| Literature DB >> 33066286 |
Lieke M van den Heuvel1,2,3, Samara M A Jansen4, Suzanne I M Alsters1, Marco C Post5,6, Jasper J van der Smagt3, Frances S Handoko-De Man4, J Peter van Tintelen1,3, Hans Gille1, Imke Christiaans7, Anton Vonk Noordegraaf4, HarmJan Bogaard4, Arjan C Houweling1.
Abstract
Pulmonary arterial hypertension (PAH) is a severe, life-threatening disease, and in some cases is caused by genetic defects. This study sought to assess the diagnostic yield of genetic testing in a Dutch cohort of 126 PAH patients. Historically, genetic testing in the Netherlands consisted of the analysis of BMPR2 and SMAD9. These genes were analyzed in 70 of the 126 patients. A (likely) pathogenic (LP/P) variant was detected in 22 (31%) of them. After the identification of additional PAH associated genes, a next generation sequencing (NGS) panel consisting of 19 genes was developed in 2018. Additional genetic testing was offered to the 48 BMPR2 and SMAD9 negative patients, out of which 28 opted for NGS analysis. In addition, this gene panel was analyzed in 56 newly identified idiopathic (IPAH) or pulmonary veno occlusive disease (PVOD) patients. In these 84 patients, NGS panel testing revealed LP/P variants in BMPR2 (N = 4), GDF2 (N = 2), EIF2AK4 (N = 1), and TBX4 (N = 3). Furthermore, 134 relatives of 32 probands with a LP/P variant were tested, yielding 41 carriers. NGS panel screening offered to IPAH/PVOD patients led to the identification of LP/P variants in GDF2, EIF2AK4, and TBX4 in six additional patients. The identification of LP/P variants in patients allows for screening of at-risk relatives, enabling the early identification of PAH.Entities:
Keywords: BMPR2; EIF2AK4; GDF2; NGS gene panel; TBX4; genetic analysis; pulmonary arterial hypertension
Year: 2020 PMID: 33066286 PMCID: PMC7602048 DOI: 10.3390/genes11101191
Source DB: PubMed Journal: Genes (Basel) ISSN: 2073-4425 Impact factor: 4.096
Figure 1Flow-chart of genetic analyses in idiopathic/pulmonary veno occlusive disease (IPAH/PVOD) patients.
Sociodemographic and clinical characteristics of patients eligible for genetic testing at diagnosis.
| All Patients | No LP/P Variant | LP/P Variant | ||
|---|---|---|---|---|
| Characteristic | ||||
| Sex | ||||
| Female | 89 (71) | 66 (70) | 23 (72) | 0.922 |
| Male | 37 (29) | 28 (30) | 9 (28) | |
| Age at diagnosis, years | 49 ± 16 | 52 ± 17 | 37 ± 13 | 0.001 |
| Clinical diagnosis b | ||||
| IPAH | 114 (90) | 84 (89) | 30 (94) | 0.031 |
| PVOD | 12 (10) | 10 (11) | 2 (6) | |
| NYHA functional class | ||||
| NYHA I-II | 36 (29) | 25 (29) | 11 (34) | 0.587 |
| NYHA III-IV | 78 (62) | 60 (71) | 18 (56) | |
| BMI, kg/m2 | 26.9 ± 5.2 | 27.0 ± 5.3 | 26.6 ± 5.0 | 0.757 |
| Hemodynamics | ||||
| mPAP, mmHg | 52 ± 17 | 50 ± 17 | 59 ± 14 | 0.008 |
| PVR, WU | 9.9 (5.7–12.7) | 8.8 (4.8–12.2) | 11.9 (9.2–15.2) | 0.022 |
| mRAP, mmHg | 9 (6–11) | 9 (6–11) | 8 (6–11) | 0.214 |
| PCWP, mmHg | 10 ± 3 | 10 ± 3 | 9 ± 3 | 0.039 |
| CI, L/min/m2 | 2.5 ± 0.8 | 2.6 ± 0.8 | 2.2 ± 0.6 | 0.061 |
| RVEDVI, mL/m2 | 84 ± 27 | 82 ± 27 | 90 ± 27 | 0.243 |
| RVESVI, mL/m2 | 53 ± 26 | 50 ± 25 | 64 ± 28 | 0.038 |
| RV EF, % | 38 ± 13 | 41 ± 12 | 30 ± 12 | <0.001 |
| Family history | ||||
| No | 68 (54) | 55 (59) | 13 (41) | 0.025 |
| Yes | 17 (13) | 8 (9) | 9 (28) | |
| Unclear | 31 (25) | 22 (23) | 9 (28) | |
| Unknown | 10 (8) | 9 (10) | 1 (3) | |
| Death | 17 (14) | 11 (12) | 6 (20) | 0.324 |
| Lung transplant | 4 (3) | 4 (4) | 0 (0) | NA c |
| Median FU, years | 3 (0–7) | 2 (0–5) | 6 (2–11) | 0.001 |
Data are given as mean (SD), median (range) or number (percentage). IPAH = Idiopathic pulmonary arterial hypertension; PVOD = pulmonary veno-occlusive disease; NYHA = New York Association functional class; BMI = body mass index; mPAP = mean pulmonary arterial pressure; PVR = pulmonary vascular resistance; mRAP = mean right atrial pressure; RVEF = right ventricular ejection fraction; RDEVI = right ventricular end-diastolic volume index; RVESVI = right ventricular end-systolic volume index. a Not all numbers add up to the total number of patients due to missing values. b Concerns p value of chi-square test performed on difference ‘idiopathic PAH’ versus ‘PVOD’, due to >20% of cells having an expected count less than 5. c Significance testing not possible due to small numbers.
Overview of the detected class 4 and 5 variants in 32 unrelated pulmonary arterial hypertension (PAH) patients.
| Gene | Nucleotide Change | Amino Acid Change | Class | Novel | Reference | Remark Pathogenicity |
|---|---|---|---|---|---|---|
|
| c.40_49del | p. (Phe14Argfs*28) | Class 5 a | No | [ | NA |
|
| c.916G > T | p.(Glu306 *) | Class 4 | Yes | NA | Premature stopcodon; not present in gnomAD and ClinVar |
|
| c.1112del | p.(Pro371Leufs*8) | Class 5 a | No | [ | NA |
|
| c.(?_-1)_(*1_?)del (entire gene) | p.0 | Class 5 | No | [ | NA |
|
| c.(?_-1)_(76 + 1_77-1)del (exon 1) | p.? e | Class 5 | No | [ | |
|
| c.76 + 2T > G | p.? e | Class 5 | No | [ | NA |
|
| c.246A > G | p.(Glu48_Gly83del) (splice defect) | Class 4 | Yes | NA | Defective splice donor site exon 2; use of a cryptic splice donor site in exon 2 (mRNA analysis performed in our lab) |
|
| c.348C > G | p.Cys116Trp | Class 4 | Yes | NA | Variant not present in controls (gnomAD). Highly conserved region; AlignGVGD: class C65; SIFT: deletious; PolyPhen2: probably damaging, score 1.000. Variant not present in ClinVar |
|
| c.350G > C | p.(Cys117Ser) | Class 5 | No | [ | NA |
|
| c.399del | p.(Pro134Leufs*18) | Class 5 | No | [ | NA |
|
| c.619dup | p.(Glu207Glyfs* 13) | Class 5 | No | [ | NA |
|
| c.690del | p.(Val231Cysfs*21) | Class 5 | Yes | [ | NA |
|
| c.852_852 + 1insA | p.(Gly285Argfs*13) | Class 4 | No | [ | NA |
|
| c.994C > T | p.(Arg332 *) | Class 5 | No | [ | NA |
|
| c.1133G > T | p.(Gly378Val) | Class 5 c | No | [ | NA |
|
| c.1217T > G | p.(Met406Arg) | Class 4 | No | [ | NA |
|
| c.1454A > G | p.(Asp485Gly) | Class 5 | No | [ | NA |
|
| c.1459G > T | p.(Asp487Tyr) | Class 4 c | Yes | NA | Not present in controls (gnomAD); Highly conserved region; AlignGVGD: class C65; SIFT: deletious; PolyPhen2: probably damaging, score 1.000. ClinVar: 1 entry, likely pathogenic (VCV000212812.2) |
|
| c.1471C > T | p.(Arg491Trp) | Class 5 | No | [ | NA |
|
| c.1487G > A | p.(Cys496Tyr) | Class 5 | No | [ | NA |
|
| c.1525G > T | p.(Glu509 *) | Class 5 | No | [ | |
|
| c.1978G > T | p.(Glu660 *) | Class 5 | No | [ | |
|
| c.2161C > T | p.(Gln721 *) | Class 5 | Yes | NA | Premature stopcodon. Not present in gnomAD or ClinVar |
|
| c.2752C > T | p.(Gln918 *) | Class 5 | No | [ | |
|
| c.(418 + 1_419-1)_(2866 + 1_2867-1)del | p.? e | Class 5 | No | [ | NA |
|
| c.(529 + 1_530-1)_(967 + 1_968-1)del (exon 5-7) | p.? e | Class 5 | No | [ | NA |
|
| c.(967 + 1_968-1)_(1128 + 1_1129-1)dup (exon 8) | p.(Val377Ilefs*12) | Class 5 | No | [ | A tandem exon duplication was confirmed by Sanger sequencing on cDNA |
|
| c.1739dup | p.(Arg581Glufs*9) | Class 5 d | No | [ | NA |
|
| c.328C > T | p.(Arg110Trp) | Class 4 | No | [ | NA |
|
| c.451C > T | p.(Arg151 *) | Class 4 | No | [ | NA |
NA not applicable. Reference sequences: BMPR2 NM_001204.6; EIF2AK4 NM_001013703.3; GDF2 NM_016204.3 and TBX4 NM_018488.2. a These patients only tested on BMPR2 and SMAD9 were reported previously in Van der Bruggen et al. [23] and/or Girerd et al. [25]. b This patient was previously reported by Gräf et al. [9].c Both parents tested negative for this variant. d Homozygotic. e An effect on the protein level is expected, but it is not possible to give a reliable prediction of the consequences. * Was previously tested on BMPR2/SMAD9.
Figure 2Kaplan–Meier curve for difference in age at diagnosis between patients with and without a LP/P variant.