)号：WO2010127338A1

公开(公告)日：2010-11-04

申请号：PCT/US2010/033359

申请日：2010-05-03

Applicant: NUVERA BIOSCIENCES, INC. ,  THE BOARD OF REGENTS OF THE UNIVERSITY OF TEXAS SYSTEM ,  SYMMANS, W., Fraser ,  HATZIS, Christos ,  PUSZTAI, Lajos

Inventor： SYMMANS, W., Fraser ,  HATZIS, Christos ,  PUSZTAI, Lajos

IPC: C12Q1/68

CPC classification number: C12Q1/6886 ,  C12Q2600/106 ,  C12Q2600/112 ,  C12Q2600/158 ,  G06F19/20

Abstract: The present invention provides the identification and combination of genes that are expressed in tumors that are responsive to a given therapeutic agent and whose combined expression can be used as an index that correlates with responsiveness to that therapeutic agent. One or more of the genes of the present invention may be used as markers (or surrogate markers) to identify tumors that are likely to be successfully treated by that agent or class of agents such as hormonal or endocrine therapy or chemotherapy.

Abstract translation: 本发明提供了在对给定治疗剂有反应的肿瘤中表达的基因的鉴定和组合，并且其组合表达可用作与对该治疗剂的反应性相关的指标。 本发明的一个或多个基因可用作标志物（或替代标记物），以鉴定可能由该试剂或类别的试剂例如激素或内分泌治疗或化学疗法成功治疗的肿瘤。