公开(公告)号：US08428882B2

公开(公告)日：2013-04-23

申请号：US11151591

申请日：2005-06-14

Applicant: Kuo Ping Chiu ,  Yijun Ruan ,  Chia Lin Wei

Inventor： Kuo Ping Chiu ,  Yijun Ruan ,  Chia Lin Wei

IPC: G01N33/50

CPC classification number: G06F19/28 ,  G06F19/22

Abstract: There is provided a method and system for processing and/or mapping ditag nucleotide sequence(s) to a genome, the ditag sequence comprising the 5′ terminal tag and the 3′ terminal tag of a nucleic acid molecule or fragment thereof or genomic fragment. The method of processing comprises preparing a database or file comprising at least one ditag sequence. The method of mapping comprises preparing a database or file of ditag(s), and mapping the ditag sequence(s) to the genome, comprising matching the 5′ and the 3′ terminal tags of the ditag sequence to at least a portion of the genome.

Abstract translation: 提供了用于处理和/或将基因组的核苷酸序列映射到基因组的方法和系统，包括核酸分子或其片段的5'末端标签和3'末端标签的基因组序列或基因组片段。 所述处理方法包括准备包含至少一个ditag序列的数据库或文件。 映射方法包括准备数据库或文件的一个或多个ditag序列，并将该ditag序列映射到基因组，包括将ditag序列的5'和3'末端标签与至少一部分 基因组

公开(公告)号：US08829172B2

公开(公告)日：2014-09-09

申请号：US13416764

申请日：2012-03-09

Applicant: Kuo Ping Chiu ,  Yi Chou ,  Sheng-Chung Chen

Inventor： Kuo Ping Chiu ,  Yi Chou ,  Sheng-Chung Chen

IPC: C07H21/00 ,  G01N33/487 ,  C12P19/34 ,  C12N15/66 ,  C12N15/65

CPC classification number: C12N15/66 ,  C12N15/65 ,  C12P19/34

Abstract: A method of generating a barcoded Paired-End Ditag (bPED) nucleic acid fragment is disclosed. The method comprises: a) performing a first ligation by ligating a half-adaptor with one or two 3′-overhanging ends to a target nucleic acid to obtain a nucleic acid fragment with two ends each attached to one of the half-adaptor, the half adaptor comprising a half-barcode and a restriction enzyme (RE) recognition site; b) performing a second ligation by ligating two of the half-adaptor at the two ends of the nucleic acid fragment to form a circularized nucleic acid construct, wherein the circularized nucleic acid construct comprises a full-size barcoded adaptor; and c) digesting the circularized nucleic acid construct with a RE that cleaves at a defined distance from the RE recognition site, and thereby generating the bPED nucleic acid fragment.

Abstract translation: 公开了一种产生条形码配对末端分析（bPED）核酸片段的方法。 该方法包括：a）通过将半适配子与一个或两个3'-突出末端连接至靶核酸来进行第一次连接，以获得核酸片段，其两端分别连接到半适配器之一， 半适配器，其包含半条形码和限制酶（RE）识别位点; b）通过在核酸片段的两端连接两个半连接体以形成环化的核酸构建体来进行第二次连接，其中所述环化的核酸构建体包含全尺寸条形码适配器; 和c）用在RE识别位点定义的距离处切割的RE消化环化的核酸构建体，从而产生bPED核酸片段。

公开(公告)号：US08481699B2

公开(公告)日：2013-07-09

申请号：US12610749

申请日：2009-11-02

Applicant: Kuo Ping Chiu

Inventor： Kuo Ping Chiu

IPC: C07H21/00 ,  G01N33/487

CPC classification number: C40B50/06 ,  C12N15/1093 ,  C12N15/66 ,  C40B40/06

Abstract: Multiplex barcoded Paired-End Ditag (mbPED) library construction for ultra high throughput sequencing is disclosed. The mbPED library comprises multiple types of barcoded Paired-End Ditag (bPED) nucleic acid fragment constructs, each of which comprises a unique barcoded adaptor, a first tag, and a second tag linked to the first tag via the barcoded adaptor. The two tags are the 5′- and 3′-ends of a nucleic acid molecule from which they originate. The barcoded adaptor comprises a barcode, a first polynucleotide sequence comprising a first restriction enzyme (RE) recognition site, and a second polynucleotide sequence comprising a second RE recognition site and covalently linked to the first polynucleotide sequence via the barcode. The two REs lead to cleavage of a nucleic acid at a defined distance from their recognition sites. The length of the adaptor is set so that the bPED nucleic acid fragment fits one-step sequencing.

Abstract translation: 公开了用于超高通量测序的多路复用条形码配对结束Ditag（mbPED）库构建。 mbPED库包含多种类型的条形码配对结束分析（bPED）核酸片段构建体，每个构建体包含独特的条形码适配器，第一标签和通过条形码适配器链接到第一标签的第二标签。 两个标签是来源于其的核酸分子的5'和3'末端。 条形适配器包括条形码，包含第一限制酶（RE）识别位点的第一多核苷酸序列和包含第二RE识别位点的第二多核苷酸序列，并经由条形码共价连接到第一多核苷酸序列。 两个RE导致在与其识别位点限定距离处的核酸裂解。 适配器的长度设定为使得bPED核酸片段适合一步测序。