公开(公告)号：US20180276338A1

公开(公告)日：2018-09-27

申请号：US15928202

申请日：2018-03-22

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Paolo Vatta ,  Onur Sakarya ,  Heinz Breu ,  Liviu Popescu ,  Asim Siddiqui ,  Fiona Hyland

IPC: G06F19/22

CPC classification number: G16B30/00

Abstract: Systems and methods are used to identify an exon junction from a single read of a transcript. A transcript sample is interrogated and a read sequence is produced using a nucleic acid sequencer. A first exon sequence and a second exon sequence are obtained using the processor. The first exon sequence is mapped to a prefix of the read sequence using the processor. The second exon sequence is mapped to a suffix of the read sequence using the processor. A sum of a number of sequence elements of the first exon sequence that overlap the prefix of the read sequence, of a number of sequence elements of the second exon sequence that overlap the suffix of the read sequence, and of a constant is calculated using the processor. If the sum equals a length of the read sequence, a junction is identified in the read using the processor.

公开(公告)号：US09546405B2

公开(公告)日：2017-01-17

申请号：US14309865

申请日：2014-06-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Olga Petrauskene ,  Craig Cummings ,  Paolo Vatta ,  Robert Tebbs ,  Priya Balachandran ,  Patrick Zoder ,  Lily Wong

IPC: C12Q1/68

CPC classification number: C12Q1/689 ,  C12Q2600/156 ,  C12Q2600/16

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract translation: 本公开的实施方案涉及分离的核酸序列，其使用方法和用于检测样品中的几种利斯特氏菌物种的工作流程，特别是在食品或环境样品中。 本公开的实施方案还可以用于彼此检测李斯特氏菌的一种或多种物种或菌株，例如，可以独立于其他李斯特菌属物种检测L.crilli。 一些实施方案还描述了可以检测单核细胞增生李斯特氏菌（L. innocua），威尔逊氏乳杆菌（L.welshimeri），塞贝尔氏球菌（L.ceelgeri），马氏，（L.marthii）（以前称为incertae-sedis），伊卡诺菌（L. ivanovii）和L. 还描述了用于检测李斯特菌的试剂盒。 在一些实施方案中，本公开的方法和试剂盒可以包括TAQMAN测定。 在一些实施方案中，0.2-2cfu的李斯特菌属 在24-28小时浓缩期后使用组合物，方法和试剂盒检测。

公开(公告)号：US20220284986A1

公开(公告)日：2022-09-08

申请号：US17699439

申请日：2022-03-21

Applicant: Life Technologies Corporation

Inventor： Paolo Vatta ,  Onur Sakarya ,  Heinz Breu ,  Liviu Popescu ,  Asim Siddiqui ,  Fiona Hyland

IPC: G16B30/10 ,  G16B30/00

Abstract: Identification of exon junctions includes obtaining a first read sequence based on a detected plurality of signals of a first sequence. A list of exon prefix and suffix sequences are generated by identifying exons of the human genome with a prefix sequence mapping to a suffix sequence of the first read sequence and by identifying exons with a suffix sequence mapping to a prefix sequence of the first read sequence. A pair of exon sequences is selected, with a first exon sequence being one of the exon suffix sequences and a second exon sequence being one of the exon prefix sequences. Summing a number of sequence elements of the first exon sequence that overlap the prefix of the first read sequence, a number of sequence elements of the second exon sequence that overlap the suffix of the first read sequence, and a constant is used to identify a fusion junction.

公开(公告)号：US20150045242A1

公开(公告)日：2015-02-12

申请号：US14309865

申请日：2014-06-19

Applicant: LIFE TECHNOLOGIES CORPORATION

Inventor： Olga PETRAUSKENE ,  Craig Cummings ,  Paolo Vatta ,  Robert Tebbs ,  Priya Balachandran ,  Patrick Zoder ,  Lily Wong

IPC: C12Q1/68

CPC classification number: C12Q1/689 ,  C12Q2600/156 ,  C12Q2600/16

Abstract: Embodiments of the disclosure relate to isolated nucleic acid sequences, methods of use thereof, and workflows for detection of several Listeria species in a sample, particularly in a food or environmental sample. Embodiments of the disclosure may also be used to detect one or more species or strains of Listeria from each other, for example L. grayi may be detected independently of other Listeria spp. Some embodiments also describe a duplexed assay that can detect L. monocytogenes, L. innocua, L. welshimeri, L. seelgeri, L. marthii (formerly incertae-sedis), L. ivanovii, and L. grayi. Kits for detection of Listeria are also described. In some embodiments, methods and kits of the disclosure may comprise a TAQMAN® assay. In some embodiments, 0.2-2 cfu of Listeria spp. are detected using the compositions, methods and kits after a 24-28 hour enrichment period.

Abstract translation: 本公开的实施方案涉及分离的核酸序列，其使用方法和用于检测样品中的几种利斯特氏菌物种的工作流程，特别是在食品或环境样品中。 本公开的实施方案还可以用于彼此检测李斯特氏菌的一种或多种物种或菌株，例如，可以独立于其他李斯特菌属物种检测L.crilli。 一些实施方案还描述了可以检测单核细胞增生李斯特氏菌（L. innocua），威尔逊氏乳杆菌（L.welshimeri），塞贝尔氏球菌（L.ceelgeri），马氏，（L.marthii）（以前称为incertae-sedis），伊卡诺菌（L. ivanovii）和L. 还描述了用于检测李斯特菌的试剂盒。 在一些实施方案中，本公开的方法和试剂盒可以包括TAQMAN测定。 在一些实施方案中，0.2-2cfu的李斯特菌属 在24-28小时浓缩期后使用组合物，方法和试剂盒检测。

公开(公告)号：US08906628B2

公开(公告)日：2014-12-09

申请号：US13870779

申请日：2013-04-25

Applicant: Life Technologies Corporation

Inventor： Paolo Vatta ,  Olga Petrauskene ,  Manohar Furtado ,  Pius Brzoska ,  Lily Wong ,  Melissa Barker ,  Craig Cummings

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: C12Q1/689 ,  C12Q2600/142

Abstract: Disclosed are methods and kits for the specific detection of E. coli O157:H7 and not E. coli O55:H7 from samples such as: complex food matrices, water, beverages, fermentation broths, forensic & biological samples, and environmental samples including food processing and manufacturing surfaces. In some embodiments, a method of the disclosure comprises: hybridizing at least a first pair of polynucleotide primers to at least a first target polynucleotide sequence, hybridizing at least a second pair of polynucleotide primers to at least a second target polynucleotide sequence, amplifying the at least first and at least second target polynucleotide sequences, and detecting the first and second amplified target polynucleotide sequence products, wherein the detection of both the first amplified target polynucleotide sequence product and the second amplified target polynucleotide sequence product is indicative of the presence of E. coli O157:H7 in a sample and not E. coli O55:H7.

Abstract translation: 公开了用于特异性检测大肠杆菌O157：H7而不是大肠杆菌O55：H7的方法和试剂盒，来自样品如：复合食物基质，水，饮料，发酵液，法医和生物样品以及包括食物在内的环境样品 加工和制造表面。 在一些实施方案中，本公开的方法包括：使至少第一对多核苷酸引物与至少第一靶多核苷酸序列杂交，将至少第二对多核苷酸引物与至少第二靶多核苷酸序列杂交， 至少第一和至少第二靶多核苷酸序列，以及检测第一和第二扩增的靶多核苷酸序列产物，其中第一扩增的目标多核苷酸序列产物和第二扩增的靶多核苷酸序列产物的检测指示E. 大肠杆菌O157：H7在样品中，而不是大肠杆菌O55：H7。