PulmoGene Panel (64 Genes) Test Details
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Background
The PulmoGene Panel contains 64 pulmonary disease genes that are associated with several defined hereditary syndromes, as well as non-syndromic presentations, including cystic lung disease, bronchiectasis, idiopathic pulmonary fibrosis, and pulmonary hypertension. The PulmoGene Panel uses a combination of next-generation sequencing technology and Sanger sequencing.
Read More...Available Pulmonary Disease Panel Tests
PulmoGene Panel - 64 genes
Gene Information
Read More for expanded gene table.
Read More...Gene | Protein | OMIM# | Locus |
ABCA3 | ATP-Binding Cassette, Sub-Family A (Abc1), Member 3 | 601615 | 16p13.3 |
ACVRL1 | Activin A Receptor Type II-Like 1 | 601284 | 12q13.13 |
AP3B1 | Adaptor-Related Protein Complex 3, Beta 1 Subunit | 603401 | 5q14.1 |
ASCL1 | Achaete-Scute Complex Homolog 1 (Drosophila) | 100790 | 12q23.2 |
BDNF | BDNF Antisense RNA | 611468 | 11p14.1 |
BLOC1S3 | Biogenesis Of Lysosomal Organelles Complex-1, Subunit 3 | 609762 | 19q13.32 |
BLOC1S6 | Biogenesis Of Lysosomal Organelles Complex-1, Subunit 6, Pallidin | 604310 | 15q21.1 |
BMPR2 | Bone Morphogenetic Protein Receptor, Type Ii (Serine/Threonine Kinase) | 600799 | 2q33-q34 |
CCDC39 | Coiled-Coil Domain Containing 39 | 613798 | 3q26.33 |
CCDC40 | Coiled-Coil Domain Containing 40 | 613799 | 17q25.3 |
CFTR | Cystic Fibrosis Transmembrane Conductance Regulator | 602421 | 7q31.2 |
CSF2RA | Colony Stimulating Factor 2 Receptor, Alpha, Low-Affinity (Granulocyte-Macrophage) | 306250 | Xp22.32 |
CSF2RB | Granulocyte-Macrophage Colony-Stimulating Facotr Receptor, Beta | 138981 | 22q12.3 |
DNAAF1 | Dynein, Axonemal, Assembly Factor 1 | 613190 | 16q24.1 |
DNAAF2 | Dynein, Axonemal, Assembly Factor 2 | 612517 | 14q21.3 |
DNAH11 | Dynein, Axonemal, Heavy Chain 11 | 603339 | 7p21 |
DNAH5 | Dynein, Axonemal, Heavy Chain 5 | 603335 | 5p15.2 |
DNAI1 | Dynein, Axonemal, Intermediate Chain 1 | 604366 | 9p13.3 |
DNAI2 | Dynein, Axonemal, Intermediate Chain 2 | 605483 | 17q25 |
DNAL1 | Dynein, Axonemal, Light Chain 1 | 610062 | 14q24.3 |
DOCK8 | Dedicator Of Cytokinesis 8 | 611432 | 9p24.3 |
DTNBP1 | Dystrobrevin-Binding Protein 1 | 607145 | 6p22.3 |
EDN3 | Endothelin 3 | 131242 | 20q13.2-q13.3 |
EFEMP2 | Egf Containing Fibulin-Like Extracellular Matrix Protein 2 | 604633 | 11q13.1 |
ELMOD2 | Elmo/Ced-12 Domain Containing 2 | 610196 | 4q31.1 |
ELN | Elastin | 130160 | 7q11.23 |
ENG | Endoglin | 131195 | 9q34.11 |
FBLN5 | Fibulin 5 | 604580 | 14q32.1 |
FBN1 | Fibrilin 1 | 134797 | 15q21.1 |
FLCN | Folliculin | 607273 | 17p11.2 |
FOXF1 | Forkhead Box F1 | 601089 | 16q24.1 |
GDNF | Glial Cell Derived Neurotrophic Factor | 600837 | 5p13.1-p12 |
HPS1 | Hermansky-Pudlak Syndrome 1 | 604982 | 10q23.1-q23.3 |
HPS3 | Hermansky-Pudlak Syndrome 3 | 606118 | 3q24 |
HPS4 | Hermansky-Pudlak Syndrome 4 | 606682 | 22cen-q12.3 |
HPS5 | Hermansky-Pudlak Syndrome 5 | 607521 | 11p14 |
HPS6 | Hermansky-Pudlak Syndrome 6 | 607522 | 10q24.32 |
HRAS | Harvey RAT Sarcoma Viral Oncogene Homolog | 190020 | 11p15.5 |
LTBP4 | Latent Transforming Growth Factor Beta Binding Protein 4 | 604710 | 19q13.1-q13.2 |
MUC5B | Mucin 5B, Oligomeric Mucus/Gel-Forming | 600770 | 11p15.5 |
NF1 | Neurofibromin 1 | 613113 | 17q11.2 |
NKX2.1 | NK2 Homeobox1 (Thyroid Transcription Factor 1) | 600635 | 14q13.2 |
NME8 | NME/NM23 Family Member 8 | 607421 | 7p14.1 |
PHOX2B | Paired-Like Homeobox 2B | 603851 | 4p12 |
RET | RET Proto-Oncogene | 164761 | 10q11.2 |
RPGR | Retinitis Pigmentosa GTPase Regulator | 312610 | Xp11.4 |
RSPH1 | Radial Spoke Head 1 Homolog (Chlamydomonas) | 609314 | 21q22.3 |
RSPH4A | Radial Spoke Head 4 Homolog A (Chlamydomonas) | 612647 | 6q22.1 |
RSPH9 | Radial Spoke Head 9 Homolog (Chlamydomonas) | 612648 | 6p21.1 |
SCNN1A | Sodium Channel, Nonvoltage-Gated 1 Alpha | 600228 | 12p13 |
SCNN1B | Sodium Channel, Nonvoltage-Gated 1, Beta | 600760 | 16p12.2-p12.1 |
SCNN1G | Sodium Channel, Nonvoltage-Gated 1, Gamma | 600761 | 16p12 |
SERPINA1 | Serpin Peptidase Inhibitor, Clade A (Alpha-1 Antiproteinase, Antitrypsin), Member 1 | 107400 | 14q32.1 |
SFTPA1 | Surfactant Protein A1 | 178630 | 10q22.3 |
SFTPA2 | Surfactant Protein A2 | 178642 | 10q22.3 |
SFTPB | Surfactant Protein B | 178640 | 2p12-p11.2 |
SFTPC | Surfactant Protein C | 178620 | 8p21 |
SFTPD | Surfactant Protein D | 178635 | 10q22.2-q23.1 |
SMAD9 | Smad Family Member 9 | 603295 | 13q12-q14 |
STAT3 | Signal Transducer And Activator Of Transcription 3 (Acute-Phase Response Factor) | 102582 | 17q21.31 |
TERC | Telomerase RNA Component | 602322 | 3q26 |
TERT | Telomerase Reverse Transcriptase | 187270 | 5p15.33 |
TSC1 | Tuberous Sclerosis 1 | 605284 | 9q34 |
TSC2 | Tuberous Sclerosis 2 | 191092 | 16p13.3 |
Methodology
The PulmoGene Panel includes 64 genes: ABCA3, ACVRL1, AP3B1, ASCL1 (excludes exon 1 in NM_004316.3), BDNF, BLOC1S3, BLOC1S6, BMPR2, CCDC39, CCDC40 (excludes exon 18A* in NM_001243342.1), (includes deep intronic c.3718-2477C>T variant, also known as 3849+10kbC>T), CSF2RA (excludes exon 09A* in NM_001161530.1), CSF2RB, DNAAF1, DNAAF2, DNAH11, DNAH5, DNAI1, DNAI2, DNAL1, DOCK8, DTNBP1, EDN3, EFEMP2, ELMOD2, ELN, ENG, FBLN5, FBN1, FLCN, FOXF1, GDNF, HPS1, HPS3, HPS4, HPS5, HPS6, HRAS, LTBP4, MUC5B (only the c.-3133G>T variant is reported), NF1 (excludes exon 15 in NM_001128147.2), NKX2-1, NME8, PHOX2B, RET, RPGR (excludes exons 13 and 15 in NM_001034853.1), RSPH1, RSPH4A, RSPH9, SCNN1A, SCNN1B, SCNN1G, SERPINA1, SFTPA1, SFTPA2, SFTPB, SFTPC, SFTPD, SMAD9, STAT3, TERC, TERT, TSC1, TSC2. *Exon from an alternate transcript. For additional information on reference sequences and exon coverage, please click here.
Read More...This assay is performed using the PerkinElmer Sciclone® G3 Workstation combined with the Agilent SureSelect Clinical Research Exome capture kit (#G9496A 5190-7344; targeting coding regions (exons) and canonical splice sites) followed by sequencing on the Illumina NextSeq 550 (High-Output v2 kit). Reads are aligned to the GRCh37 reference sequence using the Burrows-Wheeler Aligner (BWA 0.7.17), and variant calls are made using the Genomic Analysis Tool Kit (GATK v4.0.3.0). Detection of copy number variants (CNVs) encompassing 2 or more exons is performed using next-generation sequencing read data and the VisCap algorithm. CNV analysis is only performed when data meets necessary quality standards and may not be available for all cases. Variant calls are limited bioinformatically to the associated region of interest for the assay (see above for details). Sanger sequencing is used for fill in when bases have <12x coverage. All clinically significant variants are confirmed by Sanger sequencing or droplet digital PCR; variants classified as likely benign or benign are not confirmed.
Variant classifications are based on ACMG/AMP criteria (Richards et al. 2015) with ClinGen rule specifications (https://www.clinicalgenome.org/working-groups/sequence-variant-interpretation/). Variants are reported according to HGVS nomenclature (www.hgvs.org/mutnomen). Likely benign and benign variants are not included in this report but are available upon request.
This test does not routinely detect variants in non-coding regions (aside from the canonical splice sites), triplet repeat expansions, translocations, inversions, and copy number variants encompassing less than 2 consecutive exons. There is reduced detection for larger indels, variants in low complexity regions, and variants in regions with high homology.
This test was developed, and its performance characteristics determined by the Laboratory for Molecular Medicine at Partners HealthCare Personalized Medicine (LMM, 65 Landsdowne St, Cambridge, MA 02139; 617-768-8500; CLIA#22D1005307). It has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary.
LessAnalytical and Clinical Sensitivity
This test is 99.93% sensitive (95% CI =99.92-99.94%) to detect variants changing a single base and 96.75% sensitive to detect insertion/deletions (95% CI =96.28-97.22%) within covered regions. Technical positive predictive value for single nucleotide variant changes is 99.42% (95% CI = 99.37-99.48%) and 94.16% (95% CI = 93.34-94.97%) for insertion/deletion changes within covered regions. There is demonstrated reduced detection for larger indels, especially in low complexity regions with corresponding low sequence coverage and in regions with high homology.
Given the recent launch of this disease area, the detection rate for the PulmoGene Panel remains unknown at this point.