Male fetus cffDNA content calculation method based on X chromosome

Abstract

The invention discloses a male fetus cffDNA content calculation method based on an X chromosome. The male fetus cffDNA content calculation method comprises the following steps: S1, obtaining an original sequencing gene sequence; s2, counting the sequencing gene sequences; s3, standardizing the number of sequencing gene sequences; s4, recognizing the gender of the fetus; s5, calculating a copy baseline in a female fetal X chromosome window; s6, calculating a male fetus X chromosome predictive factor and detecting an abnormal point; and step S7, obtaining the cffDNA content of the male fetus. The method has the advantages of simple principle, simplicity and convenience in operation, high accuracy, high detection efficiency and the like.

Description

technical field [0001] The invention mainly relates to the technical fields of gene sequencing and biological information analysis, in particular to a method for calculating cffDNA content of male fetuses based on X chromosome. Background technique [0002] The discovery of cell-free fetal DNA molecules in pregnant women's plasma has brought prenatal testing into the non-invasive era, and circulating cell-free fetal DNA (cffDNA for short) is gradually considered to be an important carrier for non-invasive detection of fetal abnormalities. Various approaches for high-throughput sequencing-based noninvasive prenatal testing (NIPT) have been developed and are now rapidly being translated into medical practice. In these scenarios, cffDNA is a critical parameter in controlling test result performance and in appropriate clinical interpretation of test results. [0003] The existing methods for estimating and predicting cffDNA content based on bioinformatics methods mainly include...

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Problems solved by technology

The result of this method is very close to the above method (2). The disadvantage of this method is that it needs to perform ultra-high-depth sequencing on the sample, and the sequencing depth usually needs to reach more than 120x to detect fetal alleles, and targeted sequencing can only It can cover a part of the genome and cannot detect chromosomal abnormalities at the level of the whole genome of the fetus, so it is also limited in practical application

Usually, the ratio of the number of fragments in the interval [100,150] to [163,169] is used as a predictor, and the cffDNA content is estimated by fitting a linear model. The correlation coefficient between this method and the cffDNA content calculated by Y is 0.83, and the accuracy is difficult to meet the requirements of non-invasive prenatal testing. Require

[0011] (8) Based on the cell-free DNA nucleosome positioning method, existing studies have shown that the main peak of the fragment length of cell-free DNA in the peripheral blood of pregnant women is 166bp, and there are some small peaks similar to spikes at intervals of 10bp, while The main peak of fetal cell-free DNA molecule length is 143bp; scientists speculate that 166bp contains the nucleosome body and a linker, on the contrary, the DNA molecule of the 143bp main peak lacks the linker as its component. A method for predicting cffDNA has been developed by body mapping method, but the accuracy of this method is not high enough to meet the clinical requirements

[0012] In summary, the method based on low-depth massive parallel sequencing of cell-free DNA in pregnant women's peripheral blood is still the mainstream method of non-invasive prenatal detection, and the calculation method based on Y chromosome is considered to be the gold standard method for cffDNA calculation of male fetuses. However, this method Male cell-free DNA is needed as a control to accurately estimate the Y chromosome content calculated by a specific sequencing platform and bioinformatics processing flow, and then accurately infer the cffDNA content; however, testing male control samples in routine non-invasive prenatal testing will increase the cost and process of sequencing The complexity of management, in addition, if the fetus has Y chromosome aneuploidy abnormalities (such as the absence of Y chromosome, or the presence of multiple Y chromosomes), the cffDNA content cannot be accurately estimated

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