Interstitial Lung Disease Panel

Summary and Pricing

Test Method

Exome Sequencing with CNV Detection
Test Code Test Copy Genes Gene CPT Codes Copy CPT Codes
5211 ABCA3 81479,81479 Order Options and Pricing
CFTR 81223,81222
CSF2RB 81479,81479
DKC1 81479,81479
FLCN 81479,81479
HPS1 81479,81479
HPS4 81479,81479
ITGA3 81479,81479
NF1 81408,81479
NKX2-1 81479,81479
PARN 81479,81479
RTEL1 81479,81479
SFTPA2 81479,81479
SFTPB 81479,81479
SFTPC 81479,81479
SLC34A2 81479,81479
SLC7A7 81479,81479
SMPD1 81479,81479
STAT3 81479,81479
TERC 81479,81479
TERT 81479,81479
TINF2 81479,81479
TSC1 81406,81405
TSC2 81407,81406
Test Code Test Copy Genes Panel CPT Code Gene CPT Codes Copy CPT Code Base Price
5211Genes x (24)81479 81222, 81223, 81405, 81406, 81407, 81408, 81479 $1210 Order Options and Pricing

Pricing Comments

We are happy to accommodate requests for testing single genes in this panel or a subset of these genes. The price will remain the list price. If desired, free reflex testing to remaining genes on panel is available. Alternatively, a single gene or subset of genes can also be ordered via our PGxome Custom Panel tool.

An additional 25% charge will be applied to STAT orders. STAT orders are prioritized throughout the testing process.

For Reflex to PGxome pricing click here.

Turnaround Time

18 days on average for standard orders or 14 days on average for STAT orders.

Once a specimen has started the testing process in our lab, the most accurate prediction of TAT will be displayed in the myPrevent portal as an Estimated Report Date (ERD) range. We calculate the ERD for each specimen as testing progresses; therefore the ERD range may differ from our published average TAT. View more about turnaround times here.

Targeted Testing

For ordering sequencing of targeted known variants, go to our Targeted Variants page.

EMAIL CONTACTS

Genetic Counselors

Geneticist

Clinical Features and Genetics

Clinical Features

Interstitial lung diseases (ILDs), or diffuse parenchymal lung diseases, are a heterogeneous group of disorders that affect the tissue and spaces between the air sacs of the lungs (the interstitium). They include over 200 different pulmonary disorders (Schraufnagel 2010). ILDs can be associated with disorders that primarily affect the lung as well as systemic disorders affecting multiple organs. Many of the ILDs cause thickening of the interstitium due to inflammation, scarring (fibrosis), or edema, thus leading to irreversible architectural distortion and impaired gas exchange. The most common ILD is idiopathic pulmonary fibrosis (IPF) that can cluster in families and often defined as familial pulmonary fibrosis. Patients affected by ILD usually present with shortness of breath which may get worse over time. Other symptoms include dry cough and weight loss (Devine et al. 2012).

Genetics

Idiopathic pulmonary fibrosis (IPF), the most common interstitial lung disease (ILD), has been associated with pathogenic variants in genes encoding telomerases (TERT, TERC). These pathogenic variants lead to telomerase dysfunction, impaired maintenance of telomeres, and reduced telomere length. Surfactant protein-associated genes SFTPC, SFTPA2, ABCA3 and CSF2RB are also found in cases with idiopathic pulmonary fibrosis. Autosomal dominant pathogenic variants in four genes (TERT, TERC, SFTPC, and SFTPA2) are known to count for ~15% of cases with familial pulmonary fibrosis (Talbert et al. 2015). Moreover, this panel contains a substantial set of other genes associated with syndromes that may also present with interstitial lung disease (Devine et al. 2012). The FLCN, NF1, NKX2-1, PARN, SFTPA2, SFTPC, TERC, TINF2, TSC1, TSC2 and STAT3 genes are associated with autosomal dominant pulmonary disorders. The ABCA3, CFTR, CSF2RB, HPS1, HPS4, ITGA3, SFTPB, SLC7A7, SLC34A2, and SMPD1 genes are associated with autosomal recessive disorders. The DKC1 gene is associated with X-linked recessive disorders. The TERT and RTEL1 gene are associated with both autosomal dominant or recessive disorders. See individual gene test descriptions for information on molecular biology of gene products.

Phenotypes covered by this panel include:

Dyskeratosis congenita: DKC1, TERC, TERT, TINF2, RTEL1

Familial Pulmonary Fibrosis: TERT, TERC, SFTPA2, RTEL1, PARN

Neurofibromatosis, type I: NF1

Tuberous Sclerosis: TSC1, TSC2

Birt-Hogg-Dubé Syndrome: FLCN

Hyper IgE syndrome: STAT3

Cystic Fibrosis: CFTR

Hermansky-Pudlak syndrome: HPS1, HPS4

Niemann-Pick disease, type B: SMPD1

Lysinuric Protein Intolerance: SLC7A7

Surfactant metabolism dysfunction: SFTPB, SFTPC, ABCA3, CSF2RB

Pulmonary Alveolar Microlithiasis: SLC34A2, ITGA3

Congenital Interstitial lung disease with Nephrotic syndrome and Epidermolysis Bullosa: ITGA3

Choreoathetosis, hypothyroidism, and neonatal respiratory distress: NKX2-1

Clinical Sensitivity - Sequencing with CNV PGxome

This multi-gene panel analyzes 24 genes associated with disorders that primarily affect the lung as well as systemic disorders affecting multiple organs. The clinical sensitivity for this test is hard to predict at this time, but it should detect causative variants in ~15-20% of familial pulmonary fibrosis patients (Diaz de Leon et al. 2011; Garcia et al. 2011; van Moorsel et al. 2010).

Gross deletions or duplications have been reported in ABCA3, DKC1, FLCN, NF1,NKX2-1, PARN, SFTPB, SFTPC,SLC7A7, SLC34A2 TERC,TERT, TSC1, and TSC2 (Human Gene Mutation Database). Overall clinical sensitivity is difficult to predict due to the paucity of documented cases, but is expected to be low.

Testing Strategy

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 98.9% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as >20X NGS reads or Sanger sequencing.

Genes without complete coverage: CFTR, DKC1, NF1, SLC34A2, SMPD1, TERT, and TSC2. A full list of regions not covered by NGS or Sanger sequencing is available upon request.

Since this test is performed using exome capture probes, a reflex to any of our exome based tests is available (PGxome, PGxome Custom Panels).

Indications for Test

This test is recommended for individuals with clinical suspicion of familial idiopathic pulmonary fibrosis or other interstitial pulmonary diseases.

Genes

Official Gene Symbol OMIM ID
ABCA3 601615
CFTR 602421
CSF2RB 138981
DKC1 300126
FLCN 607273
HPS1 604982
HPS4 606682
ITGA3 605025
NF1 613113
NKX2-1 600635
PARN 604212
RTEL1 608833
SFTPA2 178642
SFTPB 178640
SFTPC 178620
SLC34A2 604217
SLC7A7 603593
SMPD1 607608
STAT3 102582
TERC 602322
TERT 187270
TINF2 604319
TSC1 605284
TSC2 191092
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Related Test

Name
PGxome®

Citations

  • Devine M.S., Garcia C.K. 2012. Clinics in Chest Medicine. 33: 95-110. PubMed ID: 22365249
  • Diaz de Leon A. et al. 2011. Chest. 140: 753-763. PubMed ID: 21349926
  • Garcia C.K. 2011. Proceedings of the American Thoracic Society. 8: 158-62. PubMed ID: 21543794
  • Human Gene Mutation Database (Bio-base).
  • Schraufnagel D. 2010. American Thoracic Society.
  • Talbert J.L.. et al. 2015. Pulmonary Fibrosis, Familial. In: Pagon RA, Adam MP, Bird TD, Dolan CR, Fong C-T, and Stephens K, editors. GeneReviews™, Seattle (WA): University of Washington, Seattle. PubMed ID: 20301408
  • van Moorsel C.H. et al. 2010. American Journal of Respiratory and Critical Care Medicine. 182: 1419-25. PubMed ID: 20656946

Ordering/Specimens

Ordering Options

We offer several options when ordering sequencing tests. For more information on these options, see our Ordering Instructions page. To view available options, click on the Order Options button within the test description.

myPrevent - Online Ordering

  • The test can be added to your online orders in the Summary and Pricing section.
  • Once the test has been added log in to myPrevent to fill out an online requisition form.

Requisition Form

  • A completed requisition form must accompany all specimens.
  • Billing information along with specimen and shipping instructions are within the requisition form.
  • All testing must be ordered by a qualified healthcare provider.

For Requisition Forms, visit our Forms page


Specimen Types

Specimen Requirements and Shipping Details

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ORDER OPTIONS

View Ordering Instructions

1) Select Test Type


2) Select Additional Test Options

STAT and Prenatal Test Options are not available with Patient Plus.

No Additional Test Options are available for this test.

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