- Is a 77 gene panel that includes assessment of non-coding variants
Is ideal for clinically complex patients with pulmonary involvement.
The Blueprint Genetics Comprehensive Pulmonology Panel (test code PU0701):
- Blood (min. 1ml) in an EDTA tube
- Extracted DNA, min. 2 μg in TE buffer or equivalent
- Saliva (Oragene DNA OG-500 kit/OGD-500 or OG-575 & OGD-575)
Label the sample tube with your patient's name, date of birth and the date of sample collection.
Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue. Read more about our sample requirements here.
Inherited pulmonary diseases are a group of lung disorders with variable clinical presentation and frequently have significant phenotypic overlap. The diseases can affect the airways (e.g. cystic fibrosis and primary ciliary dyskinesia), parenchyma (pulmonary fibrosis, Birt Hogg Dube syndrome and tuberous sclerosis) and vasculature of the lung. Rare lung diseases generally affect individuals from birth through about age 60. They are in many cases serious, chronic, and can be devastating. Once properly diagnosed, they often require expensive, long-term treatments. The most common genetic respiratory disease is cystic fibrosis. Misdiagnosis can lead to inappropriate care and an increased risk of complications. Genetic diagnostics by NGS offers a rapid approach to correct clinical diagnosis and early and personalized intervention.
Genes in the Comprehensive Pulmonology Panel and their clinical significance
|ABCA3||Interstitial lung disease, Surfactant metabolism dysfunction, pulmonary||AD/AR||11||287|
|ARHGEF1||Idiopathic bronchiectasis, Immunodeficiencies with antibody defects||AR||1|
|C11ORF70||Primary ciliary dyskinesia||AR||5|
|CFTR||Cystic fibrosis, Congenital bilateral absence of the vas deferens||AD/AR||518||1803|
|CHAT||Myasthenic syndrome, congenital||AR||24||73|
|CHRNA1||Myasthenic syndrome, congenital||AD/AR||28||35|
|COLQ||Myasthenic syndrome, congenital||AR||23||67|
|CSF2RA#*||Surfactant metabolism dysfunction, pulmonary||XL||2||17|
|CSF2RB||Surfactant metabolism dysfunction, pulmonary, 5||AR||2||6|
|DKC1||Hoyeraal-Hreidarsson syndrome, Dyskeratosis congenita||XL||48||74|
|DNAH1||Spermatogenic failure 18||AR||15||32|
|DNAH9||Primary ciliary dyskinesia||AR||6|
|EDN3||Hirschsprung disease, Central hypoventilation syndrome, congenital, Waardenburg syndrome||AD/AR||7||21|
|ELMOD2||Familial idiopathic pulmonary fibrosis||AD/AR|
|ELN||Cutis laxa, Supravalvular aortic stenosis||AD||78||113|
|FAM111B*||Hereditary Fibrosing Poikiloderma with Tendon Contracture, Myopathy, and Pulmonary Fibrosis, Lung cancer, familial, susceptibilty to||AD||7||7|
|FBLN5||Cutis laxa, Macular degeneration, age-related||AD/AR||13||22|
|FLCN||Birt-Hogg-Dube syndrome, Pneumothorax, primary spontaneous||AD||154||210|
|FOXF1||Alveolar capillary dysplasia with misalignment of pulmonary veins||AD||10||102|
|GAS2L2||Primary ciliary dyskinesia||AR||3|
|GAS8||Ciliary dyskinesia, primary, 33||AR||4||6|
|ITGA3||Interstitial lung disease with nephrotic syndrome and epidermolysis bullosa||AR||6||11|
|LTBP4||Cutis laxa with severe pulmonary, gastrointestinal, and urinary abnormalities||AR||10||17|
|MCIDAS||Primary ciliary dyskinesia||AR||4||3|
|MECP2||Angelman-like syndrome, Autism, Rett syndrome, Encephalopathy, Mental retardation||XL||506||1039|
|NF1*||Watson syndrome, Neurofibromatosis, Neurofibromatosis-Noonan syndrome||AD||1157||2901|
|NKX2-1||Thyroid cancer, nonmedullary, Choreoathetosis, hypothyroidism, and neonatal respiratory distress, Chorea, hereditary benign||AD||27||137|
|PARN*||Pulmonary fibrosis and/or bone marrow failure, Dyskeratosis congenita||AD/AR||15||29|
|PHOX2B||Central hypoventilation syndrome, congenital, Neuroblastoma, susceptiblity to, Neuroblastoma with Hirschsprung disease||AD||11||86|
|PIH1D3||Ciliary dyskinesia, primary, 36||XL||2||12|
|POLD1||Colorectal cancer, Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome, Idiopathic bronchiectasis, Immunodeficiency||AD/AR||3||31|
|RAPSN||Myasthenic syndrome, congenital||AR||26||58|
|RET||Hirschsprung disease, Central hypoventilation syndrome, congenital, Pheochromocytoma, Medullary thyroid carcinoma, Multiple endocrine neoplasia||AD/AR||122||407|
|RSPH3||Ciliary dyskinesia, primary, 32||AR||7||5|
|RTEL1||Pulmonary fibrosis and/or bone marrow failure, Dyskeratosis congenita||AD/AR||58||51|
|SCN4A||Hyperkalemic periodic paralysis, Myotonia, potassium-aggravated, Paramyotonia congenita, Myasthenic syndrome, congenital, Normokalemic potassium-sensitive periodic paralysis||AD/AR||57||126|
|SCNN1A||Pseudohypoaldosteronism, Bronchiectasis with or without elevated sweat chloride||AD/AR||10||44|
|SCNN1B||Liddle syndrome, Pseudohypoaldosteronism, Bronchiectasis with or without elevated sweat chloride||AD/AR||19||47|
|SFTPA1||Idiopathic pulmonary fibrosis||AD||2|
|SFTPA2||Pulmonary fibrosis, idiopathic||AD||2||5|
|SFTPB||Surfactant metabolism dysfunction, pulmonary||AR||5||28|
|SFTPC||Surfactant metabolism dysfunction, pulmonary||AD||8||82|
|SLC34A2||Pulmonary alveolar microlithiasis||AR||5||19|
|SLC7A7||Lysinuric protein intolerance||AR||55||67|
|STAT3||Hyper-IgE recurrent infection syndrome, Autoimmune disease, multisystem, infantile onset||AD||47||152|
|STK36||Primary ciliary dyskinesia||AR||5|
|STRA6||Microphthalmia, syndromic, Microphthalmia, isolated, with coloboma||AR||22||33|
|TERC||Aplastic anemia, Pulmonary fibrosis and/or bone marrow failure, telomere-related, Dyskeratosis congenita||AD||42||73|
|TERT||Aplastic anemia, Pulmonary fibrosis and/or bone marrow failure, telomere-related, Dyskeratosis congenita||AD/AR||48||156|
|TINF2||Revesz syndrome, Dyskeratosis congenita||AD||25||42|
|TMEM173||STING-associated vasculopathy, infantile-onsent (SAVI)||AD||4||10|
|TSC1||Lymphangioleiomyomatosis, Tuberous sclerosis||AD||177||372|
|TSC2||Lymphangioleiomyomatosis, Tuberous sclerosis||AD||396||1195|
* Some, or all, of the gene is duplicated in the genome. Read more.
# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads), and/or the gene has exons listed under Test limitations section that are not included in the panel as they are not sufficiently covered with high quality sequence reads.
The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)
Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.
Non-coding variants covered by Comprehensive Pulmonology Panel
|Gene||Genomic location HG19||HGVS||RefSeq||RS-number|
Added and removed genes from the panel
|Genes added||Genes removed|
|ARHGEF1 C11ORF70 DNAH9 FAM111B GAS2L2 MCIDAS POLD1 STK36 STRA6 TMEM173|
- CAP accredited laboratory
- CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
- Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
- Careful construction of clinically effective and scientifically justified gene panels
- Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
- Our publicly available analytic validation demonstrating complete details of test performance
- ~2,000 non-coding disease causing variants in our clinical grade NGS assay for panels (please see ‘Non-coding disease causing variants covered by this panel’ in the Panel Content section)
- Our rigorous variant classification scheme
- Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
- Our comprehensive clinical statements
The following exons are not included in the panel as they are not sufficiently covered with high quality sequence reads: CSF2RA (NM_001161530:9). Genes with suboptimal coverage in our assay are marked with number sign (#) and genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. Gene is considered to have suboptimal coverage when >90% of the gene's target nucleotides are not covered at >20x with mapping quality score (MQ>20) reads. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).
- Complex inversions
- Gene conversions
- Balanced translocations
- Mitochondrial DNA variants
- Repeat expansion disorders unless specifically mentioned
- Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).
- Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
- Stretches of mononucleotide repeats
- Indels larger than 50bp
- Single exon deletions or duplications
- Variants within pseudogene regions/duplicated segments
The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.
For additional information, please refer to the Test performance section and see our Analytic Validation.
The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.
Our panels are sectioned from our high-quality, clinical grade NGS assay. Please see our sequencing and detection performance table for details regarding our ability to detect different types of alterations (Table).
Assays have been validated for various sample types including EDTA-blood, isolated DNA (excluding from formalin fixed paraffin embedded tissue), saliva and dry blood spots (filter cards). These sample types were selected in order to maximize the likelihood for high-quality DNA yield. The diagnostic yield varies depending on the assay used, referring healthcare professional, hospital and country. Plus analysis increases the likelihood of finding a genetic diagnosis for your patient, as large deletions and duplications cannot be detected using sequence analysis alone. Blueprint Genetics’ Plus Analysis is a combination of both sequencing and deletion/duplication (copy number variant (CNV)) analysis.
Performance of Blueprint Genetics high-quality, clinical grade NGS sequencing assay for panels.
|Sensitivity % (TP/(TP+FN)||Specificity %|
|Single nucleotide variants||99.89% (99,153/99,266)||>99.9999%|
|Insertions, deletions and indels by sequence analysis|
|1-10 bps||99.2% (7,745/7,806)||>99.9999%|
|11-50 bps||99.13% (2,524/2,546)||>99.9999%|
|Copy number variants (exon level dels/dups)|
|1 exon level deletion (heterozygous)||100% (20/20)||NA|
|1 exon level deletion (homozygous)||100% (5/5)||NA|
|1 exon level deletion (het or homo)||100% (25/25)||NA|
|2-7 exon level deletion (het or homo)||100% (44/44)||NA|
|1-9 exon level duplication (het or homo)||75% (6/8)||NA|
|Simulated CNV detection|
|5 exons level deletion/duplication||98.7%||100.00%|
|Size range (0.1-47 Mb)||100% (25/25)|
|The performance presented above reached by Blueprint Genetics high-quality, clinical grade NGS sequencing assay with the following coverage metrics|
|Mean sequencing depth||143X|
|Nucleotides with >20x sequencing coverage (%)||99.86%|
The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding and regulatory variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases including, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, ordering providers have access to the details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with <20X sequencing depth if applicable. This reflects our mission to build fully transparent diagnostics where ordering providers can easily visualize the crucial details of the analysis process.
We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.
Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.
The final step in the analysis is orthogonal confirmation. Sequence variants classified as pathogenic, likely pathogenic and variants of uncertain significance (VUS) are confirmed using bi-directional Sanger sequencing when they do not meet our stringent NGS quality metrics for a true positive call. Reported heterozygous and homo/hemizygous copy number variations with a size <10 and <3 target exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen and confirmed less than three times at Blueprint Genetics.
Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references, abstracts and variant databases used to help ordering providers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.
Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification. We do not recommend using variants of uncertain significance (VUS) for family member risk stratification or patient management. Genetic counseling is recommended.
Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Our internal database and our understanding of variants and related phenotypes increases with every case analyzed. Our laboratory is therefore well-positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.