In This Section      
 

PulmZoom

Genes:
See test page

Mucociliary disorders
Genes:
ARMC4, CFAP298, CFAP300, CCDC103, CCDC114, CCDC151, CCDC39, CCDC40, CCDC65, CCNO, CFTR, DNAAF1, DNAAF2, DNAAF3, DNAAF4, DNAAF5, DNAH1, DNAH9, DNAH11, DNAH5, DNAH8, DNAI1, DNAI2, DNAJB13, DNAL1, DRC1, GAS8, HYDIN, LRRC6, MCIDAS, NME8, OFD1, PIH1D3, RPGR, RSPH1, RSPH3, RSPH4A, RSPH9, SCNN1A, SCNN1B, SCNN1G, SPAG1, SPZ1, TTC25, ZMYND10

Interstitial lung disease
Genes:
ABCA3, AP3B1, COPA, CSF2RA, CSF2RB, DKC1, ELMOD2, FLCN, FLNA, FOXF1, GATA2, GBA, HPS1, HPS4, IDUA, MARS, NAF1, NF1, NKX2-1, NPC2, OAS1, PARN, RTEL1, SFTPA1, SFTPA2, SFTPB, SFTPC, SLC34A2, SLC7A7, SMPD1, STAT3, TERC, TERT, TINF2, TMEM173, TSC1, TSC2

Pulmonary vascular disorders
Genes: ACVRL1, BMPR1B, BMPR2, CA12, CAV1, COL1A1, COL3A1, EIF2AK4, ENG, FBN1, FOXF1, GDF2, KCNA5, KCNK3, RASA1, SMAD9

Test Information

Test Method

DNA extraction (if applicable) and ultrasonic fragmentation; targeted capture of the coding regions and intron/exon boundaries of protein coding RefSeq genes using the Agilent Clinical Research Exome kit; next generation sequencing (NGS) on an Illumina HiSeq 2500 instrument; alignment to the human reference genome (GRCh37/hg19) using the Burrows-Wheeler Aligner (bwa); variant calling using GATK; Sanger sequencing to confirm low quality and/or complex indel variants related to the specified phenotype(s); Review of sequence data for the specified genes by multiple staff members; Variant classification following ACMG criteria (if applicable). Bioinformatic analysis was performed using DDL pipeline DDL.CRExome.v1.2018_04_18.

Clinical Utility

Discrimination between multiple inherited disorders that can cause diffuse lung disease; identification of causative mutations in complex cases that span multiple phenotypes; facilitation of targeted carrier or presymptomatic testing of relatives of proband and/or predictive prenatal testing.

Clinical Sensitivity

The detection rate for the PulmZoom panel is undetermined at this point, due to ongoing research in the field.

Analytic Sensitivity

>99% for single nucleotide and >92% for small insertion/deletion variants for the nucleotides evaluated. Lower limit of detection: Single nucleotide variants: 25% allele frequency (>96% sensitivity), Small insertion/deletion variants: 50% allele frequency (>94% sensitivity). This test is not validated to identify deletions/insertions of greater than 20bp, copy number changes, nucleotide repeat expansions, mitochondrial DNA variants or mosaicism. Disease-associated variants in regions that are not captured and/or sufficiently sequenced will not be detected by this assay.

Sample Requirements

3-6ml whole blood in EDTA (purple topped) tubes
Saliva collected in an appropriate collection device (Oragene®-DNA 500 or 600 device)
DNA extracted from fibroblast or lymphocyte cell line (must be extracted in a CLIA-certified laboratory)

Turn Around Time

6-8 weeks

Fee and CPT Codes

Exome Panel: $2915
CPT Code: 81479
*If you are a provider outside of Johns Hopkins we are only accepting institutional billing