公开(公告)号：EP3049539B1

公开(公告)日：2018-09-05

申请号：EP14850060.6

申请日：2014-09-25

Applicant: Bio-Id Diagnostic Inc.

Inventor： VINAYAGAMOORTHY, Thuraiayah

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: C12Q1/6806 ,  C12Q1/6853 ,  C12Q1/6858 ,  C12Q1/6886 ,  C12Q2600/156 ,  C12Q2525/186 ,  C12Q2525/155 ,  C12Q2525/161 ,  C12Q2525/207 ,  C12Q2525/307 ,  C12Q2531/113 ,  C12Q2535/122 ,  C12Q2535/125

Abstract: Provided are methods for detecting and analyzing polynucleotides in a biological sample or sample derived therefrom for example, using a synthetic template polynucleotide. In some aspects, a target polynucleotide in the sample hybridizes to the template polynucleotide and is extended by a polymerase, generating an extended target polynucleotide. In some examples, the extended target polynucleotide is amplified, for example, by polymerase chain reaction, and sequences of the target polynucleotide determined, for example, by priming in the region of the extended target polynucleotide generated by extension and sequencing towards the region having identity to the target polynucleotide. In some aspects, the target polynucleotide is thereby detected in the sample and its sequence identified. In some aspects, the provided methods can be used to capture polynucleotide fragments in a biological sample, for example, plasma, and determine respective biomarkers they carry, for example, for cancer diagnosis and prognosis.

公开(公告)号：EP3056574B1

公开(公告)日：2018-08-22

申请号：EP16151944.2

申请日：2011-02-04

Applicant: Quest Diagnostics Investments Incorporated

Inventor： HANTASH, Feras ,  SUN, Weimin ,  TSAO, David C. ,  ROOT, Dana Marie ,  STROM, Charles M.

IPC: C12Q1/68 ,  C12P19/34

CPC classification number: C12Q1/6883 ,  C12Q1/6827 ,  C12Q1/683 ,  C12Q1/6858 ,  C12Q2600/154 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16 ,  G06F19/10 ,  C12Q2525/151 ,  C12Q2525/155 ,  C12Q2525/161 ,  C12Q2537/16

Abstract: Methods for determining the presence or absence of expansion of CGG repeat sequence in the FMR1 gene presence or absence of expansion of CCG repeat sequence in the FMR2 gene are provided. The methods are useful in identifying an individual with normal/intermediate, versus premutation or full mutation allele of FMR1 gene and FMR2 gene due to the expansion of CGG repeats and CCG repeats in the 5'-untranslated region respectively. The methods are also useful for screening newborns for fragile X syndrome or for screening women to determine heterozygosity status with full premutation of the CCG repeat tract. The methods are also useful in estimating the premutation and full mutation carrier frequency and estimating the prevalence of FXTAS AND FXPOI in a population. The methods are simple, rapid and require small amount of sample.

公开(公告)号：EP3359683A1

公开(公告)日：2018-08-15

申请号：EP16775753.3

申请日：2016-10-05

Applicant: Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH)

Inventor： DRUKKER, Micha ,  OPPERER, Florian ,  KRENDL, Christian ,  SÖNMEZER, Can

IPC: C12Q1/68

CPC classification number: C12Q1/6806 ,  C12Q2525/155 ,  C12Q2525/161 ,  C12Q2563/179 ,  C12Q2565/514

Abstract: The present invention relates to a method of producing a set of primers suitable for the reverse transcription and/or amplification of a plurality (N) of nucleic acid molecules of interest, wherein for each nucleic acid molecule of interest at least one primer is produced and wherein the primers carry a bar-code, the method comprising the steps of: (a)(i) combining (1 ) a first oligonucleotide, wherein said first oligonucleotide comprises a first bar-code nucleic acid sequence linked at its 3' end to a first adapter nucleic acid sequence with (2) a plurality (N) of second oligonucleotides, wherein each second oligonucleotide comprises the reverse complementary sequence of a forward primer specific for a nucleic acid molecule of interest, wherein said reverse complementary sequence of the forward primer is linked at its 3' end to the reverse complementary sequence of the first adapter nucleic acid sequence; and/or (a)(ii) combining (1 ) a third oligonucleotide, wherein said third oligonucleotide comprises a second bar-code nucleic acid sequence linked at its 3' end to a second adapter nucleic acid sequence with (2) a plurality (N) of fourth oligonucleotides, wherein each fourth oligonucleotide comprises the reverse complementary sequence of a reverse primer specific for said nucleic acid molecule of interest, wherein said reverse complementary sequence of the reverse primer is linked at its 3' end to the reverse complementary sequence of the second adapter nucleic acid sequence; wherein steps (a)(i) and (a)(ii) are carried out under conditions that enable the annealing of the first and second adapter nucleic acid sequences to the respective reverse complementary sequences thereof; (b) extending the oligonucleotides of (a)(i) and (a)(ii) by polymerase-mediated oligonucleotide synthesis; and (c) optionally, removing the second and fourth oligonucleotides. The present invention further relates to methods of producing a plurality (M) of nucleic acid amplification products of interest carrying at least one sample-specific bar-code as well as to a method for multiplex sequencing of a plurality (M) of nucleic acid amplification products of interest from a plurality (X) of samples in a single reaction chamber and identifying the individual sample from which each nucleic acid amplification product is derived. Furthermore, the present invention relates to a target- unspecific bar-code-adapter panel, its use in the methods of the invention as well as a kit comprising same.

公开(公告)号：EP3208336A4

公开(公告)日：2018-06-20

申请号：EP14904072

申请日：2014-10-14

Applicant: MGI TECH CO LTD

Inventor： JIANG YUAN ,  GENG CHUNYU ,  ZHAO XIA ,  FU SHUJIN ,  HE LINGYU ,  LI YAQIAO ,  SU XIAOSHAN ,  WU FANZI ,  ZHANG WENWEI ,  JIANG HUI ,  ALEXEEV ANDREI ,  DRMANAC RADOJE

IPC: C12N15/11 ,  C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6855 ,  C40B40/06 ,  C40B50/06

CPC classification number: C12N15/1093 ,  C12N9/1205 ,  C12N9/1252 ,  C12N9/16 ,  C12N15/11 ,  C12Q1/68 ,  C12Q1/6806 ,  C12Q1/6855 ,  C12Y207/01078 ,  C12Y207/07007 ,  C12Y301/03001 ,  C40B40/06 ,  C40B50/06 ,  C12Q2521/531 ,  C12Q2525/155 ,  C12Q2525/186 ,  C12Q2525/191 ,  C12Q2525/307 ,  C12Q2535/122 ,  C12Q2537/162 ,  C12Q2563/131

Abstract: Provided is a linker element and a method of using the linker element to construct a sequencing library, wherein the linker element consists of a linker A and a linker B, the linker A is obtained through the complementary pairing of a long nucleic acid strand and a short nucleic acid strand, the 5' end of the long strand has a phosphoric acid modification, and the 3' end of the short strand has an enclosed modification, with enzyme sites in the short strand; and the linker B is a nucleic acid single strand, and the 3' end thereof can be in a complementary pairing with the 5' end of the long strand of the linker A. Using the linker element of the present invention for constructing a sequencing library ensures the linking directionality of the linkers while solving the problems of fragment interlinking, linker self-linking and low linking efficiency, and reducing the purification reaction between steps, shortening the linking time and reducing costs.

公开(公告)号：EP3329007A1

公开(公告)日：2018-06-06

申请号：EP16739665.4

申请日：2016-07-08

Applicant: Illumina, Inc.

Inventor： TREPAGNIER, Eliane H. ,  KHURANA, Tarun

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12Q2523/107 ,  C12Q2525/155 ,  C12Q2525/186 ,  C12Q2523/313

Abstract: A method including steps of (a) providing an array of sites, wherein each site comprises a mixture of different nucleic acid templates; (b) extending primers hybridized to the different nucleic acid templates at each of the sites with different nucleotide analogs having different reversible blocking moieties, respectively, thereby producing different primer extension products at each site; (c) detecting the different primer extension products to distinguish the different nucleotide analogs at each site; and (d) removing the different reversible blocking moieties from the primer extension products at each of the sites using a first treatment that is selective for a first of the different reversible blocking moieties and a second treatment that is selective for a second of the different reversible blocking moieties.

公开(公告)号：EP3152331A4

公开(公告)日：2018-05-09

申请号：EP15802743

申请日：2015-06-08

Applicant: UNIV CORNELL

Inventor： BARANY FRANCIS ,  EFCAVITCH JOHN WILLIAM

IPC: C12Q1/68

CPC classification number: C12Q1/6874 ,  C12N15/1068 ,  C12Q1/6806 ,  C12Q1/6809 ,  C12Q1/6816 ,  C12Q1/6844 ,  C12Q1/6848 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q2531/125 ,  C12Q2535/122 ,  C12Q2537/143 ,  C12Q2565/501 ,  C12Q2521/319 ,  C12Q2521/325 ,  C12Q2521/331 ,  C12Q2521/501 ,  C12Q2525/155 ,  C12Q2525/161 ,  C12Q2525/179 ,  C12Q2525/191 ,  C12Q2525/307 ,  C12Q2563/179

Abstract: The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single-stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism. These chimeric constructs are suitable for identifying and enumerating mutations, copy changes, translocations, and methylation changes. In other embodiments, input mRNA, IncRNA, or miRNA is used to generate circular DNA products that reflect the presence and copy number of specific mRNA's, IncRNA's splice-site variants, translocations, and miRNA.

公开(公告)号：EP3037552B1

公开(公告)日：2018-04-25

申请号：EP15197029.0

申请日：2013-03-06

Applicant: Illumina Cambridge Limited

Inventor： GORMLEY, Niall Anthony ,  FRASER, Louise ,  KOKKO-GONZALES, Paula

IPC: C12Q1/68

CPC classification number: G01N33/58 ,  C12Q1/6806 ,  C12Q1/6834 ,  C12Q1/6855 ,  C12Q1/6869 ,  C12Q2521/301 ,  C12Q2521/319 ,  C12Q2521/327 ,  C12Q2525/155 ,  C12Q2525/191 ,  C12Q2535/122 ,  C12Q2565/518

Abstract: Provided herein is a method of using transposition to improve methods of sequencing RNA molecules. Provided herein is a method of tagging nucleic acid duplexes, such as DNA:RNA duplexes or DNA: DNA duplexes. The method includes the steps of providing a transposase and a transposon composition, providing one or more nucleic acid duplexes immobilized on a support, and contacting the transposase and transposon composition with the one or more nucleic acid duplexes under conditions wherein the one or more nucleic acid duplexes and transposon composition undergo a transposition reaction to produce one or more tagged nucleic acid duplexes, wherein the transposon composition comprises a double stranded nucleic acid molecule comprising a transferred strand and a non-transferred strand.

公开(公告)号：EP2859124B1

公开(公告)日：2018-04-25

申请号：EP13744827.0

申请日：2013-06-12

Applicant: Centre National de la Recherche Scientifique (C.N.R.S.) ,  Ecole Normale Supérieure de Cachan ,  Université Paris Diderot - Paris 7

Inventor： MUNIR, Soundasse ,  THIERRY, Sylvain ,  SUBRA, Frédéric ,  DEPREZ, Eric ,  DELELIS, Olivier

IPC: C12Q1/70 ,  C12Q1/68

CPC classification number: C12Q1/703 ,  C12Q1/6855 ,  C12Q2525/155 ,  C12Q2545/114 ,  C12Q2600/136 ,  C12Q2600/158

公开(公告)号：EP2893034B9

公开(公告)日：2018-04-18

申请号：EP12883998.2

申请日：2012-09-10

Applicant: Genesky Diagnostics (Suzhou) Inc. ,  Shanghai Genesky Biotechnologies Inc.

Inventor： JIANG, Zhengwen ,  YU, Feng ,  LI, Caihua

IPC: C12Q1/68 ,  G01N21/64

CPC classification number: C12Q1/6827 ,  C12Q1/6858 ,  C12Q1/6862 ,  C12Q1/6883 ,  C12Q2600/156 ,  C12Q2600/16 ,  C12Q2525/204 ,  C12Q2537/143 ,  C12Q2561/125 ,  C12Q2535/125 ,  C12Q2525/155 ,  C12Q2537/16 ,  C12Q2563/107 ,  C12Q2565/125

Abstract: Here provided is a method for multiplex nucleic acid analysis. The method includes steps of hybridizing sets of probes to target nucleic acids in a sample, ligating the hybridized probes, amplifying the ligated probes, and assaying the amplification products to determining the presence, absence, or quantity of the target nucleic acids in the sample. The multiplexity is made available in part by adding detectable moieties and inserting stuffer sequences in primers so that amplification products may be identified on the basis of the detectable moieties and fragment sizes. Also provided is a sensitive method of detecting small copy number changes by measuring the copy number of a plurality of target sites in the nucleic acid in a test sample in comparison to a control sample and then determining the copy number of the nucleic acid based on the measured copy number of the plurality of target sites. Further provided is a kit for multiplex nucleic acid analysis and for small copy number change determination.

公开(公告)号：EP3298171A1

公开(公告)日：2018-03-28

申请号：EP16800544.5

申请日：2016-05-20

Applicant: Sigma-Aldrich Co. LLC

Inventor： WARD, Brian

IPC: C12Q1/68 ,  C12P19/34 ,  C07H21/04 ,  C40B20/04

CPC classification number: C12Q1/68 ,  C12Q1/6855 ,  C40B20/04 ,  C12Q2521/307 ,  C12Q2525/155 ,  C12Q2525/179 ,  C12Q2525/204 ,  C12Q2535/122 ,  C12Q2563/179

Abstract: Methods are provided herein for identifying rare and/or unknown DNA sequences by next-generation sequencing approaches. Isolated double-stranded (ds), single-stranded (ss), or ds/ss DNA is fragmented and the fragments are polished, phosphorylated, and tailed, as necessary. Fragmentation can be enzymatic or mechanical. A universal adapter sequence is ligated to each fragment, wherein the adapter can have a top strand without a 5' phosphate, a 3' with an -H in place of the -OH, and/or a 3' extra base complementary to any base added to the polished fragments. The ligatamers may then serve as templates for ampli?cation using a forward primer complementary to the adapter sequence and a reverse primer targeted to the fragment sequence. Compositions produced by these methods and kits adapted for performing these methods are also described herein.