Targeted Resequencing Reveals Genetic Risks In Patients With Sporadic Idiopathic Pulmonary Fibrosis

Part1:High Rapid Molecular Genetic Diagnosis of Idiopathic Pulmonary Fibrosis by High-Throughput Ampliseq Semiconductor Sequencing Objective: Idiopathic Pulmonary Fibrosis(IPF)is progressive pulmonary interstitial fibrosis of unknown specific causes.Clinically there are no reliable tools to help diagnosisthis disease at the early stage.Once diagnosed,the IPF patients are often with no promising prognosis and a short life expectance.Thus,identify the complex pathogenesis underlying IPF is important to providepersonalized therapies to eachpatients,to realize precise medicine.Methods :We designed a pulmonary fibrosis-associated 92 genes panel(SFTPC,SFTPA1,SFTPA2,MUC5 B,TERC,TERT,RTEL1,PARN,ELMOD2 et al)to sequence 25 clinically diagnosed IPF patients used the Ion torrent High-Throughput Ampliseq Semiconductor Sequencing.Resul:By using the High-Throughput sequencing to sequence the 25 subjects,we got 15 G data in these 92 targeted genes.Totally 15 G data,98.4% average coverage,95762858 total reads(with 71.6 usable reads)were obtained.The mean read length was 157 bp and 1320 fold base mean depth and the uniformity was 81.44%.Conclusions: This study is the first time to perform the High-Throughputsequencing to study idiopathic pulmonary fibrosis.It provides a rapid and reliable,cost-effective genetic diagnosis tool for IPF patients.Part2:Targeted resequencing reveals genetic risks in patients with sporadic idiopathic pulmonary fibrosis.Objective:Idiopathic pulmonary fibrosis(IPF)is a genetic heterogeneous disease with high mortality and poor prognosis.However,a large fraction of genetic cause remains unexplained,especially in sporadic IPF(?80% IPF).Methods:By using the designed 92 pulmonary fibriosis-related gene panel,we sequenced genomic DNAs of 253 sporadic IPF patients and 125 matched health controls based on the targeted massively parallel next-generation sequencing.The identified riskvariants were confirmed by Sanger sequencing.This study aimed to reveal the genetic profile of Chinese IPF patients and find the new pathogenetic locus.Resul:We identified two new identified pathogenic and 10 other loss-of-function(LOF)candidate variants,accounting for 4.74%(12 out of 253)of all the IPF cases.In burden tests,rare missense variants in three genes(CSF3R,DSP,and LAMA3)were identified that have a statistically significant relationship with IPF.Four common SNPs(rs3737002,rs2296160,rs1800470,and rs35705950)were observed to be statistically associated with increased risk of IPF.In the cumulative risk model,high risk subjects had 3.47-fold(95%CI: 2.07-5.81,P = 2.34 × 10-6)risk of developing IPF compared with low risk subjects.Conclusions: We drafted a comprehensive map of genetic risks(including both rare and common candidate variants)in patients with IPF,which could provide insights to help in understanding mechanisms,providing genetic diagnosis,and predicting risk for IPF.