title: A rapid NGS strategy for comprehensive molecular diagnosis of Birt-Hogg-Dubé syndrome in patients with primary spontaneous pneumothorax.
abstract: Primary spontaneous pneumothorax (PSP) or pulmonary cysts is one of the manifestations of Birt-Hogg-Dube syndrome (BHDS) that is caused by heterozygous mutations in FLCN gene. Most of the mutations are SNVs and small indels, and there are also approximately 10 % large intragenic deletions and duplications of the mutations. These molecular findings are generally obtained by disparate methods including Sanger sequencing and Multiple Ligation-dependent Probe Amplification in the clinical laboratory. In addition, as a genetically heterogeneous disorder, PSP may be caused by mutations in multiple genes include FBN1, COL3A1, CBS, SERPINA1 and TSC1/TSC2 genes. For differential diagnosis, these genes should also be screened which makes the diagnostic procedure more time-consuming and labor-intensive.
  
  
  
  Forty PSP patients were divided into 2 groups. Nineteen patients with different pathogenic mutations of FLCN previously identified by conventional Sanger sequencing and MLPA were included in test group, 21 random PSP patients without any genetic screening were included in blinded sample group. 7 PSP genes including FLCN, FBN1, COL3A1, CBS, SERPINA1 and TSC1/TSC2 were designed and enriched by Haloplex system, sequenced on a Miseq platform and analyzed in the 40 patients to evaluate the performance of the targeted-NGS method.
  
  
  
  We demonstrated that the full spectrum of genes associated with pneumothorax including FLCN gene mutations can be identified simultaneously in multiplexed sequence data. Noteworthy, by our in-house copy number analysis of the sequence data, we could not only detect intragenic deletions, but also determine approximate deletion junctions simultaneously.
  
  
  
  NGS based Haloplex target enrichment technology is proved to be a rapid and cost-effective screening strategy for the comprehensive molecular diagnosis of BHDS in PSP patients, as it can replace Sanger sequencing and MLPA by simultaneously detecting exonic and intronic SNVs, small indels, large intragenic deletions and determining deletion junctions in PSP-related genes.
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China.
authors.forename: Xinxin
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China.
authors.forename: Dehua
authors.initials: D
authors.lastname: Ma
authors.affiliation: Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Zou
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China.
authors.forename: Yibing
authors.initials: Y
authors.lastname: Ding
authors.affiliation: Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China.
authors.forename: Chengchu
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China.
authors.forename: Haiyan
authors.initials: H
authors.lastname: Min
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhang
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China.
authors.forename: Baofu
authors.initials: B
authors.lastname: Chen
authors.affiliation: Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China.
authors.forename: Minhua
authors.initials: M
authors.lastname: Ye
authors.affiliation: Department of Cardiothoracic Surgery, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China.
authors.forename: Minghui
authors.initials: M
authors.lastname: Cai
authors.affiliation: Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, People's Republic of China.
authors.forename: Yanqing
authors.initials: Y
authors.lastname: Pan
authors.affiliation: Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Cao
authors.affiliation: Department of Thoracic Surgery, Nanjing Chest Hospital, Nanjing, People's Republic of China.
authors.forename: Yueming
authors.initials: Y
authors.lastname: Wan
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China.|Nanjing Children's Hospital, Nanjing, People's Republic of China.
authors.forename: Yu
authors.initials: Y
authors.lastname: Jin
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China. qian_gao@nju.edu.cn.|Center for Translational Medicine, Nanjing University Medical School, 22 Hankou Rd, Nanjing, 210093, People's Republic of China. qian_gao@nju.edu.cn.
authors.forename: Qian
authors.initials: Q
authors.lastname: Gao
authors.affiliation: Jiangsu Key Laboratory for Molecular Medicine, Nanjing University Medical School, Nanjing, People's Republic of China. yilong@nju.edu.cn.|Center for Translational Medicine, Nanjing University Medical School, 22 Hankou Rd, Nanjing, 210093, People's Republic of China. yilong@nju.edu.cn.
authors.forename: Long
authors.initials: L
authors.lastname: Yi
mesh_terms: D000328:Adult; D058249:Birt-Hogg-Dube Syndrome / Q000150:complications / Q000175:diagnosis* / Q000235:genetics*; D019295:Computational Biology; D004247:DNA / Q000235:genetics; D005260:Female; D005784:Gene Amplification; D017353:Gene Deletion; D018628:Gene Dosage; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D009154:Mutation / Q000235:genetics; D011030:Pneumothorax / Q000150:complications / Q000175:diagnosis* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D011786:Quality Control; D025521:Tumor Suppressor Proteins / Q000235:genetics*
chemical_list: C476078:FLCN protein, human; D011518:Proto-Oncogene Proteins; D025521:Tumor Suppressor Proteins; D004247:DNA
keywords: BHD syndrome; CNV analysis; FLCN; Primary spontaneous pneumothorax; Targeted next generation sequencing