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Interstitial Lung Disease Sequencing Panel
- Summary and Pricing
- Clinical Features and Genetics
- Citations
- Methods
- Ordering/Specimens
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TEST METHODS
Sequencing
| Test Code | Test | CPT Code Copy CPT Codes | |
|---|---|---|---|
| 5211 | ABCA3 | 81479 | Add |
| CFTR | 81223 | ||
| CSF2RB | 81479 | ||
| DKC1 | 81479 | ||
| FLCN | 81479 | ||
| HPS1 | 81479 | ||
| HPS4 | 81479 | ||
| ITGA3 | 81479 | ||
| NF1 | 81408 | ||
| NKX2-1 | 81479 | ||
| PARN | 81479 | ||
| RTEL1 | 81479 | ||
| SFTPA2 | 81479 | ||
| SFTPB | 81479 | ||
| SFTPC | 81479 | ||
| SLC34A2 | 81479 | ||
| SLC7A7 | 81479 | ||
| SMPD1 | 81479 | ||
| STAT3 | 81479 | ||
| TERC | 81479 | ||
| TERT | 81479 | ||
| TINF2 | 81479 | ||
| TSC1 | 81406 | ||
| TSC2 | 81407 | ||
| Full Panel Price* | $1770.00 | ||
| Test Code | Test | Total Price | CPT Codes Copy CPT Codes | |
|---|---|---|---|---|
| 5211 | Genes x (24) |
$1770.00 | 81223, 81406, 81407, 81408, 81479(x20) | Add |
Pricing Comment
If you would like to order a subset of these genes contact us to discuss pricing.
Targeted Testing
For ordering targeted known variants, please proceed to our Targeted Variants landing page.
Turnaround Time
The great majority of tests are completed within 28 days.
Clinical Sensitivity
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).
Deletion/Duplication Testing via aCGH
| Test Code | Test | Individual Gene Price | CPT Code Copy CPT Codes | |
|---|---|---|---|---|
| 600 | ABCA3 | $690.00 | 81479 | Add |
| CFTR | $690.00 | 81222 | ||
| DKC1 | $690.00 | 81479 | ||
| FLCN | $690.00 | 81479 | ||
| HPS1 | $690.00 | 81479 | ||
| HPS4 | $690.00 | 81479 | ||
| ITGA3 | $690.00 | 81479 | ||
| NF1 | $540.00 | 81479 | ||
| NKX2-1 | $690.00 | 81479 | ||
| SFTPB | $690.00 | 81479 | ||
| SFTPC | $690.00 | 81479 | ||
| SMPD1 | $690.00 | 81479 | ||
| STAT3 | $690.00 | 81479 | ||
| TERT | $690.00 | 81479 | ||
| TINF2 | $690.00 | 81479 | ||
| TSC1 | $540.00 | 81405 | ||
| TSC2 | $540.00 | 81406 | ||
| Full Panel Price* | $1290.00 | |||
| Test Code | Test | Total Price | CPT Codes Copy CPT Codes | |
|---|---|---|---|---|
| 600 | Genes x (17) |
$1290.00 | 81222, 81405, 81406, 81479(x14) | Add |
Pricing Comment
NF1, TSC1, and TSC2 are analyzed by Multiplex Ligation-dependent Probe Amplification.
Turnaround Time
The great majority of tests are completed within 28 days.
Clinical Sensitivity
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.
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
Testing Strategy
For this Next Generation Sequencing (NGS) test, sequencing is accomplished by capturing specific regions with an optimized solution-based hybridization kit, followed by massively parallel sequencing of the captured DNA fragments. Additional Sanger sequencing is performed for regions not captured or with insufficient number of sequence reads. All reported pathogenic, likely pathogenic, and variants of uncertain significance are confirmed by Sanger sequencing.
For Sanger sequencing, polymerase chain reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.
This panel provides at least 98.15% coverage of all coding exons of the genes listed, plus ~20 bases of flanking noncoding DNA. We define coverage as >20X NGS reads for coding regions and 0-10 bases of flanking DNA, >10X NGS reads for 11-20 bases of flanking DNA, 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.
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 |
Diseases
Related Tests
CONTACTS
Genetic Counselors
- Genetic Counselor Team - clinicaldnatesting@preventiongenetics.com
Geneticist
- Fang Xu, PhD, FACMG - fang.xu@preventiongenetics.com
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
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TEST METHODS
NextGen Sequencing
Test Procedure
We use a combination of Next Generation Sequencing (NGS) and Sanger sequencing technologies to cover the full coding regions of the listed genes plus ~20 bases of non-coding DNA flanking each exon. As required, genomic DNA is extracted from the patient specimen. For NGS, patient DNA corresponding to these regions is captured using an optimized set of DNA hybridization probes. Captured DNA is sequenced using Illumina’s Reversible Dye Terminator (RDT) platform (Illumina, San Diego, CA, USA). Regions with insufficient coverage by NGS are covered by Sanger sequencing. All pathogenic, likely pathogenic, or variants of uncertain significance are confirmed by Sanger sequencing.
For Sanger sequencing, Polymerase Chain Reaction (PCR) is used to amplify targeted regions. After purification of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit. PCR products are resolved by electrophoresis on an ABI 3730xl capillary sequencer. In nearly all cases, cycle sequencing is performed separately in both the forward and reverse directions.
Patient DNA sequence is aligned to the genomic reference sequence for the indicated gene region(s). All differences from the reference sequences (sequence variants) are assigned to one of five interpretation categories, listed below, per ACMG Guidelines (Richards et al. 2015).
(1) Pathogenic Variants
(2) Likely Pathogenic Variants
(3) Variants of Uncertain Significance
(4) Likely Benign Variants
(5) Benign, Common Variants
Human Genome Variation Society (HGVS) recommendations are used to describe sequence variants (http://www.hgvs.org). Rare variants and undocumented variants are nearly always classified as likely benign if there is no indication that they alter protein sequence or disrupt splicing.
Analytical Validity
As of March 2016, 6.36 Mb of sequence (83 genes, 1557 exons) generated in our lab was compared between Sanger and NextGen methodologies. We detected no differences between the two methods. The comparison involved 6400 total sequence variants (differences from the reference sequences). Of these, 6144 were nucleotide substitutions and 256 were insertions or deletions. About 65% of the variants were heterozygous and 35% homozygous. The insertions and deletions ranged in length from 1 to over 100 nucleotides.
In silico validation of insertions and deletions in 20 replicates of 5 genes was also performed. The validation included insertions and deletions of lengths between 1 and 100 nucleotides. Insertions tested in silico: 2200 between 1 and 5 nucleotides, 625 between 6 and 10 nucleotides, 29 between 11 and 20 nucleotides, 25 between 21 and 49 nucleotides, and 23 at or greater than 50 nucleotides, with the largest at 98 nucleotides. All insertions were detected. Deletions tested in silico: 1813 between 1 and 5 nucleotides, 97 between 6 and 10 nucleotides, 32 between 11 and 20 nucleotides, 20 between 21 and 49 nucleotides, and 39 at or greater than 50 nucleotides, with the largest at 96 nucleotides. All deletions less than 50 nucleotides in length were detected, 13 greater than 50 nucleotides in length were missed. Our standard NextGen sequence variant calling algorithms are generally not capable of detecting insertions (duplications) or heterozygous deletions greater than 100 nucleotides. Large homozygous deletions appear to be detectable.
Analytical Limitations
Interpretation of the test results is limited by the information that is currently available. Better interpretation should be possible in the future as more data and knowledge about human genetics and this specific disorder are accumulated.
When Sanger sequencing does not reveal any difference from the reference sequence, or when a sequence variant is homozygous, we cannot be certain that we were able to detect both patient alleles. Occasionally, a patient may carry an allele which does not amplify, due to a large deletion or insertion. In these cases, the report will contain no information about the second allele. Our Sanger and NGS Sequencing tests are generally not capable of detecting Copy Number Variants (CNVs).
We sequence all coding exons for each given transcript, plus ~20 bp of flanking non-coding DNA for each exon. Test reports contain no information about other portions of the gene, such as regulatory domains, deep intronic regions or any currently uncharacterized alternative exons.
In most cases, we are unable to determine the phase of sequence variants. In particular, when we find two likely causative mutations for recessive disorders, we cannot be certain that the mutations are on different alleles.
Our ability to detect minor sequence variants due to somatic mosaicism is limited. Sequence variants that are present in less than 50% of the patient’s nucleated cells may not be detected.
Runs of mononucleotide repeats (eg (A)n or (T)n) with n >8 in the reference sequence are generally not analyzed because of strand slippage during PCR.
Unless otherwise indicated, DNA sequence data is obtained from a specific cell-type (usually leukocytes from whole blood). Test reports contain no information about the DNA sequence in other cell-types.
We cannot be certain that the reference sequences are correct.
Rare, low probability interpretations of sequencing results, such as for example the occurrence of de novo mutations in recessive disorders, are generally not included in the reports.
We have confidence in our ability to track a specimen once it has been received by PreventionGenetics. However, we take no responsibility for any specimen labeling errors that occur before the sample arrives at PreventionGenetics.
Deletion/Duplication Testing Via Array Comparative Genomic Hybridization
Test Procedure
Equal amounts of genomic DNA from the patient and a gender matched reference sample are amplified and labeled with Cy3 and Cy5 dyes, respectively. To prevent any sample cross contamination, a unique sample tracking control is added into each patient sample. Each labeled patient product is then purified, quantified, and combined with the same amount of reference product. The combined sample is loaded onto the designed array and hybridized for at least 22-42 hours at 65°C. Arrays are then washed and scanned immediately with 2.5 µM resolution. Only data for the gene(s) of interest for each patient are extracted and analyzed.
Analytical Validity
PreventionGenetics' high density gene-centric custom designed aCGH enables the detection of relatively small deletions and duplications within a single exon of a given gene or deletions and duplications encompassing the entire gene. PreventionGenetics has established and verified this test's accuracy and precision.
Analytical Limitations
Our dense probe coverage may allow detection of deletions/duplications down to 100 bp; however due to limitations and probe spacing this cannot be guaranteed across all exons of all genes. Therefore, some copy number changes smaller than 100-300 bp within a targeted large exon may not be detected by our array.
This array may not detect deletions and duplications present at low levels of mosaicism or those present in genes that have pseudogene copies or repeats elsewhere in the genome.
aCGH will not detect balanced translocations, inversions, or point mutations that may be responsible for the clinical phenotype.
Breakpoints, if occurring outside the targeted gene, may be hard to define.
The sensitivity of this assay may be reduced when DNA is extracted by an outside laboratory.
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Ordering Options
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.
SPECIMEN TYPES
WHOLE BLOOD
(Delivery accepted Monday - Saturday)
- Collect 3 ml -5 ml (5 ml preferred) of whole blood in EDTA (purple top tube) or ACD (yellow top tube). For Test #500-DNA Banking only, collect 10 ml -20 ml of whole blood.
- For small babies, we require a minimum of 1 ml of blood.
- Only one blood tube is required for multiple tests.
- Ship blood tubes at room temperature in an insulated container. Do not freeze blood.
- During hot weather, include a frozen ice pack in the shipping container. Place a paper towel or other thin material between the ice pack and the blood tube.
- In cold weather, include an unfrozen ice pack in the shipping container as insulation.
- At room temperature, blood specimen is stable for up to 48 hours.
- If refrigerated, blood specimen is stable for up to one week.
- Label the tube with the patient name, date of birth and/or ID number.
DNA
(Delivery accepted Monday - Saturday)
- Send in screw cap tube at least 5 µg -10 µg of purified DNA at a concentration of at least 20 µg/ml for NGS and Sanger tests and at least 5 µg of purified DNA at a concentration of at least 100 µg/ml for gene-centric aCGH, MLPA, and CMA tests, minimum 2 µg for limited specimens.
- For requests requiring more than one test, send an additional 5 µg DNA per test ordered when possible.
- DNA may be shipped at room temperature.
- Label the tube with the composition of the solute, DNA concentration as well as the patient’s name, date of birth, and/or ID number.
- We only accept genomic DNA for testing. We do NOT accept products of whole genome amplification reactions or other amplification reactions.
CELL CULTURE
(Delivery preferred Monday - Thursday)
- PreventionGenetics should be notified in advance of arrival of a cell culture.
- Culture and send at least two T25 flasks of confluent cells.
- Some panels may require additional flasks (dependent on size of genes, amount of Sanger sequencing required, etc.). Multiple test requests may also require additional flasks. Please contact us for details.
- Send specimens in insulated, shatterproof container overnight.
- Cell cultures may be shipped at room temperature or refrigerated.
- Label the flasks with the patient name, date of birth, and/or ID number.
- We strongly recommend maintaining a local back-up culture. We do not culture cells.
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