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NGS Targeted Gene Panels for Genetic Testing of the Respiratory System


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The respiratory system comprises of the respiratory tract and the lung. A number of lung diseases are associated with certain genetic factors. Some of the most common known single gene factorial lung disorders are α1-anti-trypsin deficiency and cystic fibrosis (CF) (CFTR gene).

Other respiratory diseases are caused by environmental and genetic factors and thus are complex or multifactorial disorders. Asthma is one of these complex disorders with different environmental factors influencing the occurrence of the disease and more than 100 candidate genes (identified by genome-wide association studies (GWAS)) that are associated or believed to be associated with the occurrence of asthma. Some genes wherein mutations are associated with asthma are ORMDL3, PDE4D, ADAM33, DPP10, GPR154, PHF11, HLA-G (Putra et al. 2012). 

Another multifactorial disease of the respiratory system is the chronic obstructive pulmonary disease (COPD). Some well described candidate genes wherein mutations are associated with higher risk of COPD occurrence are GSTP1, CHRNA, TNF, EPHX1, and HHIP.

Idiopathic pulmonary fibrosis (IPF) represents a group of different lung diseases. Different genes and genetic factors are discussed wherein mutations are associated with the elevated risk for the occurrence of IPF these are SFTPC, TNF-α, IL-1RN, CR1, ACE, TGF-β1, and TERT as well as the telomere length.

Lung cancer is well described as genetic disease, for more information on lung cancer we refer to the lung cancer NGS panels page.

Host genetic factors can also play a role in respiratory tract infectious diseases, for more information we recommend the review of Patarčić et al.

On this website a number of NGS targeted gene panels for diagnosis or screening of hereditary respiratory disorders are listed. For more information on the targeted genes please contact the corresponding panel provider.

For more information on genetics of the respiratory diseases we recommend the review of Putra et al.


Cystic Fibrosis - NGS Panels

CF AMPLIFIED

CF AMPLIFIED is the most comprehensive test available, detecting ~99% of disease-causing CFTR changes (or mutations), including gross deletions and duplications. Testing begins with CFTR full sequence analysis, which detects 97-98% of mutations. If two pathogenic or likely pathogenic genetic alterations are found in a symptomatic patient, or if one is found on a carrier screen in a patient without symptoms, results are presumed to be informative and no further analysis is performed.
Source: Ambry Genetics

CFTR MASTR™ Dx

The CFTR MASTR™ Dx is a molecular diagnostic assay for identification of sequence variants covering the complete CFTR gene in individuals with increased risk for CF, in CF-carriers or CF-related phenotypes.
Multiplicom’s CFTR MASTR™ Dx assay is provided as a ready-to-use kit that offers robust performance with minimum hands-on time. All reagents necessary to enable multiplex amplification of 48 amplicons (300-450 bp) in two PCR reactions are included, targeting all coding exons, selected intronic regions and part of the promoter region. The assay is validated for DNA derived from whole blood, as well as from dried blood spots. The assay is compatible with all current Massively Parallel Sequencing (MPS) systems, providing the flexibility to choose your preferred method.
Source: Multiplicom

Website


Pulmonology and Respiratory System - NGS Panels

Bronchiectasis NGS Panel

Targeted Genes: CCDC39, CCDC40, CFTR, DNAAF1, DNAAF2, DNAH11, DNAH5, DNAI1, DNAI2, DNAL1, NME8, RSPH4A, RSPH9, SCNN1A, SCNN1B, SCNN1G
Source: Fulgent Diagnostics

Central hypoventilation syndrome panel

Targeted genes: RET, GDNF, EDN3, BDNF, ASCL1, PHOX2A, PHOX2B, ZEB2, GFRA1, ECE1, MECP2

Source: Centogene

Ciliary (primary) dyskinesia panel

Targeted genes: DNAI1, DNAAF2, DNAAF3, DNAAF5, DNAH5, HYDIN, NME8, DNAH11, DNAI2, RSPH4A, RSPH9, DNAAF1, CCDC39, CCDC40, DNAL1, CCDC103, LRRC6, CCDC114

Source: Centogene

Cystic Lung Disease NGS Panel

Targeted Genes: EFEMP2, ELN, FBLN5, FLCN, LTBP4, SERPINA1, TSC1, TSC2
Source: Fulgent Diagnostics

Central Hypoventilation Syndrome NGS Panel

Targeted Genes: ASCL1, BDNF, EDN3, GDNF, PHOX2B, RET
Source: Fulgent Diagnostics

Invitae Pulmonary Arterial Hypertension Panel

This test is for individuals with a clinical diagnosis of pulmonary arterial hypertension (PAH). The primary Invitae Pulmonary Arterial Hypertension Panel includes four genes that are definitively associated with PAH.

In addition to the primary panel, clinicians can also choose to include genes that have limited evidence of association with PAH. At this time, the association of these genes with PAH remains uncertain.
Source: Invitae

Invitae Primary Ciliary Dyskinesia Panel

The Invitae Primary Ciliary Dyskinesia Panel analyzes 30 genes that are associated with primary ciliary dyskinesia (PCD), a condition with phenotypic features that include chronic respiratory tract infections, fertility problems, and a reversal of the internal organs (known as situs inversus). These genes were selected based on the available evidence to date to provide Invitae’s most comprehensive test for PCD.
Source: Invitae

Lung Disorders NGS Panel

Targeted Genes: (51) ABCA3, ACVRL1, AP3B1, ASCL1, BDNF, BLOC1S3, BLOC1S6, BMPR2, CCDC39, CCDC40, CFTR, DNAAF1, DNAAF2, DNAH11, DNAH5, DNAI1, DNAI2, DNAL1, DTNBP1, EDN3, EFEMP2, ELN, ENG, FBLN5, FLCN, GDNF, HPS1, HPS3, HPS4, HPS5, HPS6, LTBP4, MUC5B, NME8, PHOX2B, RET, RSPH4A, RSPH9, SCNN1A, SCNN1B, SCNN1G, SERPINA1, SFTPA1, SFTPA2, SFTPB, SFTPC, SMAD9, TERC, TERT, TSC1, TSC2
Source: Fulgent Diagnostics

Primary ciliary dyskinesia (NGS panel)

Targeted genes (27): ARMC4, C21orf59, CCDC103, CCDC114, CCDC39, CCDC40, CCDC65, CCNO, DNAAF1, DNAAF2, DNAAF3, DNAH11, DNAH5, DNAI1, DNAI2, DNAL1, DRC1, DYX1C1, HEATR2, HYDIN, LRRC6, NME8, RSPH1, RSPH4A, RSPH9, SPAG1, ZMYND10

Source: CGC Genetics

PRIMARY CILIARY DYSKINESIA TESTING

Primary ciliary dyskinesia (PCD) is a disorder of the lungs and other body systems.
Ambry’s PCD and Related Disorders Panel includes analysis of DNAI1, DNAI2, DNAH5, DNAH11, NME8 (formerly TXNDC3), RSPH4A, RSPH9, DNAAF1, DNAAF (autosomal genes),7-12 as well as RPGR and OFD (X-linked genes).13,14 In addition to these genes, CFTR has been added to the panel due to the relatively high incidence of cystic fibrosis (CF) in people with ciliary dysfunction and the phenotypic overlap between PCD and CF.
Source: Ambry Genetics

Pulmonary Arterial Hypertension (PAH) Panel

Pulmonary Arterial Hypertension (PAH) Panel, Sequencing and Deletion/Duplication, Multigene
Preferred test to confirm diagnosis of pulmonary arterial hypertension (PAH), especially in those with known family history.
Genes tested: ACVRL1/ALK1, BMPR2, CAV1, EIF2AK4, ENG, KCNK3
Source: Arup Laboratories

Pulmonary Arterial Hypertension Panel

Targeted genes: ACVRL1 (ALK1), BMPR2, CAV1, ENG, SMAD9

Source: GeneDx

Pulmonary surfactant metabolism dysfunction (NGS panel)

Targeted genes: ABCA3, CSF2RA, CSF2RB, SFTPA1, SFTPB,SFTPC, SFTPD

Source: CGC Genetics

SURFACTANT DYSFUNCTION TESTING

Genetic disorders of surfactant dysfunction are lung disorders that can cause breathing problems that vary widely in severity. Often times, these concerns can impact infants immediately after birth; they can benefit from a quick and accurate diagnosis to help direct clinical care.
Ambry Genetics offers gene sequencing of the three most common genes involved in inherited surfactant dysfunction. These may be ordered individually or concurrently as a panel. A quick and accurate diagnosis to help target medical treatment and care.
Source: Ambry Genetics


Putra A, Tanimotoa K, Syahruddin E, Andarini S, Hosoi Y, and Hiyama K (2012) A step forward into respiratory genetics: overview contribution of genetics in respiratory diseases |Asian Biomedicine |

Patarčić I, Gelemanović A, Kirin M, Kolčić I, Theodoratou E,
Baillie K, de Jong M, Rudan I, Campbell H and Polašek O (2015) The role of host genetic factors in respiratory tract infectious diseases: systematic review, meta-analyses and field synopsis |Nature |


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