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【资讯翻译】The Utility of Whole Exome Sequencing in Prenatal Diagnosis

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发表于 2016-3-17 09:57:51 | 显示全部楼层 |阅读模式
The Utility of Whole Exome Sequencing in Prenatal Diagnosis

During the past several years clinical whole-exome sequencing (WES) has been utilized for patients with complex clinical presentations. With a molecular diagnosis rate of about 30%, clinical WES is an effective way of ending the expensive and time-consuming diagnostic odyssey. With the continuous improvement of WES methodology including updated sequencing instrumentation and shorter turnaround time (TAT), improved analysis, clinical exome is now also considered a suitable test for critically ill patients. This shortened TAT allows for WES utilization in prenatal diagnosis. Here, we report the first 43 consecutive prenatal cases. Prenatal cases are defined as a fetal sample obtained through either an invasive procedure or a product of conception (POC). This cohort includes 34 cases with WES preformed for the proband only (proband WES) followed by Sanger sequencing studies of both parental samples and 9 trio WES, where both the proband’s and parental samples underwent whole exome sequencing. For the final report, all contributing changes are confirmed by Sanger sequencing for trio cases. The exome sequencing was performed on the Illumina HiSeq2500 with an average of ~11.4 Gb data per exome and more than 97% of the targeted exome regions are sequenced at a depth of 20X. Exome sequencing data were analyzed for small nucleotide changes as well as large CNVs. Individual DNA samples were also analyzed by the Illumina HumanExome-12v1 array for quality control and potential detection of large CNVs. The proband WES yielded a diagnosis of 32% (11/34) cases and the trio WES provided diagnosis in 33% (3/9) cases. Although the molecular diagnosis rate is almost identical, the TAT is dramatically different; the average TAT for proband WES is currently 12 weeks whereas it is 1 to 3 weeks for prenatal trio WES. We divided our patient cohort into three categories; patient’s with brain anomaly detected by ultrasound (5 cases), patient’s with brain anomaly and other organ system anomaly detected by ultrasound (16 cases), and ultrasound anomaly not including the brain (22 cases). Additional ultrasound anomalies include the following, but are not limited to: cardiac, kidney, limb, and bladder anomalies, diaphragmatic hernia, heterotaxy, cystic hygroma, and edema.  For the 5 patients with brain anomaly on ultrasound we were able to provide diagnosis for 3 individuals (60%), for the 16 patients with brain anomaly and other organ system involved we provided diagnosis for 6 patients (38%), and for the 22 patients with anomaly not including the brain we provided a diagnosis for 5 patients (23%). Furthermore for individuals with brain, cardiac defect, and other organ system anomaly (7 patients) we were able to provide a molecular diagnosis for 3 individuals (43%). Additionally, for individuals with cardiac anomaly and other organ system anomaly we were able to provide diagnosis for 1 individual (25%). For 24 of our patients this was the first presentation in the family and diagnosis was made for 9 individuals (38%). For the remaining 19 individuals, two or more family members had a similar phenotype and diagnosis was made for 5 cases (26%). With rapid turnaround time and comprehensive analysis, the prenatal trio WES may be a valuable tool in prenatal diagnosis. The next step in improving the current test will include analysis of DNA from direct chorionic villus sampling or amniotic fluid to further reduce the TAT.

信源地址:https://acmg.expoplanner.com/ind ... amp;session_id=1778

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发表于 2016-3-17 10:06:17 | 显示全部楼层
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发表于 2016-3-18 11:37:52 | 显示全部楼层
全外显子组测序用于产前诊断

       在过去的几年,临床全外显子组测序(WES)已被用于具有复杂临床表现的患者。由于临床WES的分子诊断率约为30%,它是一种结束昂贵和耗时的诊断过程的有效方式。由于WES方法学的持续改进使得临床外显子检测适用于危重病人,这些改进的地方包括测序仪器的更新和周转时间(TAT)的减少,分析方法的改善等。TAT的减少使得WES适用于产前诊断。在这里,我们第一次报告了由43个连续的产前病例组成的案例。产前诊断病例的定义为通过侵入性手术或妊娠产物(POC)获得的胎儿样品。该队列包括34例只进行预制的WES的先证者病例(先证者WES,其父母的样本进行Sanger测序)和9例三重WES(先证者及父母的样本都进行了全外显子组测序)。在最终研究报告中,三重病例的所有有价值的变化都被确定。用Illumina HiSeq2500进行外显子测序,平均每个外显子获得11.4 GB的数据,97%以上的目标外显子区域的测序深度为20X。对外显子组测序数据进行小核苷酸的变化以及大型拷贝数变异(CNV)分析。个别DNA样品进行Illumina humanexome-12v1阵列分析,用于质量控制和大型CNVs检测。先证者WES的诊断率为32%(11/34),三重WES的诊断率为33%(3/9)。虽然分子诊断率几乎是相同的,但是TAT是大不相同的;目前先证者WES的平均TAT达12周,而产前三重WES的平均TAT是1至3周。我们将病人分为三类:父母经超声检查得出脑异常的(5例,I类)、父母经超声检查得出脑异常及其他器官系统异常的(16例,II类)和父母超声异常但不包括脑异常的(22例,II类)。其他超声异常包括(不局限于以下情况):心、肾、肢体、膀胱异常、膈疝、内脏、囊性淋巴水肿。我们确诊了5例I类病中的3例(60%),16例II类病例中的6例(38%),和22II类病例中的5例(23%)。此外,7例大脑,心脏缺陷,和其他器官系统异常的病例中,我们对其中的3人给出了分子诊断(43%)。此外,对于心脏异常和其他器官系统异常的病例,我们能够提供的诊断为1人(25%)。24例患者是第一次加入研究,其诊断率为9例(38%)。其余的19例病例(2个或更多的家庭成员有同样表型)的诊断率为5例(26%)。随着快速周转时间和综合分析,产前三重WES可能是一个有价值的产前诊断工具。接下来,进一步减少TAT的改进措施包括从绒毛膜绒毛或羊水直接取样用于DNA分析。

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 楼主| 发表于 2016-3-18 13:39:37 | 显示全部楼层
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