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1. 发明申请

WO2015181718A1 METHOD OF PRENATAL DIAGNOSIS 审中-公开
标题翻译：临床诊断方法
公开(公告)号：WO2015181718A1
公开(公告)日：2015-12-03
申请号：PCT/IB2015/053926
申请日：2015-05-26
申请人： EBIOS FUTURA S.R.L.
发明人： BENELLI, Matteo , GERUNDINO, Francesca , GIACHINI, Claudia , PESCUCCI, Chiara
IPC分类号： C12Q1/68 , G06F19/18 , G06F19/22 , G06F19/24
CPC分类号： C12Q1/6869 , C12Q2537/159 , C12Q2537/16 , C12Q2537/165 , G06F19/18 , G06F19/22 , G06F19/24
摘要： Method of prenatal diagnosis comprising the steps of: acquiring (1) reads of fragments of genomic libraries obtained from circulating free total DNA in a sample of maternal plasma, the DNA representing a plurality of chromosomes; aligning (2) the reads with respect to a predetermined reference genome obtaining a first dataset (SAM); converting (4) the first dataset (SAM) into a second dataset (BAM) so as to allow sorting thereof according to chromosomal coordinates and successive duplicate removal, obtaining a third dataset containing all the reads aligned and devoid of duplicates; subdividing (6) at least one chromosome into windows of predetermined dimensions, so as to count the reads which have a "mapping validity" greater than or equal to a threshold value in each reading window, obtaining a total number of above-threshold reads (N W ); normalizing, for each reading window, the total number of above-threshold reads (N W ) with respect to the total number (N tot ) of reads of the fragment of genomic library obtaining a first normalized datum (N W,lib ); normalizing (8), for each reading window, the first normalized datum (N W,lib ) with respect to a systematic error due to the content of G and C bases, obtaining a second normalized datum (N W,lib,GC ); calculating (10), for each chromosome, a median of all the second normalized data (N W,lib,GC ) obtaining a final value (N ji ); calculating (12) an aneuploidy parameter (Z) for at least one chromosome; determining the aneuploidy parameter (Z) of at least one chromosome so as to evaluate whether the sample of maternal plasma is aneuploid.
摘要翻译：产前诊断方法，包括以下步骤：（1）读取母体血浆样本中循环游离总DNA获得的基因组文库片段，DNA代表多条染色体; 对准（2）相对于获得第一数据集（SAM）的预定参考基因组的读取; 将所述第一数据集（SAM）转换（4）到第二数据集（BAM）中，以便根据染色体坐标和连续的重复删除来对其进行排序，获得包含所有对齐和没有重复的读出的第三数据集; 将至少一个染色体（6）细分为预定尺寸的窗口，以便对每个阅读窗口中具有大于或等于阈值的“映射有效性”的读数进行计数，获得高于阈值读数的总数（ NW）; 归一化，对于每个阅读窗口，相对于获得第一标准化数据（NW，lib）的基因组文库的片段的读数的总数（Ntot）的阈值读数（NW）的总数; 对于每个阅读窗口，归一化（8）关于由于G和C基数的内容导致的系统误差的第一归一化数据（NW，lib），获得第二归一化数据（NW，lib，GC）; 对于每个染色体，计算（10）所有第二归一化数据（NW，lib，GC）的中值，获得最终值（Nji）; 计算（12）至少一个染色体的非整倍体参数（Z）; 确定至少一条染色体的非整倍性参数（Z），以评估母体血浆样品是否为非整倍体。

2. 发明公开

EP3149202A1 METHOD OF PRENATAL DIAGNOSIS 审中-公开
标题翻译： VERFAHREN ZURPRÄNATALENDIAGNOSE
公开(公告)号：EP3149202A1
公开(公告)日：2017-04-05
申请号：EP15736606.3
申请日：2015-05-26
申请人： Ebios Futura S.r.l.
发明人： BENELLI, Matteo , GERUNDINO, Francesca , GIACHINI, Claudia , PESCUCCI, Chiara
IPC分类号： C12Q1/68 , G06F19/18 , G06F19/22 , G06F19/24
CPC分类号： C12Q1/6869 , C12Q2537/159 , C12Q2537/16 , C12Q2537/165 , G06F19/18 , G06F19/22 , G06F19/24
摘要： Method of prenatal diagnosis comprising the steps of: acquiring (1) reads of fragments of genomic libraries obtained from circulating free total DNA in a sample of maternal plasma, the DNA representing a plurality of chromosomes; aligning (2) the reads with respect to a predetermined reference genome obtaining a first dataset (SAM); converting (4) the first dataset (SAM) into a second dataset (BAM) so as to allow sorting thereof according to chromosomal coordinates and successive duplicate removal, obtaining a third dataset containing all the reads aligned and devoid of duplicates; subdividing (6) at least one chromosome into windows of predetermined dimensions, so as to count the reads which have a "mapping validity" greater than or equal to a threshold value in each reading window, obtaining a total number of above-threshold reads (NW); normalizing, for each reading window, the total number of above-threshold reads (NW) with respect to the total number (Ntot) of reads of the fragment of genomic library obtaining a first normalized datum (NW,lib); normalizing (8), for each reading window, the first normalized datum (NW,lib) with respect to a systematic error due to the content of G and C bases, obtaining a second normalized datum (NW,lib,GC); calculating (10), for each chromosome, a median of all the second normalized data (NW,lib,GC) obtaining a final value (Nji); calculating (12) an aneuploidy parameter (Z) for at least one chromosome; determining the aneuploidy parameter (Z) of at least one chromosome so as to evaluate whether the sample of maternal plasma is aneuploid.
摘要翻译：产前诊断方法，包括以下步骤：（1）读取母体血浆样本中循环游离总DNA获得的基因组文库片段，DNA代表多条染色体; 对准（2）相对于获得第一数据集（SAM）的预定参考基因组的读取; 将所述第一数据集（SAM）转换为第二数据集（BAM），以便根据染色体坐标和连续的重复删除来进行排序，从而获得包含所有对齐和没有重复的读取的第三数据集; 将至少一个染色体（6）细分为预定尺寸的窗口，以便对每个阅读窗口中具有大于或等于阈值的“映射有效性”的读数进行计数，获得高于阈值读数的总数（ NW）; 归一化，对于每个阅读窗口，相对于获得第一标准化数据（NW，lib）的基因组文库的片段的读数的总数（Ntot）的阈值读数（NW）的总数; 对于每个阅读窗口，归一化（8）关于由于G和C基数的内容导致的系统误差的第一归一化数据（NW，lib），获得第二归一化数据（NW，lib，GC）; 对于每个染色体，计算（10）所有第二归一化数据（NW，lib，GC）的中值，获得最终值（Nji）; 计算（12）至少一个染色体的非整倍体参数（Z）; 确定至少一条染色体的非整倍性参数（Z），以评估母体血浆样品是否为非整倍体。

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