Accurate genetic diagnosis of Finnish pulmonary arterial hypertension patients using oligonucleotide‐selective sequencing

Abstract

The genetic basis of pulmonary arterial hypertension (PAH) among Finnish PAH patients is poorly understood. We adopted a novel-targeted next-generation sequencing (NGS) approach called Oligonucleotide-Selective Sequencing (OS-Seq) and developed a custom data analysis and interpretation pipeline to identify pathogenic base substitutions, insertions, and deletions in seven genes associated with PAH (BMPR2, BMPR1B, ACVRL1, ENG, SMAD9, CAV1, and KCNK3) from Finnish PAH patients. This study represents the first clinical study with OS-Seq technology on patients suffering from a rare genetic disorder. We analyzed DNA samples from 21 Finnish PAH patients, whose BMPR2 and ACVRL1 mutation status had been previously studied using Sanger sequencing. Our sequencing panel covered 100% of the targeted base pairs with >15× sequencing depth. Pathogenic base substitutions were identified in the BMPR2 gene in 29% of the Finnish PAH cases. Two of the pathogenic variant-positive patients had been previously tested negative using Sanger sequencing. No clinically significant variants were identified in the six other PAH genes. Our study validates the use of targeted OS-Seq for genetic diagnostics of PAH and revealed pathogenic variants that had been previously missed using Sanger sequencing.

Whole‐exome sequencing improves genetic testing accuracy in pulmonary artery hypertension

“…Human error is also increased especially when interpreting the raw sequencing results due to ambiguities in the capillary electrophoresis readouts. 13 This factor could have caused the failure to identify the mutation site (c.76 + 1 G > C). Artifact misjudgment should be minimized, but it cannot be completely avoided.…”

“…12 With the advent of NGS, more and more studies have made a comparison of NGS with Sanger sequencing in various diseases. [13][14][15] However, few studies have directly compared the accuracy of WES with Sanger sequencing in PAH. The aim of the present study is to evaluate whether WES can provide more accurate results (defined by fewer false-negative/-positive results) than Sanger sequencing in the routine genetic testing of BMPR2 in PAH patients.…”

Genetic testing and blood biomarkers in paediatric pulmonary hypertension. Expert consensus statement on the diagnosis and treatment of paediatric pulmonary hypertension. The European Paediatric Pulmonary Vascular Disease Network, endorsed by ISHLT and DGPK

“…In current PAH guidelines, brain natriuretic peptide (BNP) and N-terminal fragment of pro-BNP (NT-proBNP) have been recommended 19. Other prognostic markers such as growth differentiation factor-15, osteopontin and red cell distribution width, are considered emerging biomarkers of PAH.…”

New pathogenic variant ofBMPR2in pulmonary arterial hypertension

“…15 With the development of molecular genetics, scholars detect the germline variants of activin A receptor type II-like 1 (ACVRL1), Notch homolog 3(NOTCH3), endoglin (ENG), caveolin 1 (CAV1), potassium channel of subfamily K member 3 (KCNK3),THBS1, and SMAD family members even in a small number of patients with pulmonary arterial hypertension. [16][17][18][19][20][21][22][23][24] In this study, we used next-generation high-throughput sequencing to investigate the genetic background of 7 cases of idiopathic pulmonary arterial hypertension and 34 cases of CHD associated with pulmonary arterial hypertension patients to evaluate the variant frequency of pulmonary arterial hypertension-related genes and provide theoretical basis for screening of patients with pulmonary arterial hypertension further.…”