Chu Tianjiao, Yeniterzi Suveyda, Rajkovic Aleksandar, Hogge W Allen, Dunkel Mary, Shaw Patricia, Bunce Kimberly, Peters David G
Department of Obstetrics, Gynecology and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA; Center for Fetal Medicine, Magee-Womens Research Institute, Pittsburgh, PA, USA.
Prenat Diagn. 2014 May;34(5):469-77. doi: 10.1002/pd.4331. Epub 2014 Feb 27.
BACKGROUND/OBJECTIVE: The non-invasive prenatal detection of fetal microdeletions becomes increasingly challenging as the size of the mutation decreases, with current practical lower limits in the range of a few megabases. Our goals were to explore the lower limits of microdeletion size detection via non-invasive prenatal tests using Minimally Invasive Karyotyping (MINK) and introduce/evaluate a novel statistical approach we recently developed called the GC Content Random Effect Model (GCREM).
Maternal plasma was obtained from a pregnancy affected by a 4.2-Mb fetal microdeletion and three normal controls. Plasma DNA was subjected to capture an 8-Mb sequence spanning the breakpoint region and sequence. Data were analyzed with our published method, MINK, and a new method called GCREM.
The 8-Mb capture segment was divided into either 38 or 76 non-overlapping regions of 200 and 100 Kb, respectively. At 200 Kb resolution, using GCREM (but not MINK), we obtained significant adjusted p-values for all 20 regions overlapping the deleted sequence, and non-significant p-values for all 18 reference regions. At 100 Kb resolution, GCREM identified significant adjusted p-values for all but one 100-Kb region located inside the deleted region.
Targeted sequencing and GCREM analysis may enable cost effective detection of fetal microdeletions and microduplications at high resolution.
背景/目的：随着突变大小的减小，胎儿微缺失的无创产前检测变得越来越具有挑战性，目前实际的下限在几兆碱基范围内。我们的目标是通过使用微创核型分析（MINK）的无创产前检测来探索微缺失大小检测的下限，并介绍/评估我们最近开发的一种名为GC含量随机效应模型（GCREM）的新统计方法。
从一例受4.2兆碱基胎儿微缺失影响的妊娠以及三个正常对照中获取母血血浆。对血浆DNA进行捕获，以获取跨越断点区域的8兆碱基序列并进行测序。使用我们已发表的方法MINK和一种名为GCREM的新方法对数据进行分析。
8兆碱基的捕获片段分别被分成38个或76个不重叠的区域，大小分别为200千碱基和100千碱基。在200千碱基分辨率下，使用GCREM（而非MINK），我们获得了与缺失序列重叠的所有20个区域的显著校正p值，以及所有18个参考区域的非显著p值。在100千碱基分辨率下，GCREM识别出除了位于缺失区域内的一个100千碱基区域外，所有其他区域的显著校正p值。
靶向测序和GCREM分析可能能够以高分辨率经济高效地检测胎儿微缺失和微重复。
