McInerney-Leo Aideen M, Marshall Mhairi S, Gardiner Brooke, Coucke Paul J, Van Laer Lut, Loeys Bart L, Summers Kim M, Symoens Sofie, West Jennifer A, West Malcolm J, Paul Wordsworth B, Zankl Andreas, Leo Paul J, Brown Matthew A, Duncan Emma L
The University of Queensland Diamantina Institute, Translational Research Institute, Princess Alexandra Hospital , Brisbane, Queensland, Australia.
Medical Genetics, The University Hospital Ghent , Gent, Belgium.
Bonekey Rep. 2013 Dec 4;2:456. doi: 10.1038/bonekey.2013.190. eCollection 2013.
Osteogenesis imperfecta (OI) and Marfan syndrome (MFS) are common Mendelian disorders. Both conditions are usually diagnosed clinically, as genetic testing is expensive due to the size and number of potentially causative genes and mutations. However, genetic testing may benefit patients, at-risk family members and individuals with borderline phenotypes, as well as improving genetic counseling and allowing critical differential diagnoses. We assessed whether whole exome sequencing (WES) is a sensitive method for mutation detection in OI and MFS. WES was performed on genomic DNA from 13 participants with OI and 10 participants with MFS who had known mutations, with exome capture followed by massive parallel sequencing of multiplexed samples. Single nucleotide polymorphisms (SNPs) and small indels were called using Genome Analysis Toolkit (GATK) and annotated with ANNOVAR. CREST, exomeCopy and exomeDepth were used for large deletion detection. Results were compared with the previous data. Specificity was calculated by screening WES data from a control population of 487 individuals for mutations in COL1A1, COL1A2 and FBN1. The target capture of five exome capture platforms was compared. All 13 mutations in the OI cohort and 9/10 in the MFS cohort were detected (sensitivity=95.6%) including non-synonymous SNPs, small indels (<10 bp), and a large UTR5/exon 1 deletion. One mutation was not detected by GATK due to strand bias. Specificity was 99.5%. Capture platforms and analysis programs differed considerably in their ability to detect mutations. Consumable costs for WES were low. WES is an efficient, sensitive, specific and cost-effective method for mutation detection in patients with OI and MFS. Careful selection of platform and analysis programs is necessary to maximize success.
成骨不全症（OI）和马凡综合征（MFS）是常见的孟德尔遗传病。这两种病症通常通过临床诊断，因为由于潜在致病基因和突变的大小及数量，基因检测费用高昂。然而，基因检测可能使患者、高危家庭成员和具有临界表型的个体受益，同时改善遗传咨询并有助于进行关键的鉴别诊断。我们评估了全外显子组测序（WES）是否是检测OI和MFS突变的灵敏方法。对13名已知患有OI的参与者和10名已知患有MFS的参与者的基因组DNA进行了WES，先进行外显子捕获，然后对多重样本进行大规模平行测序。使用基因组分析工具包（GATK）调用单核苷酸多态性（SNP）和小插入缺失，并使用ANNOVAR进行注释。使用CREST、exomeCopy和exomeDepth检测大片段缺失。将结果与先前的数据进行比较。通过筛查来自487名个体的对照人群的WES数据中COL1A1、COL1A2和FBN1的突变来计算特异性。比较了五个外显子捕获平台的目标捕获情况。在OI队列中的所有13个突变以及MFS队列中的9/10个突变均被检测到（灵敏度=95.6%），包括非同义SNP、小插入缺失（<10 bp）以及一个大的UTR5/外显子1缺失。由于链偏倚，GATK未检测到一个突变。特异性为99.5%。捕获平台和分析程序在检测突变的能力上有很大差异。WES的耗材成本较低。WES是一种用于检测OI和MFS患者突变的高效、灵敏、特异且具有成本效益的方法。仔细选择平台和分析程序对于实现最大成功率是必要的。
