公开(公告)号：WO2021127184A1

公开(公告)日：2021-06-24

申请号：PCT/US2020/065617

申请日：2020-12-17

Applicant: THE JOHNS HOPKINS UNIVERSITY ,  VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  HSIUE, Emily Han-Chung ,  DOUGLASS, Jacqueline ,  HWANG, Michael S. ,  PEARLMAN, Alexander ,  PAPADOPOULOS, Nickolas ,  ZHOU, Shibin ,  MOG, Brian ,  WRIGHT, Katharine M. ,  GABELLI, Sandra B.

Inventor： VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  HSIUE, Emily Han-Chung ,  DOUGLASS, Jacqueline ,  HWANG, Michael S. ,  PEARLMAN, Alexander ,  PAPADOPOULOS, Nickolas ,  ZHOU, Shibin ,  MOG, Brian ,  WRIGHT, Katharine M. ,  GABELLI, Sandra B.

IPC: C07K14/82 ,  C07K16/32 ,  A61K39/395 ,  A61P35/00

Abstract: This document provides methods and materials for assessing a mammal having or suspected of having cancer and/or for treating a mammal having cancer. For example, molecules including one or more antigen-binding domains (e.g., a single-chain variable fragment (scFv)) that can bind to a modified peptide (e.g., a tumor antigen), as well as method for using such molecules, are provided.

公开(公告)号：WO2021163546A1

公开(公告)日：2021-08-19

申请号：PCT/US2021/017937

申请日：2021-02-12

Applicant: THE JOHNS HOPKINS UNIVERSITY ,  PAPADOPOULOS, Nickolas ,  KINZLER, Kenneth W. ,  VOGELSTEIN, Bert ,  COHEN, Joshua David

Inventor： PAPADOPOULOS, Nickolas ,  KINZLER, Kenneth W. ,  VOGELSTEIN, Bert ,  COHEN, Joshua David

IPC: C12Q1/686

Abstract: Provided herein are systems, kits, compositions and methods for sequencing library preparation and sequencing workflow (e.g., for the identification of mutations). In certain embodiments, provides herein systems and methods to identically barcode both strands of templates, and PCR-based enrichment of each strand that does not require hybridization capture.

公开(公告)号：WO2012142213A2

公开(公告)日：2012-10-18

申请号：PCT/US2012/033207

申请日：2012-04-12

Applicant: THE JOHNS HOPKINS UNIVERSITY ,  VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  PAPADOPOULOS, Nickolas ,  KINDE, Isaac

Inventor： VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  PAPADOPOULOS, Nickolas ,  KINDE, Isaac

IPC: C12Q1/68 ,  C12N15/11

CPC classification number: C12Q1/6874 ,  C12Q1/6806 ,  C12Q1/6869 ,  C12Q1/6876 ,  C12Q2563/179 ,  C12Q2600/158 ,  C12Q2535/122 ,  C12Q2565/514

Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called "Safe-SeqS" for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant ("super-mutants") if ≥95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro , and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.

Abstract translation: 存在于DNA模板的一小部分中的突变的鉴定对于在几个生物医学研究领域的进展是必不可少的。 尽管大规模并行测序仪器原则上非常适合于此任务，但是这些仪器中的错误率通常太高，无法确定罕见的变体。 我们在这里描述了一种可以显着增加大规模并行测序仪器对此目的的灵敏度的方法。 这种方法的一个例子是（Safe-Sequencing System），称为“Safe-SeqS”，包括（i）将唯一标识符（UID）分配给每个模板分子; （ii）每个唯一标记的模板分子的扩增以产生UID家族; 和（iii）扩增产物的冗余测序。 具有相同UID的PCR片段是真正的突变体（“超突变体”），如果其中95％含有相同的突变。 我们说明了这种方法用于确定聚合酶的保真度，体外合成的寡核苷酸的准确性以及正常细胞的核和线粒体基因组中突变的流行率的效用。

公开(公告)号：WO2012071096A2

公开(公告)日：2012-05-31

申请号：PCT/US2011/050487

申请日：2011-09-06

Applicant: THE JOHNS HOPKINS UNIVERSITY ,  VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  VELCULESCU, Victor ,  PAPADOPOULOS, Nickolas ,  JONES, Sian

Inventor： VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  VELCULESCU, Victor ,  PAPADOPOULOS, Nickolas ,  JONES, Sian

IPC: C12Q1/68 ,  C12N5/09 ,  G01N33/68 ,  A61K31/7088 ,  C12N15/11

CPC classification number: C12Q1/6886 ,  A61K31/7088 ,  A61K31/711 ,  C12Q2600/156 ,  G01N33/5011

Abstract: Two genes, ARID1A (AT-rich interactive domain-containing protein 1A) and PPP2R1A (protein-phosphatase 2, regulatory subunit 1, alpha), can be used in methods which are useful for detecting cancer, diagnosing cancer, contributing to a diagnosis of cancer, confirming a diagnosis of cancer, identifying appropriate treatments for cancer, monitoring treatment of cancer, and evaluating treatment protocols for cancer, including ovarian clear cell carcinoma, breast cancer, colon cancer, gastric cancer, lung cancer, medulloblastoma, pancreatic cancer, and prostate cancer.

Abstract translation: 在可用于检测癌症的方法中可以使用两种基因，即ARID1A（富含AT的交互结构域的蛋白质1A）和PPP2R1A（蛋白质磷酸酶2，调节亚基1，α） 诊断癌症，有助于诊断癌症，确认癌症的诊断，鉴别癌症的适当治疗，监测癌症的治疗，以及评估癌症的治疗方案，包括卵巢透明细胞癌，乳腺癌，结肠癌，胃癌，肺癌 癌症，成神经管细胞瘤，胰腺癌和前列腺癌。

公开(公告)号：WO2010028098A3

公开(公告)日：2010-06-10

申请号：PCT/US2009055802

申请日：2009-09-03

Applicant: UNIV JOHNS HOPKINS ,  VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PARSONS D WILLIAMS ,  JONES SIAN ,  ZHANG XIAOSONG ,  LIN JIMMY CHANG-HO ,  LEARY REBECCA J ,  ANGENENDT PHILIPP ,  PAPADOPOULOS NICKOLAS ,  VELCULESCU VICTOR ,  PARMIGIANI GIOVANNI ,  KARCHIN RACHEL ,  KERN SCOTT ,  HRUBAN RALPH ,  ESHLEMAN JAMES R ,  GOGGINS MICHAEL ,  KLEIN ALISON

Inventor： VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PARSONS D WILLIAMS ,  JONES SIAN ,  ZHANG XIAOSONG ,  LIN JIMMY CHANG-HO ,  LEARY REBECCA J ,  ANGENENDT PHILIPP ,  PAPADOPOULOS NICKOLAS ,  VELCULESCU VICTOR ,  PARMIGIANI GIOVANNI ,  KARCHIN RACHEL ,  KERN SCOTT ,  HRUBAN RALPH ,  ESHLEMAN JAMES R ,  GOGGINS MICHAEL ,  KLEIN ALISON

IPC: C12Q1/68

CPC classification number: G01N33/57438 ,  C12Q1/6886 ,  C12Q2600/156 ,  G01N2800/50

Abstract: This invention relates to new insights into the pathogenesis of pancreatic cancers by analyzing the genes altered in 24 pancreatic tumors. First, we determined the sequences of 23,781 transcripts, representing 20,583 protein-encoding genes, in DNA from these tumors. Second, we searched for homozygous deletions and amplifications using microarrays querying one million single nucleotide polymorphisms in each sample. Third, we analyzed the transcriptomes of the same samples using SAGE and next-generation sequencing-by-synthesis technologies We found that pancreatic cancers contain an average of 63 genetic alterations, of which 49 are point mutations, 8 are homozygous deletions, and 6 are amplifications. Further analyses revealed a core set of 12 regulatory processes or pathways that were each genetically altered in 70 % to 100 % of the samples. The data suggest that dysregulation of this core set of pathways is responsible for the major features of pancreatic tumorigenesis.

Abstract translation: 本发明涉及通过分析24个胰腺肿瘤中改变的基因对胰腺癌发病机理的新见解。 首先，我们从这些肿瘤的DNA中确定了23,781个转录本，代表20,583个蛋白质编码基因的序列。 其次，我们使用微阵列查询了每个样本中一百万个单核苷酸多态性的纯合缺失和扩增。 第三，我们使用SAGE和下一代合成技术分析相同样品的转录组我们发现胰腺癌平均含有63个遗传改变，其中49个是点突变，8个是纯合缺失，6个是 扩增。 进一步的分析揭示了一组核心的12个调节过程或途径，在70％至100％的样品中进行了遗传改变。 数据表明，这种核心途径的失调导致了胰腺肿瘤发生的主要特征。

公开(公告)号：WO2013003585A3

公开(公告)日：2013-03-28

申请号：PCT/US2012044634

申请日：2012-06-28

Applicant: UNIV JOHNS HOPKINS ,  VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS ,  WU JIAN

Inventor： VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS ,  WU JIAN

IPC: C12Q1/68 ,  C12N15/11

CPC classification number: C12Q1/6806 ,  C12Q2535/122 ,  C12Q2563/131 ,  C12Q2563/149 ,  C12Q2565/518

Abstract: Assays can be used to detect mutations found in neoplasms of the pancreas, as well as for other neoplasms and other uses. Nucleic acids can be captured from body fluids such as cyst fluids. Thousands of oligonucleotides can be synthesized in parallel, amplified and ligated together. The ligated products can be further amplified. The amplified, ligated products are used to capture complementary DNA sequences, which can be analyzed, for example by massively parallel sequencing.

Abstract translation: 分析可用于检测胰腺肿瘤中发现的突变，以及其他肿瘤和其他用途。 核酸可以从体液如囊肿液中捕获。 数千个寡核苷酸可以平行合成，扩增并连接在一起。 连接产物可以进一步扩增。 扩增的连接产物用于捕获互补DNA序列，其可以通过例如大规模平行测序进行分析。

公开(公告)号：WO2012099881A2

公开(公告)日：2012-07-26

申请号：PCT/US2012021553

申请日：2012-01-17

Applicant: UNIV JOHNS HOPKINS ,  VOGELSTEIN BERT ,  WANG QING ,  PANDEY AKHILESH ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS

Inventor： VOGELSTEIN BERT ,  WANG QING ,  PANDEY AKHILESH ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS

IPC: G01N33/68 ,  G01N33/551 ,  G01N33/574

CPC classification number: G01N33/6893 ,  G01N33/574 ,  G01N33/6848

Abstract: Altered protein products resulting from somatic mutations are directly identified and quantified by mass spectrometry. The peptides expressed from normal and mutant alleles are detected by Selected Reaction Monitoring (SRM) of their product ions using a triple quadrupole mass spectrometer. As a prototypical example of this approach, we quantify the number and fraction of mutant Ras protein present in cancer cell lines. There were an average of 1.3 million molecules of Ras protein per cell and the ratio of mutant to normal Ras proteins ranged from 0.49 to 5.6. Similarly, we detected and quantified mutant Ras proteins in clinical specimens such as colorectal and pancreatic tumor tissues as well as in pre-malignant pancreatic cyst fluids. These methods are useful for diagnostic applications.

Abstract translation: 通过质谱法直接鉴定和定量由体细胞突变产生的改变的蛋白质产物。 使用三重四极质谱仪通过其产物离子的选择性反应监测（SRM）来检测从正常和突变等位基因表达的肽。 作为这种方法的原型实例，我们量化了存在于癌细胞系中的突变型Ras蛋白的数量和分数。 每个细胞平均有130万个Ras蛋白分子，突变体与正常Ras蛋白的比例范围为0.49至5.6。 同样，我们在临床标本如结直肠癌和胰腺肿瘤组织以及恶变前胰腺囊液中检测并定量了突变型Ras蛋白。 这些方法对诊断应用程序很有用。

公开(公告)号：WO2012064721A2

公开(公告)日：2012-05-18

申请号：PCT/US2011059751

申请日：2011-11-08

Applicant: UNIV JOHNS HOPKINS ,  UNIV DUKE ,  VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS ,  PARSONS DONALD WILLIAMS ,  LEARY REBECCA J ,  LI MENG ,  ZHANG XIAOSONG ,  JONES SIAN ,  RIGGINS GREGORY J ,  VELCULESCU VICTOR ,  BIGNER DARELL ,  YAN HAI

Inventor： VOGELSTEIN BERT ,  KINZLER KENNETH W ,  PAPADOPOULOS NICKOLAS ,  PARSONS DONALD WILLIAMS ,  LEARY REBECCA J ,  LI MENG ,  ZHANG XIAOSONG ,  JONES SIAN ,  RIGGINS GREGORY J ,  VELCULESCU VICTOR ,  BIGNER DARELL ,  YAN HAI

IPC: G01N33/574 ,  C12Q1/68 ,  G01N33/50

CPC classification number: C12Q1/6886 ,  C12Q2600/112 ,  C12Q2600/156 ,  G01N33/57407

Abstract: Medulloblastoma (MB) is the most common malignant brain tumor of children. To identify the genetic alterations in this tumor type, we searched for copy number alterations using high density microarrays and sequenced all known protein-coding genes and miRNA genes using Sanger sequencing. We found that, on average, each tumor had 11 gene alterations, markedly fewer than in common adult cancers. In addition to alterations in the Hedgehog and Wnt pathways, our analysis led to the discovery of genes not previously known to be altered in MBs. Most notably, inactivating mutations of the histone H3K4 trimethylase genes MLL2 or MLL3 were identified in 16% of MB patients. These results demonstrate key differences between the genetic landscapes of adult and childhood cancers, highlight dysregulation of developmental pathways as an important mechanism underlying MBs, and identify a role for a specific type of histone methylation in human tumorigenesis.

Abstract translation: 髓母细胞瘤（MB）是儿童最常见的恶性脑肿瘤。 为了鉴定这种肿瘤类型的遗传改变，我们使用高密度微阵列搜索拷贝数改变，并使用Sanger测序对所有已知的蛋白质编码基因和miRNA基因进行测序。 我们发现平均而言，每个肿瘤有11个基因改变，明显少于常见的成人癌症。 除了Hedgehog和Wnt途径的改变之外，我们的分析还导致发现以前不知道在MB中改变的基因。 最值得注意的是，在16％的MB患者中鉴定出组蛋白H3K4三甲基化酶基因MLL2或MLL3的失活突变。 这些结果表明成人和儿童癌症的遗传景观之间的主要区别，突出发展途径的失调作为潜在的MB的重要机制，并确定在人类肿瘤特定类型的组蛋白甲基化的作用。

公开(公告)号：WO2010118016A2

公开(公告)日：2010-10-14

申请号：PCT/US2010/030084

申请日：2010-04-06

Applicant: THE JOHNS HOPKINS UNIVERSITY ,  CASE WESTERN RESERVE UNIVERSITY ,  VOGELSTEIN, Bert ,  KINZLER, Kenneth, W. ,  LI, Meng ,  DIAZ, Luis ,  PAPADOPOULOS, Nickolas ,  MARKOWITZ, Sanford

Inventor： VOGELSTEIN, Bert ,  KINZLER, Kenneth, W. ,  LI, Meng ,  DIAZ, Luis ,  PAPADOPOULOS, Nickolas ,  MARKOWITZ, Sanford

IPC: C12Q1/68 ,  C12N15/11 ,  G01N33/52

CPC classification number: C12Q1/6816 ,  C12Q1/6886 ,  C12Q2600/154 ,  C12Q2565/501 ,  C12Q2527/125 ,  C12Q2523/125

Abstract: Abnormal DNA methylation can be used as a biomarker in cancer patients. For such purposes, it is important to determine precisely the fraction of methylated molecules in an analyzed sample. A technology we term Methyl-BEAMing achieves this goal. Individual bisulfite-treated DNA molecules can be PCR-amplified within aqueous nanocompartments containing beads, resulting in a population of beads each containing thousands of copies of the template molecule. After hybridization with probes specific for methylated sequences, the beads can be analyzed by flow cytometry. This approach enables detection and enumeration of one methylated molecule in a population of ~5000 unmethylated molecules. Methyl-BEAMing provides digital quantification of rare methylation events and is generally applicable to the assessment of methylated genes in clinical samples.

Abstract translation: DNA甲基化异常可用作癌症患者的生物标志物。 为此目的，重要的是精确测定分析样品中甲基化分子的分数。 我们称之为甲基BEAMing的技术实现了这一目标。 单独的亚硫酸氢盐处理的DNA分子可以在含有珠粒的含水纳米间隔内进行PCR扩增，导致每个珠粒群含有数千份拷贝的模板分子。 与特异于甲基化序列的探针杂交后，可以通过流式细胞术分析珠粒。 这种方法能够检测和计数一个约5000个非甲基化分子的一个甲基化分子。 甲基BEAMing提供罕见甲基化事件的数字量化，通常适用于临床样品中甲基化基因的评估。

公开(公告)号：WO2010065576A3

公开(公告)日：2010-06-10

申请号：PCT/US2009/066313

申请日：2009-12-02

Applicant: THE JOHNS HOPKINS UNIVERSITY ,  VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  HE, Yiping ,  VELCULESCU, Victor ,  PAPADOPOULOS, Nickolas

Inventor： VOGELSTEIN, Bert ,  KINZLER, Kenneth W. ,  HE, Yiping ,  VELCULESCU, Victor ,  PAPADOPOULOS, Nickolas

IPC: C12N15/11 ,  C12Q1/68 ,  G06F19/00

Abstract: Transcription in mammalian cells can be assessed at a genome-wide level, but it has been difficult to reliably determine whether individual transcripts are derived from the Plus- or Minus-strands of chromosomes. This distinction can be critical for understanding the relationship between known transcripts (sense) and the complementary antisense transcripts that may regulate them. Here we describe a technique that can be used to (i) identify the DNA strand of origin for any particular RNA transcript and (ii) quantify the number of sense and antisense transcripts from expressed genes at a global level. We examined five different human cell types and in each case found evidence for antisense transcripts in 2900 to 6400 human genes. The distribution of antisense transcripts was distinct from that of sense transcripts, was non-random across the genome, and differed among cell types. Antisense transcripts thus appear to be a pervasive feature of human cells, suggesting that they are a fundamental component of gene regulation.