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    METHODS OF EQUALIZING REPRESENTATION LEVELS OF NUCLEIC ACID TARGETS
    2.
    发明申请
    METHODS OF EQUALIZING REPRESENTATION LEVELS OF NUCLEIC ACID TARGETS 有权
    平衡核酸指标代表水平的方法

    公开(公告)号：US20090246760A1

    公开(公告)日：2009-10-01

    申请号：US12058032

    申请日：2008-03-28

    Applicant: Timothy D. Harris ,  John J. Boyce, IV

    Inventor： Timothy D. Harris ,  John J. Boyce, IV

    IPC: C12Q1/68 ,  C07H21/00

    CPC classification number: C12Q1/6851 ,  C12Q2537/165

    Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).

    Abstract translation: 本公开提供了减少核酸靶标的表达水平范围的方法。 这些方法对于受益于靶表现的低方差（例如单分子测序和/或杂合基因分型）和病原体诊断的多靶标分析特别有用。 提供了两种一般方法。 在方法1中，调节探针的起始浓度。 在方法2中，目标特异性探针被“分类”，即，基于相似的表示级别来选择几个探针子集。 此后，使用样本的单独部分（即，分离的血管），提取具有或不具有扩增的相应靶标的每个子集。

    METHODS AND COMPOSITIONS FOR REDUCING NUCLEOTIDE IMPURITIES
    3.
    发明申请
    METHODS AND COMPOSITIONS FOR REDUCING NUCLEOTIDE IMPURITIES 审中-公开
    降低核苷酸含量的方法和组合物

    公开(公告)号：US20090226906A1

    公开(公告)日：2009-09-10

    申请号：US12113501

    申请日：2008-05-01

    Applicant: David Z. Xie ,  Philip R. Buzby ,  Timothy D. Harris

    Inventor： David Z. Xie ,  Philip R. Buzby ,  Timothy D. Harris

    IPC: C12Q1/68 ,  C12N9/00 ,  C12P19/34

    CPC classification number: C12P19/34 ,  C12Q1/6806 ,  C12Q1/6874 ,  C12Q2565/518 ,  C12Q2525/301 ,  C12Q2535/113

    Abstract: The disclosure provides methods and compositions for reducing nucleotide impurities in reagents and reaction mixtures. Generally, the methods of the invention involve the inclusion of so-called “scrubbing oligonucleotides” (or “scrubbers”) that preferentially incorporate nucleotide impurities, thereby reducing available free impurities. The disclosure further provides methods of sequencing a target nucleic acid by synthesis that utilize “live” scrubbing. Scrubbing oligonucleotides of various structures are disclosed, including hairpin scrubbers and homopolymeric scrubbers.

    Abstract translation: 本公开提供了用于减少试剂和反应混合物中的核苷酸杂质的方法和组合物。 通常，本发明的方法包括优先掺入核苷酸杂质的所谓“洗涤寡核苷酸”（或“洗涤器”），从而减少可用的游离杂质。 本公开进一步提供了通过利用“活”洗涤的合成来测序靶核酸的方法。 公开了各种结构的洗涤寡核苷酸，包括发夹洗涤器和均聚洗涤器。

    METHODS OF EQUALIZING REPRESENTATION LEVELS OF NUCLEIC ACID TARGETS
    8.
    发明申请
    METHODS OF EQUALIZING REPRESENTATION LEVELS OF NUCLEIC ACID TARGETS 审中-公开
    平衡核酸指标代表水平的方法

    公开(公告)号：US20110027790A1

    公开(公告)日：2011-02-03

    申请号：US12871978

    申请日：2010-08-31

    Applicant: Timothy D. Harris ,  John J. Boyce, IV

    Inventor： Timothy D. Harris ,  John J. Boyce, IV

    IPC: C12Q1/68 ,  C12P19/34 ,  C07H21/00

    CPC classification number: C12Q1/6851 ,  C12Q2537/165

    Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).

    Abstract translation: 本公开提供了减少核酸靶标的表达水平范围的方法。 这些方法对于受益于靶表现的低方差（例如单分子测序和/或杂合基因分型）和病原体诊断的多靶标分析特别有用。 提供了两种一般方法。 在方法1中，调节探针的起始浓度。 在方法2中，目标特异性探针被“分类”，即，基于相似的表示级别来选择几个探针子集。 此后，使用样本的单独部分（即，分离的血管），提取具有或不具有扩增的相应靶标的每个子集。

    PAIRED-END READS IN SEQUENCING BY SYNTHESIS
    9.
    发明申请
    PAIRED-END READS IN SEQUENCING BY SYNTHESIS 审中-公开
    通过合成进行顺序读取

    公开(公告)号：US20100304447A1

    公开(公告)日：2010-12-02

    申请号：US12839609

    申请日：2010-07-20

    Applicant: Timothy D. Harris

    Inventor： Timothy D. Harris

    IPC: C12P19/34

    CPC classification number: C12Q1/6869 ,  C12Q2525/15

    Abstract: The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35 bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.

    Abstract translation: 本公开提供了在逐个合成过程中产生配对读取的方法，特别是在具有相对较短读取长度（例如15-35个碱基）的系统中，例如通过合成的单分子测序。 提供了几种方法的实现。 特别有利的是允许对模板进行重排序的方法，其产生较低的错误率。 本发明还提供了使用配对读取的方法，例如，将它们重复重复或用于组装成包括全基因组组装在内的大序列。

    Methods of equalizing representation levels of nucleic acid targets
    10.
    发明授权
    Methods of equalizing representation levels of nucleic acid targets 有权
    平衡核酸靶标表达水平的方法

    公开(公告)号：US07790391B2

    公开(公告)日：2010-09-07

    申请号：US12058032

    申请日：2008-03-28

    Applicant: Timothy D. Harris ,  John J. Boyce, IV

    Inventor： Timothy D. Harris ,  John J. Boyce, IV

    IPC: C12Q1/68

    CPC classification number: C12Q1/6851 ,  C12Q2537/165

    Abstract: The disclosure provides methods of reducing the range of representation levels of nucleic acid targets. The methods are particularly useful for multi-target analyses benefiting from a low variance of target representations, such as, e.g., single molecule sequencing and/or heterozygous genotyping, and pathogen diagnosis. Two general methods are provided. In Method 1, starting concentrations of probes are adjusted. In Method 2, target-specific probes are “binned,” i.e., several subsets of probes are selected based on similar representation levels. Thereafter, each subset of corresponding targets is extracted, with or without amplification, using a separate portion of the sample (i.e., separate vessels).

    Abstract translation: 本公开提供了减少核酸靶标的表达水平范围的方法。 这些方法对于受益于靶表现的低方差（例如单分子测序和/或杂合基因分型）和病原体诊断的多靶标分析特别有用。 提供了两种一般方法。 在方法1中，调节探针的起始浓度。 在方法2中，目标特异性探针被“分类”，即，基于相似的表示级别来选择几个探针子集。 此后，使用样本的单独部分（即，分离的血管），提取具有或不具有扩增的相应靶标的每个子集。

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