藉由系統性重新分析全外顯子定序之同型合子序列長度以篩選罕見疾病候選基因

Reanalyze exome data to search candidate genes for rare diseases by systemic detection of runs of homozygosity

吳季謙(Chi-Chien Wu)

指導教授 ： 李妮鍾

國立臺灣大學/醫學院/分子醫學研究所/碩士(2022年)

https://doi.org/10.6342/NTU202202378

摘要

背景及目的：同型合子定位(Homozygosity mapping)是偵測人類基因組中連續的同型合子基因型區間(ROH)的有效方法。ROH是重要的遺傳標記，特別是在近親通婚的家族中。近期的研究指出同型合子會增加罹患罕見疾病的風險。本研究的目的是想透過系統性的偵測ROH來重新分析疑似罕見遺傳疾病患者的全外顯子定序(WES)資料，並找出台灣族群的ROH分布模式。
方法：針對來自台大醫院的760名疑似遺傳疾病的患者進行回顧性分析。他們的WES資料是由三種不同的定序平台所分析。我們將使用AutoMap分析軟體來找出個案的ROH區間，ROH在染色體上的分布將透過R語言的detectRUNS及RIdeogram套件來進行視覺化呈現。
結果：全外顯子組的平均ROH大小為82.78 ± 28.52 Mb，個案平均下來會有36.96 ± 7.09個ROH區間。根據近親通婚的分類標準，760名個案在非近親通婚、不確定、可能為近親通婚、近親通婚的百分比(平均大小)分別為0.4% (12.39 ± 3.90 Mb)、46.3% (66.53 ± 10.20 Mb)、50.8% (91.76 ± 9.53 Mb)以及2.5% (212.61 ± 69.40 Mb)。分析後的結果顯示有17名疑似罕見遺傳疾病患者可能是近親通婚的後代，並發現有2名個案是單親源二倍體，其兩條第五號染色體均來自父親或母親。在經過多個篩選步驟後，我們在29名發現候選基因的個案中找到8名個案的致病變異。
結論：透過系統性的偵測ROH區間在臨床上是診斷罕見疾病患者的可行方法。

關鍵字

同型合子定位 ； 同型合子基因型區間 ； 近親通婚 ； 罕見遺傳疾病 ； 單親源二倍體

並列摘要

Background Aim：Homozygosity mapping is a powerful method to detect the regions of consecutive homozygous genotypes, runs of homozygosity (ROH), in a person’s genome. The ROH patterns are crucial genetic marker, especially in consanguinity. Recently, homozygosity has been considered as an increased risk of rare diseases (RDs). Our aim was to reanalyze of whole exome sequencing (WES) data from patients with suspected rare genetic disease by systemic detection of ROH and find the ROH pattern in Taiwanese population.
Method：760 subjects with suspected genetic disorders from National Taiwan University Hospital were retrospectively analyzed. Their genome data was identified by three different exome sequencing platforms. The ROH regions were identified by using the AutoMap software. The visualization of ROH pattern on chromosomes was drawn by using R package detectRUNS and RIdeogram.
Result：Mean homozygousity region size in each exome was 82.78 ± 28.52 Mb, with average 36.96 ± 7.09 homozygous region each individual. Based on classification of consanguineous status, the percentage (mean size) in Non-consanguinity, Uncertain, Probable consanguinity, and Consanguinity were 0.4% (12.39 ± 3.90 Mb), 46.3% (66.53 ± 10.20 Mb), 50.8% (91.76 ± 9.53 Mb), and 2.5% (212.61 ± 69.40 Mb), respectively. The data implied that 17 patients were born of consanguineous union and 2 individuals with isodisomy uniparental disomy on chromosomes 5. After multistep filtering, we identified the disease-causing variant in 8 cases among 29 subjects with candidate genes.
Conclusion：Systemic detection of ROH is a useful tool for diagnosis of RD patients in clinical practice.

並列關鍵字

Homozygosity mapping ； Runs of homozygosity ； Consanguinity ； Rare genetic disease ； Uniparental disomy

參考文獻

1.Richter T, Nestler-Parr S, Babela R, et al. Rare Disease Terminology and Definitions-A Systematic Global Review: Report of the ISPOR Rare Disease Special Interest Group. Value Health 2015;18:906-14.

2.Nguengang Wakap S, Lambert DM, Olry A, et al. Estimating cumulative point prevalence of rare diseases: analysis of the Orphanet database. Eur J Hum Genet 2020;28:165-173.

3.Chien S, Su PH, Chen SJ. Development of genetic counseling services in Taiwan. J Genet Couns 2013;22:839-43.

4.Hsu JC, Wu HC, Feng WC, et al. Disease and economic burden for rare diseases in Taiwan: A longitudinal study using Taiwan's National Health Insurance Research Database. PLoS One 2018;13:e0204206.

5.Griggs RC, Batshaw M, Dunkle M, et al. Clinical research for rare disease: opportunities, challenges, and solutions. Mol Genet Metab 2009;96:20-6.