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Primary Immunodeficiency via the PIK3CD gene

  • Summary and Pricing
  • Clinical Features and Genetics
  • Citations
  • Methods
  • Ordering/Specimens
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TEST METHODS

Sequencing

Test Code Test Copy GenesIndividual Gene PriceCPT Code Copy CPT Codes
1730 PIK3CD$1310.00 81479 Add to Order
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 18 days.

Clinical Sensitivity
Clinical sensitivity cannot be estimated because only a small number of patients have been reported. Analytical sensitivity should be high because all mutations reported are detectable by this method.

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Clinical Features
Primary immunodeficiency (PID) via the PIK3CD gene is a disorder hallmarked by recurrent sinopulmonary infections, impaired vaccine response, and chronic viremia due to Epstein-Barr virus (EBV) and/or cytomegalovirus. Recurrent respiratory infections can lead to progressive airway damage resulting in bronchiectasis (Angulo et al. 2013; Lucas et al. 2014). Because of an impaired immune response to EBV, patients with PID via the PIK3CD gene are at increased risk for development of EBV-related lymphoma (Crank et al. 2014). To date, over 50 genes have been implicated in PID, with mutations in the PIK3CD gene first being described in late 2013 (Al-Herz et al. 2014). Genetic testing is helpful in the differential diagnosis of PID via PIK3CD from other PIDs including hyper-IgM syndrome, agammaglobulinemia, and common variable immunodeficiency. Treatment for disease may include immunoglobulin replacement and antibiotics during infection bouts. Allogenic stem cell transplantation is the only curative treatment (Angulo et al. 2013).
Genetics
PID via mutations in the PIK3CD gene is inherited in an autosomal dominant manner. Both familial and spontaneous forms of the disease have been documented. To date, gain of function mutations leading to hyperactivation of PIK3CD are the cause of PID with c.3061G>A (p. Glu1021Lys) and c.1573G>A (p.Glu525Lys) variants being most prevalent (Angulo et al. 2013; Lucas et al. 2014). There are no reports of nonsense, frameshift, insertion, or deletion mutations in the PIK3CD gene to date. Somatic mutations in the PIK3CD have also been found in patients with Diffuse Large B-cell lymphoma (Zhang et al. 2013; Kang et al. 2006). The PIK3CD gene encodes the p100 subunit of phosphatidylinositol-3-OH kinase which is expressed only in leukocytes (Chantry et al. 1997; VanHaesebroeck et al. 1997).

The PIK3CD protein is an important second messenger kinase involved in several functions including migration, survival, and immunoglobulin class switching (Foukas et al. 2006; Ali et al. 2004).
Testing Strategy
Our DNA sequencing test involves bidirectional Sanger sequencing of the entire PIK3CD gene plus ~20bp of flanking non-coding DNA on either side of each exon.  We will also sequence any single exon (Test#100) in family members of patients with known mutation or to confirm research results.
Indications for Test
Candidates for testing have recurrent respiratory infections and lymphoproliferation of CD3+ T-cell and CD20+ B-cell populations. Patients also tend to have decreased CD4+ helper T-cell and impaired immunoglobin class switching leading to decrease IgA levels (Lucas et al. 2013; Angulo et al. 2013).

Gene

Official Gene Symbol OMIM ID
PIK3CD 602839
Inheritance Abbreviation
Autosomal Dominant AD
Autosomal Recessive AR
X-Linked XL
Mitochondrial MT

Disease

Name Inheritance OMIM ID
Immunodeficiency 14 615513

Related Tests

Name
Adenosine Deaminase Deficiency via the ADA Gene
Autosomal Dominant Hyper IgE Syndrome via the STAT3 Gene
Common Variable Immune Deficiency/IgA Deficiency via the TNFRSF13B Gene
Severe Combined Immunodeficiency/Omenn Syndrome via the DCLRE1C (ARTEMIS) Gene
Severe Combined Immunodeficiency/Omenn Syndrome via the IL7R Gene
Severe Combined Immunodeficiency/Omenn Syndrome via the RAG1 Gene
Severe Combined Immunodeficiency/Omenn Syndrome via the RAG2 Gene
X-linked Agammaglobulinemia via the BTK Gene
X-Linked Hyper IgM Syndrome via the CD40LG gene
X-linked Severe Combined Immunodeficiency via the IL2RG Gene

CONTACTS

Genetic Counselors
Geneticist
Citations
  • Al-Herz W, Bousfiha A, Casanova J-L, Chatila T, Conley ME, Cunningham-Rundles C, Etzioni A, Franco JL, Gaspar HB, Holland SM, Klein C, Nonoyama S, et al. 2014. Corrigendum: Primary Immunodeficiency Diseases: An Update on the Classification from the International Union of Immunological Societies Expert Committee for Primary Immunodeficiency. Frontiers in Immunology 5: PubMed ID: 25309542
  • Ali K, Bilancio A, Thomas M, Pearce W, Gilfillan AM, Tkaczyk C, Kuehn N, Gray A, Giddings J, Peskett E, Fox R, Bruce I, et al. 2004. Essential role for the p110delta phosphoinositide 3-kinase in the allergic response. Nature 431: 1007–1011. PubMed ID: 15496927
  • Angulo I, Vadas O, Garcon F, Banham-Hall E, Plagnol V, Leahy TR, Baxendale H, Coulter T, Curtis J, Wu C, Blake-Palmer K, Perisic O, et al. 2013. Phosphoinositide 3-Kinase Gene Mutation Predisposes to Respiratory Infection and Airway Damage. Science 342: 866–871. PubMed ID: 24136356
  • Chantry D, Vojtek A, Kashishian A, Holtzman DA, Wood C, Gray PW, Cooper JA, Hoekstra MF. 1997. p110 , a Novel Phosphatidylinositol 3-Kinase Catalytic Subunit That Associates with p85 and Is Expressed Predominantly in Leukocytes. Journal of Biological Chemistry 272: 19236–19241. PubMed ID: 9235916
  • Crank MC, Grossman JK, Moir S, Pittaluga S, Buckner CM, Kardava L, Agharahimi A, Meuwissen H, Stoddard J, Niemela J, Kuehn H, Rosenzweig SD. 2014. Mutations in PIK3CD Can Cause Hyper IgM Syndrome (HIGM) Associated with Increased Cancer Susceptibility. Journal of Clinical Immunology 34: 272–276. PubMed ID: 24610295
  • Foukas LC, Claret M, Pearce W, Okkenhaug K, Meek S, Peskett E, Sancho S, Smith AJH, Withers DJ, Vanhaesebroeck B. 2006. Critical role for the p110α phosphoinositide-3-OH kinase in growth and metabolic regulation. Nature 441: 366–370. PubMed ID: 16625210
  • Kang S, Denley A, Vanhaesebroeck B, Vogt PK. 2006. Oncogenic transformation induced by the p110beta, -gamma, and -delta isoforms of class I phosphoinositide 3-kinase. Proc. Natl. Acad. Sci. U.S.A. 103: 1289–1294. PubMed ID: 16432180
  • Lucas CL, Kuehn HS, Zhao F, Niemela JE, Deenick EK, Palendira U, Avery DT, Moens L, Cannons JL, Biancalana M, Stoddard J, Ouyang W, et al. 2013. Dominant-activating germline mutations in the gene encoding the PI(3)K catalytic subunit p110δ result in T cell senescence and human immunodeficiency. Nature Immunology 15: 88–97. PubMed ID: 24165795
  • Vanhaesebroeck B, Welham MJ, Kotani K, Stein R, Warne PH, Zvelebil MJ, Higashi K, Volinia S, Downward J, Waterfield MD. 1997. p110δ, a novel phosphoinositide 3-kinase in leukocytes. Proceedings of the National Academy of Sciences 94: 4330–4335. PubMed ID: 9113989
  • Zhang J, Grubor V, Love CL, Banerjee A, Richards KL, Mieczkowski PA, Dunphy C, Choi W, Au WY, Srivastava G, Lugar PL, Rizzieri DA, et al. 2013. Genetic heterogeneity of diffuse large B-cell lymphoma. Proceedings of the National Academy of Sciences 110: 1398–1403. PubMed ID: 23292937
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TEST METHODS

Bi-Directional Sanger Sequencing

Test Procedure

Nomenclature for sequence variants was from the Human Genome Variation Society (http://www.hgvs.org).  As required, DNA is extracted from the patient specimen.  PCR is used to amplify the indicated exons plus additional flanking non-coding sequence.  After cleaning of the PCR products, cycle sequencing is carried out using the ABI Big Dye Terminator v.3.0 kit.  Products are resolved by electrophoresis on an ABI 3730xl capillary sequencer.  In most cases, sequencing is performed in both forward and reverse directions; in some cases, sequencing is performed twice in either the forward or reverse directions.  In nearly all cases, the full coding region of each exon as well as 20 bases of non-coding DNA flanking the exon are sequenced.

Analytical Validity

As of March 2016, we compared 17.37 Mb of Sanger DNA sequence generated at PreventionGenetics to NextGen sequence generated in other labs. We detected only 4 errors in our Sanger sequences, and these were all due to allele dropout during PCR. For Proficiency Testing, both external and internal, in the 12 years of our lab operation we have Sanger sequenced roughly 8,800 PCR amplicons. Only one error has been identified, and this was due to sequence analysis error.

Our Sanger sequencing is capable of detecting virtually all nucleotide substitutions within the PCR amplicons. Similarly, we detect essentially all heterozygous or homozygous deletions within the amplicons. Homozygous deletions which overlap one or more PCR primer annealing sites are detectable as PCR failure. Heterozygous deletions which overlap one or more PCR primer annealing sites are usually not detected (see Analytical Limitations). All heterozygous insertions within the amplicons up to about 100 nucleotides in length appear to be detectable. Larger heterozygous insertions may not be detected. All homozygous insertions within the amplicons up to about 300 nucleotides in length appear to be detectable. Larger homozygous insertions may masquerade as homozygous deletions (PCR failure).

Analytical Limitations

In exons where our sequencing did not reveal any variation between the two alleles, we cannot be certain that we were able to PCR amplify both of the patient’s alleles. Occasionally, a patient may carry an allele which does not amplify, due for example to a deletion or a large insertion. In these cases, the report contains no information about the second allele.

Similarly, our sequencing tests have almost no power to detect duplications, triplications, etc. of the gene sequences.

In most cases, only the indicated exons and roughly 20 bp of flanking non-coding sequence on each side are analyzed. Test reports contain little or no information about other portions of the gene, including many regulatory regions.

In nearly all 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 for example 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 and cycle sequencing.

Unless otherwise indicated, the sequence data that we report are based on DNA isolated from a specific tissue (usually leukocytes). Test reports contain no information about gene sequences in other tissues.

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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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