公开(公告)号：US20060292611A1

公开(公告)日：2006-12-28

申请号：US11448462

申请日：2006-06-06

申请人： Jan Berka ,  Zhoutao Chen ,  Michael Egholm ,  Brian Godwin ,  Stephen Hutchison ,  John Leamon ,  Gary Sarkis ,  Jan Simons

发明人： Jan Berka ,  Zhoutao Chen ,  Michael Egholm ,  Brian Godwin ,  Stephen Hutchison ,  John Leamon ,  Gary Sarkis ,  Jan Simons

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6806 ,  C12N15/10 ,  C12N15/1093 ,  C12Q1/6809 ,  C12Q1/6869 ,  C12Q2537/155 ,  C12Q2525/191 ,  C12Q2521/301 ,  C12Q2533/107 ,  C12Q2531/125 ,  C12Q2521/319 ,  C12Q2521/125 ,  C12Q2565/518 ,  C12Q2563/131

摘要： The present invention provides for a method of preparing a target nucleic acid fragments to produce a smaller nucleic acid which comprises the two ends of the target nucleic acid. Specifically, the invention provides cloning and DNA manipulation strategies to isolate the two ends of a large target nucleic acid into a single small DNA construct for rapid cloning, sequencing, or amplification.

公开(公告)号：US20060228721A1

公开(公告)日：2006-10-12

申请号：US11104781

申请日：2005-04-12

申请人： John Leamon ,  William Lee ,  Jan Simons ,  Brian Desany ,  Michael Ronan ,  James Drake ,  Kenton Lohman ,  Michael Egholm ,  Jonathan Rothberg

发明人： John Leamon ,  William Lee ,  Jan Simons ,  Brian Desany ,  Michael Ronan ,  James Drake ,  Kenton Lohman ,  Michael Egholm ,  Jonathan Rothberg

IPC分类号： C12Q1/68 ,  C12P19/34

CPC分类号： C12Q1/6827 ,  C12Q1/6834 ,  C12Q1/6858 ,  C12Q2565/301 ,  C12Q2531/107 ,  C12Q2531/101 ,  C12Q2565/537 ,  C12Q2565/515 ,  C12Q2545/114

摘要： The claimed invention provides for new sample preparation methods enabling direct sequencing of PCR products using pyrophosphate sequencing techniques. The PCR products may be specific regions of a genome. The techniques provided in this disclosure allows for SNP (single nucleotide polymorphism) detection, classification, and assessment of individual allelic polymorphisms in one individual or a population of individuals. The results may be used for diagnostic and treatment of patients as well as assessment of viral and bacterial population identification.

摘要翻译： 所要求保护的发明提供了使用焦磷酸测序技术直接测序PCR产物的新的样品制备方法。 PCR产物可以是基因组的特定区域。 本公开中提供的技术允许在一个个体或个体群体中的单个等位基因多态性的SNP（单核苷酸多态性）检测，分类和评估。 结果可用于患者的诊断和治疗以及病毒和细菌群体鉴定的评估。

公开(公告)号：US20070117121A1

公开(公告)日：2007-05-24

申请号：US11523120

申请日：2006-09-18

申请人： Stephen Hutchison ,  Jan Simons ,  David Willoughby

发明人： Stephen Hutchison ,  Jan Simons ,  David Willoughby

IPC分类号： C40B30/06 ,  C40B40/08

CPC分类号： C12N15/1096

摘要： New biochemical protocols for high throughput processing of mRNA samples into cDNA libraries with adaptor sequences compatible with automated sequencing systems are provided. The provided methods produces cDNA libraries which do not have 3′ bias associated with current cDNA library production methods. New methods for the production of DNA libraries from DNA are also provided.

摘要翻译： 提供了用于将mRNA样品高通量处理的新的生物化学方案转化为具有与自动测序系统相容的衔接子序列的cDNA文库。 所提供的方法产生不具有与当前cDNA文库生产方法相关的3'偏差的cDNA文库。 还提供了用于从DNA生产DNA文库的新方法。

公开(公告)号：US20070178452A1

公开(公告)日：2007-08-02

申请号：US10277951

申请日：2002-10-21

申请人： Pascal Bouffard ,  John Herrmann ,  Chunli Huang ,  Michael Jeffers ,  Jingfang Ju ,  Luca Rastelli ,  Juliette Shimkets ,  Jan Simons ,  Bruce Taillon

发明人： Pascal Bouffard ,  John Herrmann ,  Chunli Huang ,  Michael Jeffers ,  Jingfang Ju ,  Luca Rastelli ,  Juliette Shimkets ,  Jan Simons ,  Bruce Taillon

IPC分类号： C12Q1/68 ,  G06F19/00

CPC分类号： C12N15/1096 ,  C12Q2600/158 ,  G16B30/00

摘要： Disclosed is a method in which DNA sequences derived from microsome-associated mRNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification. Another embodiment of the invention uses information on the presence or absence of carefully chosen target subsequences in a single sequence clone together with DNA sequence databases to determine the clone sequence. Computer implemented methods are provided to analyze the experimental results and to determine the sample sequences in question and to carefully choose target subsequences in order that experiments yield a maximum amount of information

摘要翻译： 公开了可以确定和分类来自混合样品或排列单序列克隆中的微粒体相关mRNA序列的DNA序列而不进行测序的方法。 这些方法利用关于精确选择的目标子序列的存在的信息，通常长度为4至8个碱基对，优选样品DNA序列中目标子序列之间的长度以及含有可能存在的序列的DNA序列数据库 在样品中确定样品序列。 优选的方法是使用限制性核酸内切酶识别目标子序列并切割样品序列。 然后仔细选择识别部分连接到切割片段，扩增片段，并进行实验观察。 聚合酶链反应（PCR）是优选的扩增方法。 本发明的另一个实施方案使用关于在单个序列克隆中与DNA序列数据库一起存在或不存在仔细选择的目标子序列的信息来确定克隆序列。 提供计算机实现的方法来分析实验结果并确定所讨论的样本序列，并仔细选择目标子序列，以便实验产生最大量的信息