Methods for analyzing massively parallel sequencing data for noninvasive prenatal diagnosis
- 申请公布号：
- US9218449(B2)
- 申请号：
- US201313802268
- 申请日期：
- 2013.03.13
- 申请公布日期：
- 2015.12.22
- 申请人：
- The Chinese University of Hong Kong
- 发明人：
- Lo Yuk Ming Dennis;Chiu Wai Kwun Rossa;Chan Kwan Chee;Zheng Wenli;Sun Hao;Chen Zhang
- 分类号：
- G06F19/22;G11C17/00;G06F19/16;G06F19/18
- 主分类号：
- G06F19/22
- 代理机构：
- Kilpatrick Townsend & Stockton LLP
- 代理人：
- Kilpatrick Townsend & Stockton LLP
- 地址：
- Shatin CN
- 摘要：
- This invention provides several ways of managing GC bias that occurs during seequencing and analysis of genomic DNA. Maternal plasma can be used as a source of fetal DNA for analysis. DNA segments or tags obtained from the plasma can be aligned with a chromosomal region of interest and with an artificial reference chromosome assembled from regions of the genome having matching GC content. This technology can be used, for example, to detect and evaluate aneuploidy and other chromosomal abnormalities.
- 主权项：
- 1. A method of characterizing a test genome or portion thereof, the method comprising:
identifying a first chromosomal region having a first GC content in a reference genome; assembling an artificial reference chromosome including a plurality of disjoint regions of the reference genome, the plurality of disjoint regions being at least 50 kb in length, the artificial reference chromosome having a second GC content that is about the first GC content; aligning, by a computer system, each of a plurality of sequence tags with the first chromosomal region and with the artificial reference chromosome, wherein the sequence tags have been obtained by sequencing nucleic acids in a biological sample comprising cell-free nucleic acids from a first tissue and a second tissue; determining, by a computer system, a first amount of sequence tags that align with the first chromosomal region; determining, by a computer system, a reference amount of sequence tags that align with the artificial reference chromosome; determining a parameter from the first amount and the reference amount, the parameter including a ratio of the first amount and the reference amount; and comparing the parameter to a cutoff value, thereby determining a classification of an amplification or deletion in the first chromosomal region of the first tissue.
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