Invitae Core Carrier Screen

Test description

The Invitae Core Carrier Screen includes up to 6 genes associated with common, severe, disorders seen across ethnicities, including cystic fibrosis (CFTR), spinal muscular atrophy (SMN1), and fragile X syndrome (FMR1).

The American College of Obstetricians and Gynecologists (ACOG) and the American College of Medical Genetics (ACMG) recommend all patients who are pregnant or considering pregnancy to be screened for cystic fibrosis (CF) and spinal muscular atrophy (SMA). Additionally, screening for fragile X syndrome is recommended for women with a family history of fragile X-related disorders or intellectual disability, or women with a personal history of primary ovarian insufficiency.

The genes associated with alpha-thalassemia (HBA1, HBA2) and HBB-related hemoglobinopathies including beta-thalassemia and sickle cell disease (HBB) can also be included at no additional charge. To include these genes with your order, please select the appropriate checkboxes below.

Carrier frequency, detection rates and residual risks are available here.

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Primary panel (3 genes)
Add-on alpha-thalassemia genes (2 genes)

The genes associated with alpha-thalassemia can be added at no additional charge.


Add-on HBB-related hemoglobinopathies gene (1 gene)

The gene associated with HBB-related hemoglobinopathies (including beta-thalassemia and sickle cell disease) can be added at no additional charge.


Alternative tests to consider

Additional genes can be included with this carrier screen at no additional charge. Add this panel to your cart and then go to the carrier gene list to see the full list of available carrier genes.

Other carrier screening options:

  • alpha-thalassemia (HBA1, HBA2)
  • cystic fibrosis (CFTR)
  • fragile X syndrome (FMR1)
  • HBB-related hemoglobinopathies, including beta-thalassemia and sickle cell disease (HBB)
  • spinal muscular atrophy (SMN1)

Carrier frequency, detection rates and residual risks are available here.

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence in the transcript listed below. In addition, analysis covers the select non-coding variants specifically defined in the table below. Any variants that fall outside these regions are not analyzed. Any specific limitations in the analysis of these genes are also listed in the table below.

Based on validation study results, this assay achieves >99% analytical sensitivity and specificity for single nucleotide variants, insertions and deletions <15bp in length, and exon-level deletions and duplications. Invitae's methods also detect insertions and deletions larger than 15bp but smaller than a full exon but sensitivity for these may be marginally reduced. Invitae’s deletion/duplication analysis determines copy number at a single exon resolution at virtually all targeted exons. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. Certain types of variants, such as structural rearrangements (e.g. inversions, gene conversion events, translocations, etc.) or variants embedded in sequence with complex architecture (e.g. short tandem repeats or segmental duplications), may not be detected. Additionally, it may not be possible to fully resolve certain details about variants, such as mosaicism, phasing, or mapping ambiguity. Unless explicitly guaranteed, sequence changes in the promoter, non-coding exons, and other non-coding regions are not covered by this assay. Please consult the test definition on our website for details regarding regions or types of variants that are covered or excluded for this test. This report reflects the analysis of an extracted genomic DNA sample. In very rare cases, (circulating hematolymphoid neoplasm, bone marrow transplant, recent blood transfusion) the analyzed DNA may not represent the patient's constitutional genome.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
CFTR* NM_000492.3
FMR1* NM_002024.5
HBA1, HBA2* HBA1: NM_000558.4, HBA2: NM_000517.4
HBB NM_000518.4
SMN1* NM_000344.3

CFTR: Analysis includes the intronic variants: NM_000492.3:c.3718-2477C>T (also known as 3849+10kbC>T), c.1210-34TG[12]T[5] (also known as T5TG12), c.1210-34TG[11]T[5] (also known as T5TG11), and c.1679+1634A>G.
FMR1: This assay is designed to detect and categorize triplet repeats found at the promoter region of the FMR1 locus for all alleles reported. If two equal alleles are reported, this may indicate that both alleles are the same size, or that one allele is the reported size and the other allele is too small to be detected by this analysis. The number of AGG interruptions within the CGG repeat region is determined for females with triplet repeat sizes of 55-90. AGG analysis is not currently performed for samples originating in New York state.
HBA1/2: This assay is designed to detect deletions and duplications of HBA1 and/or HBA2, resulting from the -alpha20.5, --MED, --SEA, --FIL/--THAI, -alpha3.7, -alpha4.2, anti3.7 and anti4.2. Sensitivity to detect other copy number variants may be reduced. Detection of overlapping deletion and duplication events will be limited to combinations of events with significantly differing boundaries. In addition, this assay detects deletion of the enhancer element HS40 and the sequence variant, Constant Spring (NM_000517.4:c.427T>C).
SMN1: The SMN1 gene is identical to the SMN2 gene with the exception of exon 8 (typically referred to as exon 7). This assay unambiguously detects SMN1 exon 8 copy number. The presence of the g.27134T>G variant (also known as c.*3+80T>G or SNP analysis for enhanced SMA testing) is reported if SMN1 copy number = 2. Sequence analysis of other point mutations is not included.