公开(公告)号：US20110086772A1

公开(公告)日：2011-04-14

申请号：US12891623

申请日：2010-09-27

申请人： Lisa McDaniel ,  Blake Ballif ,  Roger Schultz ,  Brice Tebbs ,  Bassem Bejjani ,  Lisa Shaffer

发明人： Lisa McDaniel ,  Blake Ballif ,  Roger Schultz ,  Brice Tebbs ,  Bassem Bejjani ,  Lisa Shaffer

IPC分类号： C40B30/04 ,  C40B40/08

CPC分类号： C12Q1/6827 ,  C12Q2565/519 ,  C12Q2565/513 ,  C12Q2539/101

摘要： Multiplex (+/−) stranded analyses, such as array comparative genomic hybridization (aCGH), are provided for detecting chromosomal rearrangements associated with cancer and other diseases. For example, an illustrative multiplex array for CGH includes discrete plus (+) strand and minus (−) strand DNA probes, complementary to each other but separable on the CGH array. The minus (−) strand DNA probes recover diagnostic information lost to conventional microarrays, since many genes transcribe from the minus (−) strand. In an illustrative system, patient and control DNA samples are prepared for CGH by amplification and labeling using comprehensive primers that generate both plus (+) strands and minus (−) strands of DNA in the samples. The breakpoints of a translocated chromosome may be detected on a multiplex microarray by DNA probes of one polarity, while DNA copy number changes associated with the translocation region may be detected by corresponding DNA probes of the complementary polarity. Related methods for identifying translocation partner genes are also provided.

摘要翻译： 提供多重（+/-）链分析，如阵列比较基因组杂交（aCGH），用于检测与癌症和其他疾病相关的染色体重排。 例如，用于CGH的说明性多重阵列包括彼此互补但在CGH阵列上可分离的离散加（+）链和负（ - ）链DNA探针。 负（ - ）链DNA探针恢复常规微阵列损失的诊断信息，因为许多基因从负（ - ）链转录。 在说明性系统中，通过使用在样品中产生加（+）链和负（ - ）链DNA的综合引物进行扩增和标记来制备用于CGH的患者和对照DNA样品。 可以通过一个极性的DNA探针在多重微阵列上检测易位染色体的断点，而与易位区相关的DNA拷贝数变化可以通过互补极性的相应DNA探针检测。 还提供了用于鉴定易位配偶体基因的相关方法。

公开(公告)号：US20050181410A1

公开(公告)日：2005-08-18

申请号：US11057088

申请日：2005-02-11

申请人： Lisa Shaffer ,  Bassem Bejjani

发明人： Lisa Shaffer ,  Bassem Bejjani

IPC分类号： C12Q1/68 ,  G01N33/48 ,  G01N33/50 ,  G06F19/00

CPC分类号： C12Q1/6837 ,  C12Q2565/513

摘要： Methods and apparatuses for selecting and arranging clinically relevant chromosomal loci allow an exemplary diagnostic array to simultaneously test for numerous genetic alterations that occur in many different parts of the human genome. Clinically irrelevant or ineffective loci are eliminated. One implementation increases reliability and accuracy by dividing the base-pair sequence of each chromosomal locus into segments and then assigning nucleic acid clones for comparative genomic hybridization to each different segment. The segments may overlap for increased resolution and control. Clones representing segments that are adjacent on a native chromosome are placed in non-adjacent target areas of the array to avoid interfering hybridization reactions. Arrangement motifs within an array may be redundantly repeated for high availability and increased reliability and accuracy of results. Techniques, hardware, software, logic engines, loci collections, and diagnostic arrays are described.

摘要翻译： 用于选择和安排临床相关染色体基因座的方法和装置允许示例性诊断阵列同时测试发生在人类基因组的许多不同部分中的许多遗传改变。 临床无关或无效的位点被消除。 一个实现通过将每个染色体基因座的碱基对序列划分成片段，然后为每个不同的片段分配用于比较基因组杂交的核酸克隆来增加可靠性和准确性。 这些段可以重叠以提高分辨率和控制。 表示在天然染色体上相邻的片段的克隆位于阵列的不相邻靶区域，以避免干扰杂交反应。 可以冗余重复阵列中的排列图案以实现高可用性，并提高结果的可靠性和准确性。 描述了技术，硬件，软件，逻辑引擎，基因座集合和诊断阵列。

公开(公告)号：US20050202441A1

公开(公告)日：2005-09-15

申请号：US10731419

申请日：2003-12-09

申请人： Bassem Bejjani ,  Todd Christensen

发明人： Bassem Bejjani ,  Todd Christensen

IPC分类号： C07H21/04 ,  C12N20060101 ,  C12P19/34 ,  C12Q1/68

CPC分类号： C12P19/34

摘要： Subject matter includes design, synthesis, and propagation of synthetic and semi-synthetic reference nucleic acids and mixtures of reference nucleic acids for use in genetic tests, such as molecular screening, mutation testing, carrier testing, and diagnostic assays. In one implementation, methods are described for design, synthesis, and propagation of reference nucleic acid mixtures and a system is presented for using the mixtures.

摘要翻译： 主题包括用于遗传测试的合成和半合成参考核酸和参考核酸混合物的设计，合成和扩增，例如分子筛选，突变测试，载体测试和诊断测定。 在一个实施方案中，描述了参考核酸混合物的设计，合成和扩增的方法，并且提出了使用该混合物的体系。