Carrier Screening

Carrier screening tests healthy people for heterozygous variants in genes that cause autosomal recessive or X-linked conditions, so that couples can learn their chance of having an affected child before or early in pregnancy.

A carrier of an autosomal recessive disorder has no symptoms, but when both partners carry a variant in the same gene, each pregnancy has a 25% chance of an affected child, 50% chance of a carrier and 25% chance of a non-carrier. For X-linked conditions, a carrier woman has a 50% chance of an affected son and 50% chance of a carrier daughter in each pregnancy.

Methods are targeted variant panels, gene sequencing, copy number analysis (important for spinal muscular atrophy and alpha thalassaemia), and haemoglobin analysis (full blood count with HPLC or electrophoresis, which is followed by DNA studies).

Options include:

• Ethnicity based screening (haemoglobinopathies, Tay-Sachs disease in people of Ashkenazi Jewish descent, cystic fibrosis in people of northern European descent).
• Condition specific screening (cystic fibrosis, spinal muscular atrophy, fragile X).
• Expanded carrier screening, a panel of hundreds of genes offered to all couples irrespective of ancestry.

Carrier frequencies vary:

• Cystic fibrosis: about 1 in 25 in people of northern European descent and 1 in 60 to 90 in those of African or Asian descent.
• Spinal muscular atrophy: about 1 in 40 to 60.
• Sickle cell trait: 10 to 30% in parts of West and Central Africa and 8 to 10% in African-American people.
• Beta thalassaemia trait: 1 to 10% across the Mediterranean, Middle East, South Asia and South-East Asia.
• Alpha thalassaemia carriers: up to 30 to 40% in some areas of Africa and South-East Asia.
• Tay-Sachs disease carrier: 1 in 30 in Ashkenazi Jewish people (1 in 250 in others).
• Fragile X premutation: about 1 in 150 to 250 in women.

Overall, about 1 in 4 to 1 in 3 people carry a variant in an expanded panel gene, and 1 in 300 to 1 in 100 couples is at risk.

Indications. Couples planning pregnancy or in early pregnancy (preconception is best, because it allows the widest range of choices). Known family history of a recessive or X-linked condition. Consanguineous couples. Ancestry with a high carrier frequency of a particular disorder. Reproductive partners using donor sperm or eggs, and donors themselves.

A partner whose first degree relative is a known carrier (cascade testing). Not for children, and not for conditions of adult onset in the context of routine screening without counselling.

Specimen. Peripheral blood 2 to 5 mL in EDTA (DNA, and full blood count for haemoglobinopathy screening), or saliva or buccal swab. Haemoglobinopathy screening needs EDTA blood with red cell indices (mean cell volume and mean cell haemoglobin); iron deficiency must be corrected or excluded for interpretation.

Record ancestry, family history, consanguinity, previous affected children, and the partner's result. Written consent is needed for expanded panels and for non-paternity or incidental findings.

Reference values. No pathogenic or likely pathogenic variant in the genes tested. A negative result lowers but does not remove the chance of being a carrier (residual risk). Haemoglobin variants: haemoglobin A2 under 3.5% and mean cell volume over 80 fL are normal; carriers of beta thalassaemia have haemoglobin A2 of 3.5 to 7% with a mean cell volume under 80 fL and mean cell haemoglobin under 27 pg.

Interpretation.

• Carrier of a single variant in an autosomal recessive gene: no risk to the individual's own health in most conditions, but there is a 50% chance of passing it on. Partner testing is the next step, and the couple's risk is assessed from both results.
• Both partners carriers of the same condition: couple at 25% risk in each pregnancy. Options are prenatal diagnosis (chorionic villus sampling or amniocentesis), preimplantation genetic testing with in vitro fertilisation, donor gametes, adoption, or continuing without testing and preparing for an affected child.
• Residual risk after a negative result: depends on the detection rate of the panel in the person's ancestry.
• For example, a negative cystic fibrosis panel with 90% detection in a person of northern European descent reduces the carrier chance from 1 in 25 to about 1 in 240.
• A negative spinal muscular atrophy test reduces the carrier chance from 1 in 40 to about 1 in 700 (silent carriers with two copies on one chromosome and none on the other are missed).
• Spinal muscular atrophy: SMN1 exon 7 copy number of 0 (affected), 1 (carrier), 2 (usually non-carrier), 3 or more (non-carrier, with the possibility of a silent carrier state).
• Cystic fibrosis: pathogenic CFTR variants include severe variants (F508del, G542X) and variants with variable clinical consequences (R117H, 5T allele); partner testing and counselling must separate classical disease from milder forms.
• Haemoglobinopathies: sickle cell trait (haemoglobin AS, 35 to 45% haemoglobin S), haemoglobin C trait, beta thalassaemia trait (raised haemoglobin A2), alpha thalassaemia trait (normal haemoglobin A2, low mean cell volume), and structural variants such as haemoglobin E and haemoglobin Lepore.
• Couples with sickle cell trait and beta thalassaemia trait, or both with beta thalassaemia trait or haemoglobin E and thalassaemia, are at risk of a child with a severe disorder.
• X-linked conditions (fragile X, Duchenne muscular dystrophy, haemophilia, X-linked hydrocephalus): carrier women have a 50% chance of an affected son.
• For fragile X, CGG repeat 55 to 200 is a premutation and expands to a full mutation in a daughter with probability related to maternal repeat size (up to over 90% for repeats over 100).
• Premutation carriers have a risk of premature ovarian insufficiency and tremor ataxia syndrome.
• Variants of uncertain significance in a carrier gene are not used in reproductive decisions, but need partner results and periodic review.
• Incidental findings in expanded panels (a carrier who is affected, or a heterozygote with symptoms, which occurs in X-linked conditions) require counselling.

Critical values and findings needing immediate action.

• Both partners carriers of the same severe recessive disorder, found in pregnancy: urgent counselling and offer of prenatal diagnosis within the gestational window.
• Woman with beta thalassaemia trait or sickle cell trait whose partner is not yet tested, in early pregnancy: partner testing without delay, so that prenatal diagnosis can be offered before 12 to 14 weeks.
• Detection of a full mutation or premutation of fragile X in a pregnant woman: prenatal diagnosis and counselling.
• Carrier detected in an egg or sperm donor: use for recipients with non-carrier partners only, or choose another donor.
• Homozygous or compound heterozygous result in an apparently healthy adult (for example, mild cystic fibrosis variants or haemoglobin disorders): clinical review for undiagnosed disease.

Interferences and pitfalls.

• A negative screen reduces but never eliminates the risk; panels detect only the variants included, and detection rates differ greatly with ancestry because most panels were designed on populations of European descent.
• Silent carriers of spinal muscular atrophy (2+0), alpha thalassaemia deletions and small deletions in CFTR are missed by panels that do not use copy number analysis.
• Iron deficiency lowers haemoglobin A2 and can hide beta thalassaemia trait; coexisting delta thalassaemia, haemoglobin E and haemoglobin S can also produce misleading patterns. Alpha thalassaemia trait is missed by HPLC and needs DNA analysis. Recent transfusion invalidates haemoglobin analysis.
• Variants of uncertain significance are common in sequencing panels, and a variant labelled likely pathogenic may be downgraded; laboratories should state the database version and date.
• Non-paternity may be revealed incidentally, and consanguinity (shared ancestry) raises the risk for rare recessive conditions not on the panel.
• Expanded panels create anxiety, because most couples find at least one carrier variant; counselling about what the result means and about conditions with mild or variable severity is required, and conditions of adult onset should be excluded from the panel unless desired.
• Privacy, insurance and stigma issues apply to communities with high carrier frequencies, and screening of populations requires culturally sensitive services.
• Testing at birth or in children should be avoided unless there is a medical reason, to protect the child's future autonomy.
• Preimplantation genetic testing is costly and has a limited success rate, which restricts the choices of couples in many settings.

Special groups.

• Consanguineous couples: increased risk for many recessive disorders; use exome based carrier testing for known familial variants and offer genetic counselling.
• Couples using donor gametes: test the donor and the recipient for the same conditions.
• Women with known fragile X, Duchenne or haemophilia families: test for the familial variant, and offer prenatal diagnosis or preimplantation testing.
• Haemoglobinopathy screening: offered to all women in high prevalence regions at the first antenatal visit, with early partner testing.
• Pregnancy: testing in early pregnancy is acceptable but time limits the options; sequential testing of the partner only when the woman is a carrier is used by many programmes.
• Regions: in sub-Saharan Africa, the Middle East, India and South-East Asia, haemoglobinopathy and G6PD screening is the priority, and premarital screening programmes have lowered the birth incidence of thalassaemia in several countries. Cystic fibrosis is rarer in people of African and Asian descent but is under recognised.

Follow up tests.

• Partner testing for the same gene or condition.
• Haemoglobin electrophoresis or HPLC with DNA studies for alpha and beta globin.
• SMN1 and SMN2 copy number.
• CFTR full gene sequencing or deletion and duplication analysis.
• FMR1 CGG repeat sizing.
• Familial variant testing in relatives.
• Prenatal diagnosis (chorionic villus sampling or amniocentesis).
• Preimplantation genetic testing.
• Pre-test and post-test genetic counselling.