以Exome CNV再分析全外顯子定序個案之致病性拷貝數變異

Abstract

背景 基因變異常造成許多臨床疾病，小自單一或數個核苷酸變異、大至數千或數萬個鹼基對的拷貝數異常、甚至是染色體數目異常，在臨床基因診斷時均須納入鑑別。全外顯子定序(WES)可精準地分析單一核苷酸異常(SNV)或小範圍的核苷酸插入或缺失(small indel)，亦可利用讀深法(read of coverage)產生gCNV檔，分析較大範圍的拷貝數異常(exome CNV)。 目的 本研究旨於利用exome CNV再次分析WES的個案資料，搭配Decipher線上資料庫，探討是否可以偵測SNV及small indel之外的拷貝數異常(CNV)，並提升基因診斷率。 方法 將WES原始資料以GATK gCNV caller工具產出gCNV檔，利用MViewer篩選>5 Kb並包含Mendeliome基因或OMIM基因的CNV片段，查詢Decipher是否有已知的CNV syndrome與該片段重疊，並篩選每段CNV是否帶有高pLI/pHaplo/pTriplo值的Mendeliome或OMIM基因。最後比對高pLI/pHaplo/pTriplo值的Mendeliome或OMIM基因之表現型，嘗試找出與個案表現型符合的致病CNV片段，並計算診斷率。 結果 在130位再次分析的個案中，共有5位利用Exome CNV找到CNV syndrome或致病CNV(包含Klinefelter syndrome、Vissers-Bodmer syndrome、1q21.1 recurrent microdeletion、17p11.2 duplication syndrome)，針對拷貝數異常的診斷率為3.85%。利用exome CNV，可將WES的診斷率自44.62提升至47.69，共3.07%。 結論 Exome CNV可以成功利用WES原始資料偵測拷貝數異常，搭配Decipher資料庫參考pLI/pHaplo/pTriplo值及Mendeliome基因、OMIM基因之表現型，可以提高WES的基因診斷率。然而，本研究流程仍需要更多個案數及驗證。

Background Genetic variations bring many clinical diseases, ranging from single nucleotide variation (SNV), small indel to copy number variation or chromosomal diseases. Genetic testing should assess all levels of variations to make precise genetic diagnosis. WES brings much information about SNV and small indel, which is also able to evaluate copy number variation by analyzing reads of coverage (exome CNV). Aim Using exome CNV to re-analyze possible pathogenic CNV from the WES cohort, and calculate the genetic yields of WES and exome CNV. Methods Total 130 cases were enrolled in the study. We reviewed all the CNVs from the 130 cases that are larger than 5 Kb and containing Mendeliome genes or OMIM genes. The pathogenic CNV was filtered out if compatible with CNV syndrome reported on Decipher, or had genes with high pLI/pHaplo/pTriplo values and similar phenotypes. The diagnostic rate of exome CNV was presented. Results 6 of 130 cases were found having pathogenic CNV from exome CNV, including Klinefelter syndrome, Vissers-Bodmer syndrome, 1q21.1 recurrent microdeletion and 17p11.2 duplication syndrome. The diagnostic rate of exome CNV was 3.85%. By adding exome CNV, the diagnostic yield of WES improved to 47.69% from 44.62%. Conclusions Exome CNV can detect pathogenic CNV and improve diagnostic rate of WES by 3.06%. However, further study that enrolls more cases is needed to complete validation.