Immunology

Confirming the Diagnosis: Flow Cytometry and Genetics

At a Glance

Doctors confirm a SCID diagnosis using flow cytometry to count missing immune cells (T, B, and NK cells) and genetic testing to find the specific DNA mutation. Identifying the exact SCID subtype is critical for determining the safest and most effective curative treatment for your baby.

After an abnormal newborn screen, doctors use more advanced tests to move from a “suspicion” to a “confirmed diagnosis.” These tests identify exactly which part of the immune system is missing and why ^[1]^[2].

Flow Cytometry: Counting the “Security Force”

Flow cytometry is a specialized blood test that acts like a high-speed scanner. It counts the different types of white blood cells in your baby’s blood to see which ones are present and in what amounts ^[3]^[4]. To understand the results, it helps to know what these cells do:

T-cells (The Commanders): These are the most important cells for fighting viruses and directing the rest of the immune system. In SCID, these are always very low or missing ^[5]^[6].
B-cells (The Archers): These cells create antibodies, which are like “arrows” that target and neutralize bacteria and viruses ^[5]^[6].
Natural Killer (NK) cells (The Specialized Guards): These are part of the body’s first line of defense, specifically attacking cells that have been infected by a virus ^[5]^[7].

Deciphering the Jargon: T, B, and NK Phenotypes

Doctors use a shorthand code to describe which cells are missing (-) and which are present (+). This is called a phenotype ^[8].

Phenotype	What it means	Common Genetic Causes
T- B+ NK-	Missing T and NK cells; has B-cells.	X-linked SCID (IL2RG) or JAK3 ^[9]^[10]
T- B- NK+	Missing T and B cells; has NK cells.	RAG1/2 or Artemis mutations ^[11]
T- B- NK-	Missing all three major cell types.	ADA-SCID (Adenosine Deaminase deficiency) ^[12]
T- B+ NK+	Missing only T-cells.	IL7Rα mutations ^[13]

Genetic Testing: Finding the “Instruction Error”

While flow cytometry counts the cells, genetic testing looks at the DNA to find the specific “typo” or mutation that caused the problem. This is critical because the specific gene involved often dictates the treatment ^[4]^[14].

Common Genetic Subtypes

X-linked SCID (IL2RG): The most common form, accounting for about 45–50% of cases. It primarily affects boys. Gene therapy is a growing alternative to transplant for this type ^[15]^[16].
ADA-SCID: Caused by a lack of the ADA enzyme, which leads to a buildup of toxins that kill immune cells. These babies can often start Enzyme Replacement Therapy (ERT) immediately as a “bridge” to keep them safe until a transplant or gene therapy can be performed ^[17]^[12].
RAG1/RAG2: These genes are responsible for “shuffling” DNA to create diverse immune cells. Without them, the body cannot make T or B cells ^[18].
Artemis SCID: This type makes the baby’s cells extra sensitive to radiation (radiosensitivity). If a baby has Artemis SCID, doctors must be very careful with the types of chemotherapy or radiation used before a transplant to avoid damaging other organs ^[19]^[20].

Knowing the specific subtype allows your medical team to customize a “blueprint” for your baby’s cure, whether that is a bone marrow transplant, enzyme therapy, or gene therapy. To learn about these treatments, visit the Curative Treatments page.

Common questions in this guide

What does flow cytometry do for a SCID diagnosis?

Flow cytometry is a specialized blood test that acts like a scanner to count your baby's white blood cells. It helps doctors confirm SCID by determining if crucial immune cells like T-cells, B-cells, and NK cells are present or missing.

What do the T, B, and NK phenotypes mean on my baby's lab report?

The phenotype is a shorthand code doctors use to describe which immune cells your baby has or is missing. For example, a T- B+ NK- phenotype means the baby is missing T and NK cells but has B cells, which is common in X-linked SCID.

Why is genetic testing important for a baby with SCID?

Genetic testing identifies the exact DNA mutation causing the immunodeficiency. Knowing the specific gene involved is critical because it helps doctors customize the safest and most effective curative treatment plan, such as choosing between gene therapy or a transplant.

Can babies with ADA-SCID receive treatment before a transplant?

Yes, babies diagnosed with the ADA-SCID genetic subtype can often start enzyme replacement therapy immediately. This acts as a protective bridge to keep them safe from toxins until a permanent cure like a bone marrow transplant or gene therapy can be performed.

Why do doctors need to know if a baby has Artemis SCID before a transplant?

Artemis SCID makes a baby's cells highly sensitive to radiation. Because of this radiosensitivity, doctors must carefully adjust the types of chemotherapy or radiation used before a bone marrow transplant to prevent damaging the baby's other healthy organs.

Curated prompts to bring to your next appointment.

1.Based on the flow cytometry, what are the absolute counts for my baby's T, B, and NK cells?
2.What specific genetic mutation was found, and how does it change the treatment plan (e.g., radiation sensitivity or enzyme therapy)?
3.If our baby has ADA-SCID, how soon can we start enzyme replacement therapy (ERT) as a bridge?
4.Does this specific subtype make our baby a candidate for gene therapy instead of a bone marrow transplant?
5.What is the next step for testing us (the parents) or other family members to see if we are carriers?

Tap a prompt to share your answer — we'll use it plus this page's context to start a tailored conversation.

References (20)

1
Newborn Screening for Severe Combined Immunodeficiency: Do Preterm Infants Require Special Consideration?
Atkins AE, Cogley MF, Baker MW
International journal of neonatal screening 2021; (7(3)) doi:10.3390/ijns7030040.
PMID: 34287233
2
Flow Cytometry Confirmation Post Newborn Screening for SCID in England.
Gilmour KC
International journal of neonatal screening 2021; (8(1)) doi:10.3390/ijns8010001.
PMID: 35076464
3
Flow cytometry-based diagnosis of primary immunodeficiency diseases.
Kanegane H, Hoshino A, Okano T, et al.
Allergology international : official journal of the Japanese Society of Allergology 2018; (67(1)):43-54 doi:10.1016/j.alit.2017.06.003.
PMID: 28684198
4
Flow cytometry-based diagnostic approach for inborn errors of immunity: experience from Algeria.
Tahiat A, Belbouab R, Yagoubi A, et al.
Frontiers in immunology 2024; (15()):1402038 doi:10.3389/fimmu.2024.1402038.
PMID: 39072316
5
An Overview of Advances in Cell-Based Cancer Immunotherapies Based on the Multiple Immune-Cancer Cell Interactions.
Zhang J, Späth SS, Weissman SM, Katz SG
Methods in molecular biology (Clifton, N.J.) 2020; (2097()):139-171 doi:10.1007/978-1-0716-0203-4_10.
PMID: 31776925
6
Flow cytometry quantification of tumor-infiltrating lymphocytes to predict the survival of patients with diffuse large B-cell lymphoma.
Yu T, Xu-Monette ZY, Lagoo A, et al.
Frontiers in immunology 2024; (15()):1335689 doi:10.3389/fimmu.2024.1335689.
PMID: 38348048
7
Immunological landscape of colorectal cancer: tumor microenvironment, cellular players and immunotherapeutic opportunities.
Andac-Aktas AB, Calibasi-Kocal G
Frontiers in molecular biosciences 2025; (12()):1687556 doi:10.3389/fmolb.2025.1687556.
PMID: 41244711
8
The diagnosis of severe combined immunodeficiency: Implementation of the PIDTC 2022 Definitions.
Dvorak CC, Haddad E, Heimall J, et al.
The Journal of allergy and clinical immunology 2023; (151(2)):547-555.e5 doi:10.1016/j.jaci.2022.10.021.
PMID: 36456360
9
Functional Characterization of an IL2RG Variant, a Case Report of X-Linked T- B + NK + SCID.
Assing K, Christensen EB, Dellgren C, et al.
Immunity, inflammation and disease 2025; (13(12)):e70307 doi:10.1002/iid3.70307.
PMID: 41462576
10
Whole-exome sequencing of T- B+ severe combined immunodeficiency in Egyptian infants, JAK3 predominance and novel variants.
El Hawary R, Meshaal S, Mauracher AA, et al.
Clinical and experimental immunology 2021; (203(3)):448-457 doi:10.1111/cei.13536.
PMID: 33040328
11
The diagnosis of severe combined immunodeficiency (SCID): The Primary Immune Deficiency Treatment Consortium (PIDTC) 2022 Definitions.
Dvorak CC, Haddad E, Heimall J, et al.
The Journal of allergy and clinical immunology 2023; (151(2)):539-546 doi:10.1016/j.jaci.2022.10.022.
PMID: 36456361
12
Long-Term Safety and Efficacy of Gene Therapy for Adenosine Deaminase Deficiency.
Booth C, Masiuk K, Vazouras K, et al.
The New England journal of medicine 2025; (393(15)):1486-1497 doi:10.1056/NEJMoa2502754.
PMID: 41092330
13
Diagnosis and Treatment of a Patient With Severe Combined Immunodeficiency Due to a Novel Homozygous Mutation in the IL-7Rα Chain.
Mansour R, Bsat YE, Fadel A, et al.
Frontiers in immunology 2022; (13()):867837 doi:10.3389/fimmu.2022.867837.
PMID: 35418989
14
Optimizing limited antibody panels for efficient hematological disorders diagnosis by flow cytometry in resource-constrained setting.
Yousafzai Y, Mir A, Hameed M, et al.
Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico 2026; doi:10.1007/s12094-025-04215-2.
PMID: 41549166
15
Preclinical ex vivo IL2RG gene therapy using autologous hematopoietic stem cells as an effective and safe treatment for X-linked severe combined immunodeficiency disease.
Hu M, Xu Q, Zhang F, et al.
Genes & diseases 2025; (12(3)):101445 doi:10.1016/j.gendis.2024.101445.
PMID: 40092492
16
Gene therapy and genome editing for primary immunodeficiency diseases.
Zhang ZY, Thrasher AJ, Zhang F
Genes & diseases 2020; (7(1)):38-51 doi:10.1016/j.gendis.2019.07.007.
PMID: 32181274
17
Consensus approach for the management of severe combined immune deficiency caused by adenosine deaminase deficiency.
Kohn DB, Hershfield MS, Puck JM, et al.
The Journal of allergy and clinical immunology 2019; (143(3)):852-863 doi:10.1016/j.jaci.2018.08.024.
PMID: 30194989
18
Partial correction of immunodeficiency by lentiviral vector gene therapy in mouse models carrying Rag1 hypomorphic mutations.
Castiello MC, Di Verniere M, Draghici E, et al.
Frontiers in immunology 2023; (14()):1268620 doi:10.3389/fimmu.2023.1268620.
PMID: 38022635
19
Radiation sensitivity in genetic tumour syndromes and how to test for them.
Distel LV, Hildebrand LS, Kuhlmann LCF, Vogel RKG
Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V 2025; (37(4)):313-320 doi:10.1515/medgen-2025-2041.
PMID: 41210219
20
Fibroblast-based radiosensitivity assays as a clinically valuable tool for (severe) combined immunodeficiency syndromes.
Beyls E, De Beul S, Bordon V, et al.
Mutation research. Genetic toxicology and environmental mutagenesis 2025; (902()):503852 doi:10.1016/j.mrgentox.2025.503852.
PMID: 40044379

This page is for educational purposes to help you understand your baby's SCID test results. Always consult your pediatric immunologist to interpret specific flow cytometry and genetic reports.

Get notified when new evidence is published on Severe combined immunodeficiency.

We monitor PubMed for new peer-reviewed studies on this topic and email a short summary when something meaningful changes.

Guide Contents