Cystic Fibrosis Testing

Cystic Fibrosis (CF) affects approximately 30,000 children and adults in the US, and at least eight million Americans are asymptomatic carriers. Ambry Genetics is committed to CF caregivers and patients through diagnostic testing, research services and community involvement.

PrintPrint

Cystic Fibrosis (CF) affects approximately 30,000 children and adults in the US, and at least eight million Americans are asymptomatic carriers. Ambry Genetics is committed to CF caregivers and patients through diagnostic testing, research services and community involvement.

 

CF 102 White Paper

The Ambry lab has analyzed the complete CF gene for more than 35,000 patients, providing the largest single-laboratory result database in the world from which to draw result interpretations.

The CF AMPLIFIED™ is the most comprehensive test available, detecting ~99% of mutations including gross deletions and duplications. The test begins with full gene sequence analysis which detects 97-98% of mutations. If two mutations are detected on a diagnostic test or one mutation detected on a carrier screen, results are presumed to be informative and no further analysis is performed. If results are not informative or if clinical suspicion remains, testing may proceed to gross deletion/duplication analysis as ordered or per request. It can be used for diagnosis in patients with a known or suspected diagnosis of CF, testing newborns who are found to have a single CF mutation on a newborn CF mutation screening test, and carrier testing for high-risk individuals and partners of CF mutation carriers.

The 508 FIRST™ test is for patients who have had no previous DNA testing. It provides a quick and inexpensive screen for deltaF508, the most common mutation.

The Ambry CF 102™ Screening Panel is a panel of > 100 CF mutations carefully selected to provide the highest overall mutation detection rate (91%) of any mutation panel currently on the market. It provides excellent sensitivity with a fast turnaround time and low cost.  It is designed for patients who are known or suspected to have CF, for carrier screening for relatives of CF patients, and for carrier testing for known familial mutations.

Ambry also offers CF 33™, a 33-mutation screening panel, as well as a number of other flexible testing options to fit the needs of your patient.

Disease Name 
Cystic Fibrosis
Disease Information 

Cystic Fibrosis (CF) is an autosomal recessive genetic disease affecting approximately 30,000 children and adults in the United States. CF has an incidence of approximately 1/3200 live births. The carrier frequency for non-Hispanic Caucasians is about one in 25, and lower in other ethnic groups. Two defective CF alleles cause the body to produce abnormally thick, sticky mucus that clogs the lungs and leads to life-threatening lung infections. People with CF have a variety of other symptoms including high sweat chloride levels, persistent coughing, wheezing or shortness of breath, and excessive appetite but poor weight gain. These thick secretions also obstruct the pancreas and prevent digestive enzymes from reaching the intestines to help break down and absorb food, contributing to pancreatitis and poor weight gain. CF mutations may also lead to congenital bilateral absence of the vas deferens (CBAVD) and infertility. The severity of symptoms varies greatly between individuals diagnosed with CF due, in part, to the more than 1,500 different CF mutations described to date.

Testing Benefits & Indication 

Genetic testing for CF is indicated for diagnosis in individuals with a known or suspected diagnosis of CF, for carrier testing in individuals at increased risk based on ethnicity and/or family history, and for carrier testing in partners of individuals who carry a CF mutation.

Test Description 

Genomic deoxyribonucleic acid (gDNA) is isolated from the patient’s specimen using standardized methodology and quantified by agarose gel electrophoresis.

508 FIRST™ Test analyzes DeltaF508 mutation first, with a potential reflex to full gene analysis.

CFTR full-gene sequence analysis is performed on a next-generation sequencing instrument. The analytical range includes: exons 1 to 27, as well as at least 20 bases into the 5’- and 3’-ends of all introns, 5’- and 3’-untranslated regions (5’UTR and 3’UTR). This assay is also capable in assessing the poly-T tract within intron 10 and in identifying the c.1679+1634A>G (c.1811+1634A>G or c.1811+1.6kb) mutation in intron 12 and the c.3717+12191C>T (c.3849+10kbC>T) mutation in intron 22.

CF AMPLIFIED™ Test includes full-gene sequence analysis plus reflexing to gross deletion/duplication. Gene deletion/duplication analysis is performed using Multiplex Ligation-dependent Probe Amplification (MLPA, MRC Holland). Gross deletion/duplication analysis determines gene copy number for any of the 27 exons.

Specific alteration(s) in the CFTR gene (other than deltaF508) is requested, traditional Sanger dideoxy terminator DNA sequencing technique and/or MLPA are used.

Please note that 508 FIRST detects only the deltaF508 mutation. Novel variants are always reported. Polymorphisms and the poly T status will be reported upon request. The following sites are used to search for previously described CF mutations and polymorphisms: Toronto Sick Children’s CF database, HGMD, and online search engines (i.e., PubMed). Sequence analysis is based on the following NCBI reference sequence: NM_000492.

The CF 102 Screening Panel targets detection of the following specific mutations in the CFTR gene: 1078delT (c.948delT),  1154insTC (c.1022_1023insTC),  1248+1G>A (c.1116+1G>A),  1288insTA (c.1153_1154insAT),  1471delA (c.1340delA),  1717-1G>A (c.1585-1G>A),  1898+1 G>A (c.1766+1G>A ),  1898+3A>G (c.1766+3A>G ),  1949del84 (c.1817_1900del84), 2055del9>A (c.1923_1931del9insA),  2143delT (c.2012delT),  2183AA>G (c.2051_2052delAAinsG),  2184delA (c.2052delA),  2184insA (c.2052insA),  2307insA (c.2175_2176insA),  2347delG (c.2215delG),  2585delT (c.2453delT),  2622+1G>A (c.2490+1G>A),  2789+2insA (c.2657+2_2657+3insA),  2789+5G>A (c.2657+5G>A),  3120+1G>A (c.2988+1G>A),  3120G>A (c.2988G>A),  3199del6 (c.3067_3072delATAGTG),  3272-26A>G (c.3140-26A>G),  3600G>A (c.3468G>A),  3659delC (c.3528delC),   3849+10kbC>T (c.3717+12191C>T),  3876delA (c.3744delA),  3905insT (c.3773_3774insT), 394delTT (c.262_263delTT),  4005+2T>C (c.3873+2T>C),  405+1G>A (c.273+1G>A),  406-1G>A (c.274-1G>A),  4209TGTT>AA (c.4077_4080delTGTTinsAA),  621+1G>T (c.489+1G>T),  663delT (c.531delT),  711+1G>T (c.579+1G>T),  935delA (c.803delA),  p.A455E (c.1364C>A),  p.D1152H (c.3454G>C), p.E116K (c.346G>A),  p.E1371X (c.4111G>T),  p.E384X (c.1150G>T),  p.E585X (c.1753G>T),  p.E60X (c.178G>T),  p.E92X (c.274G>T),  p.G1061R (c.3181G>C),  p.G1244E (c.3731G>A),  p.G178R (c.532G>A),  p.G330X (c.988G>T),  p.G480C (c.1438G>T),  p.G542X (c.1624G>T),  p.G551D (c.1652G>A),  p.G551S (c.1651G>A),  p.G85E (c.254G>A),  EX2del,   EX2_3del,  deltaF508 (c.1521_1523delCTT),  deltaI507 (c.1519_1521delATC),  p.L1077P (c.3230T>C),  p.L467P (c.1400T>C),  p.M1101K (c.3302T>A),  p.N1303K (c.3909C>G),  p.P67L (c.200C>T),  p.Q1042X (c.3124C>T),  p.Q220X (c.658C>T),  p.Q414X (c.1240C>T),  p.Q493X (c.1477C>T),  p.Q552X (c.1654C>T),  p.Q98R (c.293A>G),  p.Q98X (c.292C>T),  p.R1066C (c.3196C>T),  p.R1066H (c.3197G>A),  p.R1070W (c.3208C>T),  p.R1158X (c.3472C>T),  p.R1162X (c.3484C>T),  p.R117C (c.349C>T),  p.R117H (c.350G>A),  p.R334Q (c.1001G>A),  p.R334W (c.1000C>T),  p.R347H (c.1040G>A),  p.R347P (c.1040G>C),  p.R553X (c.1657C>T),  p.R560T (c.1679G>C),  p.R709X (c.2125C>T),  p.R75X (c.223C>T),  p.R764X (c.2290C>T),  p.S1196X (c.3587C>G),  p.S1251N (c.3752G>A),  p.S466X (c.1397C>G and c.1397C>A),  p.S489X (c.1466C>A),  p.S549N (c.1646G>A),  p.S912X (c.2735C>A), p.S945L (c.2834C>T), p.T338I (c.1013C>T), p.T351I (c.1052C>T), p.V520F (1558G>T), p.W1089X (c.3266G>A), p.W1204X (c.3612G>A), p.W1282X (c.3846G>A), p.Y1032C (c.3095A>G), p.Y1092X (c.3276C>A), p.Y563N (c.1687T>A).

In the CF 33 Screening Panel, only the following 33 known disease-causing mutations on CFTR listed below are analyzed and reported; I507del,1717-1G>A, 1898+1G>A, 2184delA, 2789+5G>A, 3120+1G>A, 3659delC, 3849+10kbC>T, 3876delA, 394delTT, 621+1G>T, 711+1G>T, A455E, F508del, G542X, G551D, G85E, N1303K, Q493X, R1162X, R117H, R334W, R347P, R553X, R560T, S549N, W1282X, 2055del9>A, 406?1G>A, E60X, R1066C, S492F,2105-2117del13insAGAAA.

For the CF 102 and CF 33 screening panels, if p.R117H is detected, then reflex poly T / TG repeat analysis is performed.

The following sites are used to search for previously described CF mutations and polymorphisms: Toronto Sick Childrens CF database, HGMD, and online search engines (i.e., PubMed).

Mutation Detection Rate 

508 First™ detects approximately 99% of CFTR mutations, including gross deletions and duplications, in patients of all ethnicities.

Specimen Requirements 

Blood: Collect 3-5 cc from adult or 2 cc minimum from child into EDTA purple-top tube (first choice) or ACD yellow-top tube (second choice). Store at room temperature or refrigerate. Ship at room temperature.
Blood spot: Minimum of one complete spot approximately 0.5 inch in diameter on S&S 903 collection paper or similar. Store in a clean plastic bag at room temperature. Ship at room temperature.
Saliva: Collect 2 ml into Oragene™ DNA Self-Collection container. Store and ship at room temperature.
DNA: Send 5 μg in TE at 50-100 ng/μl. Store frozen and ship on ice or dry ice.
Prenatal: Prenatal testing is available. Please call an Ambry Genetic Counselor to discuss your case.

Billing Codes 
TEST CODE                                                            TECHNIQUE
1000  CFTR gene sequence
1002 508 FIRST (deltaF508 reflex to CFTR Amplified)
1004 CFTR deletion / duplication
1006 CFTR Amplified (CFTR gene sequence reflex deletion / duplication) 
1007 CFTR Amplified (CFTR gene sequence and deletion / duplication)  (concurrent)
1010 CF TG Repeat (CFTR)
1012 508 ONLY (CFTR)
1018 CFTR Screening Panel (CF 102)
2000 CFTR Screening Panel (CF33)

 

Turnaround Time 
Technique Days
CFTR Gene Sequence Analysis 5-13
508 FIRST Reflex to CFTR Sequence Analysis and Deletion / Duplication     5-13
CFTR Deletion / Duplication Analysis     5-13
CFTR Sequence Analysis Reflex Option to Deletion / Duplication     5-13
CFTR Sequence Analysis Concurrent to Deletion / Duplication 5-13
CF TG Repeat (CFTR) 7-14
508 ONLYTM (CFTR) 5-13
CFTR Screening Panel (CF102)     7-14
CFTR Screening Panel (CF33)     7-14

 

Genes