SMA affects individuals of all ethnicities. The estimated pan-ethnic disease frequency, (a
derived from our carrier frequency data (1/11
000, ) is consistent with the reported prevalence estimate of 1/10
000 reported for clinically typical SMA derived from larger population studies.4
Previous reports on SMA carrier frequencies in limited populations have identified a discrepancy between the estimated disease prevalence (1/10
000) and that extrapolated from observed carrier frequency estimates (1/6000) under Hardy–Weinberg equilibrium. Although possible explanations for the earlier discrepancies have been proposed,4
our present study is the first to report a pan-ethnic carrier frequency that is most consistent with the reported incidence of SMA.
For purposes of genetic counseling within the setting of population-based carrier screening, pan-ethnic carrier frequency (1/54) and carrier detection rate (91%) data are particularly useful when ethnicity is unknown or reflects admixture. When ethnicity is known, however, it may be possible to further refine the carrier frequency or detection rate provided in pre-test education and counseling, as well as provide more accurate estimates of residual risk following identification of a 2- or 3-copy SMN1 result. For instance, a Caucasian individual with a 2-copy result following carrier screening would have an ~1/800 residual risk to be a carrier, whereas an African American individual with the same result would have a 1/130 risk to be a carrier.
Testing 4883 African American individuals with no family history of SMA confirmed earlier observations24
of a higher frequency of the 2-copy allele (c
) in this population as compared with other populations. This suggests a higher frequency of [2+0] carriers who would not be identified by an assay designed to detect deletion carriers who have 1 copy of SMN1
. This is accurately reflected by the lower detection rate of 71% in this population. The a priori
risk for an African American individual to be a carrier (1/72) is, however, comparable to other populations and supports the inclusion of African Americans among those being offered carrier screening for SMA, with appropriate counseling regarding the limitations of testing and associated residual risks.
In this study of 7655 Hispanic individuals, the observed SMN1
1-copy frequency did not differ significantly from that observed in our earlier study24
of 1030 individuals (P
=0.1869). In the Asian carrier-screening population, pair-wise comparison of observed SMN1
1-copy frequency between our current data set (n
=4647) and those of our earlier study24
=1027), as well as studies in native Chinese17
=1712) and Korean14
=326) populations, also did not yield significant differences at 1% (P
-values=0.7776, 0.0366, 0.5674, respectively). Among individuals identified as Asian Indian (n
=976), the 1-copy genotype frequency was 1.74% with a calculated a priori
carrier frequency of 1/52. We are not aware of previous studies of SMA carrier frequency in the general Asian Indian population. Similarly, the SMN1
1-copy genotype frequency distribution in our Ashkenazi Jewish population was not significantly different from that reported in the Israeli population16
=0.6575). Finally, an evaluation of genotype frequencies for individuals whose ethnic background was ‘Not Provided' on the ordering test requisition supports the conclusion that the ethnicity distribution of this group does not differ from that of the pan-ethnic population as a whole as the 1-copy genotype frequencies are similar (P
At least seven couples with no family history of SMA in our carrier-screening population were identified as carriers with a 25% risk to have an affected child. As a reference laboratory we do not have complete ascertainment of family samples, and it is possible that some partners of individuals identified as carriers via screening were tested at other laboratories. Additionally, we could have incomplete ascertainment if partners were not identified as such on ordering paperwork or if a fetal sample from carrier parents was tested at another laboratory. Of the seven couples, four had fetal testing in our laboratory and no affected fetuses were identified in this small group.
Among individuals with a family history of SMA, there have been case reports of first-degree relatives with an SMN1
copy number of 0 who are asymptomatic or mildly affected.25
This raises the question of the frequency of individuals with 0 copies of SMN1
in the general population. Among the 72
453 samples tested, we did not identify any individuals referred for carrier testing with an apparent 0-copy SMN1
The identification of 36 individuals with sequence variants in the primer/probe region underscores the importance of this additional quality assurance measure to identify potential false positive results. These individuals could be misclassified as being carriers of a deletion/gene conversion within the SMN1 gene. At present, there is insufficient evidence to classify these variants as either disease causing or benign. Therefore, although the SMN1 copy number of individuals identified with these variants can be reclassified, their SMA carrier status and associated residual risk cannot be accurately determined at present. Follow-up options, such as carrier testing of the partner can be explored. In the absence of follow-up sequencing, the estimated pan-ethnic-positive predictive value of our carrier analysis (TP (1162)/TP (1162)+FP (36)) would have been 97%.
In our prenatal testing cohort, as expected, ~25% of the at-risk fetuses were found to have 0 copies of SMN1
and were predicted to be affected with SMA. Among 54 fetal samples referred for testing due to a 25% risk to be affected, 47 were from obligate carrier parents with a previous affected child. Of these, eight obligate carriers (8.5%) had 2 copies of SMN1
and a partner with 1 copy of SMN1
. This frequency is consistent with the frequency of 7/117 (6.0%) obligate carrier parents identified to have 2 copies of SMN1
as reported by Smith et al18
=0.79). In our study, additional studies to distinguish the [2+0] versus
[1+1] status of these 2-copy obligate carrier parents were not performed. Therefore, the exact frequency of 2-copy chromosomes in our obligate carrier parent cohort cannot be determined.
A lack of agreement exists among the limited number of studies investigating a relationship between abnormal ultrasound findings and SMA. Some reports suggest an association between increased nuchal translucency and SMA,26
although this association has not been supported by all studies.27
The inclusion of abnormal ultrasound findings among indications for carrier testing and prenatal diagnosis within our study suggests possible physician interest in including SMA among the differential diagnoses for select ultrasound abnormalities, although we are unable to determine the frequency with which parents or fetuses with these findings are referred for SMA testing.
The most frequent indication for fetal testing (49%) was having one carrier parent identified during screening. In these circumstances, the other parent was identified as having 2 or 3 copies of SMN1 or was tested for carrier status concurrently with the fetal SMN1 copy number analysis. In all but six samples for which clinical indication could not be confirmed, invasive prenatal diagnosis was performed for a reason unrelated to the carrier parent's SMN1 status. It is presumed that fetal testing was pursued in the interest of time in these cases, as was the case for individuals in whom the fetal sample and the untested parent were analyzed at the same time, or for additional reassurance.
The a priori risk for a fetus to be affected with SMA, when one parent is identified as a 1-copy carrier and the other parent has an SMN1 copy number of 2, can vary by ethnic background. In a Caucasian couple, the risk to have an affected fetus is 1/2528. In contrast, the risk for an African American couple with the same parental results is 1/264. SMN1 copy number analysis for a fetus in this circumstance could reveal a 0-copy SMN1 result, consistent with a prediction for the fetus to be affected. In addition, such a result would set the parental phase for the 2-copy parent as a [2+0] carrier. Alternatively, a 1-copy fetal result in this situation would be associated with an ~1/4000 risk for the fetus to be affected with SMA, due to compound heterozygosity for a 1d (d) allele.
In a pilot study of general population carrier screening in the United States, Prior et al18
reported ~60% of individuals seeking prenatal genetic counseling accepted carrier testing for SMA. After result disclosure, 98.7% of patients were glad they pursued testing. In Israel, among women electing carrier screening for cystic fibrosis and fragile X syndrome, a large-scale population screening study found 93% requested SMA testing as well.15
Our clinical laboratory analysis of >68
000 individuals without a family history of SMA, starting before the 2008 ACMG guideline, demonstrates (1) rapid test uptake by physicians and further supports patient interest in the availability of carrier screening for this disorder; (2) the feasibility of high throughput carrier testing for SMA; and (3) new and valuable information regarding SMN1
copy number in the general United States population to permit more accurate residual carrier risk calculations based on ethnicity-specific carrier frequencies and detection rates.
Furthermore, these data address specific recommendations set forth by professional organizations such as the AMP and ACOG and fully support the ACMG recommendations to offer SMA carrier screening to all, regardless of race or ethnicity.