来自杂志 Prenatal diagnosis 的文献。
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1.
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(2024-06-30 17:33):
#paper DOI: 10.1002/pd.5620 Prenatal Diagnosis, 2019, Fetal fraction and noninvasive prenatal testing: what clinicians need to know. 这是一篇综述文章，作者总结了fetal fraction(即胎儿cfDNA浓度)在理解和解读NIPT检测结果中作为重要参数的作用。综述内容分为以下几个方面。第一，fetal freaction的定义，如何理解fetal fraction的“高”和“低”；第二fetal fraction的来源及其数值高低受到哪些生物学因素的影响；第三，NIPT流程中如何计算fetal fraction以及fetal fraction这一参数设置对NIPT结果的影响；第四，由于low fetal fraction导致NIPT结果no-call时，有什么备选方案。
Abstract:
The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal …
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The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a "plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.
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2.
半面阳光
(2024-01-31 13:17):
#paper DOI: https://doi.org/10.1002/pd.5079, Prenatal diagnosis, 2017, Comparing methods for fetal fraction determination and quality control of NIPT samples. 在无创产前筛查（NIPT）的分析流程中，胎儿游离DNA浓度（cell-free fetal DNA fraction ）是一个重要的参数，尤其是检测样本中具有高背景浓度的母亲游离DNA（maternal cell-free DNA），计算fetal fraction是NIPT流程中的一个重要环节。这篇文献比较了四种计算fetal fraction的方法，分别是DEFRAG、BAYINDIR、SEQFF、SANEFALCON。作者手机了654例外周血样本，其中279例为女胎，375例为男胎，然后进行NGS测序，再分别用4种方法计算fetal fraction。研究结果发现，DEFRAG和BAYINDIR这两种基于Y染色体测序数据进行计算的方法一致性要优于另外两种可以同时计算男女胎fetal fraction的方法。其中DEFRAG在计算低胎儿浓度的样本时，表现比BAYINDIR方法更好。而SeqFF和SANEFALCON这两种可计算女胎胎儿浓度的方法，虽然不及DEFRAG和BAYINDIR的准确性，但是SANEFALCON在计算由于胎儿浓度低而分析失败样本时表现较好，甚至优于DEFRAG。此外，作者还探讨分析了孕妇BMI指数和孕周对计算fetal fraction的影响，结果显示DEFRAG在计算fetal fraction时受到这两个参数的影响较其他方法更明显。
Abstract:
OBJECTIVE: To compare available analysis methods for determining fetal fraction on single read next generation sequencing data. This is important as the performance of non-invasive prenatal testing (NIPT) procedures depends …
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OBJECTIVE: To compare available analysis methods for determining fetal fraction on single read next generation sequencing data. This is important as the performance of non-invasive prenatal testing (NIPT) procedures depends on the fraction of fetal DNA.METHODS: We tested six different methods for the detection of fetal fraction in NIPT samples. The same clinically obtained data were used for all methods, allowing us to assess the effect of fetal fraction on the test result, and to investigate the use of fetal fraction for quality control.RESULTS: We show that non-NIPT methods based on body mass index (BMI) and gestational age are unreliable predictors of fetal fraction, male pregnancy specific methods based on read counts on the Y chromosome perform consistently and the fetal sex-independent new methods SeqFF and SANEFALCON are less reliable but can be used to obtain a basic indication of fetal fraction in case of a female fetus.CONCLUSION: We recommend the use of a combination of methods to prevent the issue of reports on samples with insufficient fetal DNA; SANEFALCON to check for presence of fetal DNA, SeqFF for estimating the fetal fraction for a female pregnancy and any Y-based method for estimating the fetal fraction for a male pregnancy. © 2017 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.
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