Genetic risk assessment in carrier testing for spinal muscular atrophy

As evidenced by the complete absence of a functionally critical sequence in exon 7, approximately 94% of individuals with clinically typical spinal muscular atrophy (SMA) lack both copies of the SMN1 gene at 5q13. Hence most carriers have only one copy of SMN1. Combining linkage and dosage analyses for SMN1, we observed unaffected individuals who have two copies of SMN1 on one chromosome 5 and zero copies of SMN1 on the other chromosome 5. By dosage analysis alone, such individuals, as well as carriers of non-deletion disease alleles, are indistinguishable from non-carrier individuals. We report that approximately 7% of unaffected individuals without a family history of SMA have three or four copies of SMN1, implying a higher frequency of chromosomes with two copies of SMN1 than previously reported. We present updated calculations for disease and non-disease allele frequencies and we describe how these frequencies can be used for genetic risk assessment in carrier testing for SMA.     

云南地区3049名育龄人群脊髓性肌萎缩症携带者筛查结果分析

目的对云南地区3049名育龄人群进行脊髓性肌萎缩症(spinal muscular atrophy,SMA)的携带者筛查,探讨本地区人群运动神经元存活基因(survival motor neuron,SMN)的拷贝数情况及携带频率。方法应用多重连接探针扩增技术(multiplex ligation-dependent probe amplification,MLPA)对SMN1及SMN2基因第7外显子的拷贝数进行检测,筛查出SMN1基因第7外显子拷贝数为1的SMA携带者。对双方均为携带者的夫妇提供产前诊断。结果在3049名育龄人群中,共检测出SMA携带者62例,携带率为1/49(2.03%)。男性携带率为1.91%(40/2094),女性携带率为2.30%(22/955),二者的差异无统计学意义(P>0.05)。SMN1杂合缺失占1.30%(41/3049),由SMN1转换为SMN2者占0.69%(21/3049)。SMN1等位基因的平均拷贝数为1.99。检出双方均为SMA携带者的夫妇2对,通过产前诊断避免了1例患病胎儿的出生。结论云南地区SMA男女携带者的频率无显著差异,符合常染色体隐性遗传模式。阐明SMA携带者的频率和SMN基因的拷贝数情况,可为遗传咨询和产前预防提供依据。     

Large-scale population screening for spinal muscular atrophy: Clinical implications

PurposeTo determine the frequency of SMN1 deletion carriers in the Israeli population and to assess the feasibility of population screening for spinal muscular atrophy.MethodsA total of 6394 individuals without family history of spinal muscular atrophy underwent genetic screening by multiplex ligation-dependent probe amplification, designed to detect SMN1 exon 7 and exon 8 copy number.ResultsOne hundred fifty-nine individuals carried an SMN1 heterozygous exon 7 deletion, yielding a carrier frequency of 1:40. About 10.8% of individuals were found to carry two or more SMN1 exon 7 copies on the same chromosome (cis configuration). This implies that some deletion carriers may not be detected by multiplex ligation-dependent probe amplification or similar quantitative methods. The acceptance of spinal muscular atrophy screening among women undergoing testing for fragile X syndrome and cystic fibrosis reached 93%.ConclusionsCurrently used molecular techniques cannot detect about 5% of spinal muscular atrophy carriers with a cis configuration or individuals with SMN1 sequence mutations and de novo deletions. Thus, it is estimated that the spinal muscular atrophy carrier detection rate is about 90%. Given the severity of spinal muscular atrophy, the relatively high carrier frequency, and the estimated detection rate, we conclude that population-based screening for spinal muscular atrophy is feasible and acceptable. Genet Med 2011:13(2):110–114.     

Cost-effectiveness of a school-based Tay-Sachs and cystic fibrosis genetic carrier screening program.

PURPOSE: To explore the cost-effectiveness of school-based multi-disease genetic carrier screening. METHOD: Decision analysis of the cost-effectiveness of a school-based Tay-Sachs disease and cystic fibrosis genetic carrier screening program, relative to no screening. Data relating to ethnicity profile, test-accepting behavior, and screening program cost were sourced from an existing program in Sydney, Australia. RESULTS: Compared to no screening, the incremental cost-effectiveness of the screening program is A dollar 5,834 per additional carrier detected. This cost-effectiveness ratio is most sensitive to changes in genetic test accuracy, and the cost of laboratory assays. The results imply a cost per affected birth avoided of approximately A dollar 530,000 (approximately US dollar 371,000). CONCLUSIONS: This preconceptional genetic carrier screening program offers comparable cost-effectiveness to prenatal screening programs for cystic fibrosis.     

应用荧光定量PCR对上海地区人群进行脊肌萎缩症携带者筛查

目的 建立脊肌萎缩症(spinal muscular atrophy,SMA)携带者筛查的技术体系,评估上海地区SMA携带者频率和携带者筛查的检出效率.方法 收集经临床和分子确诊的15例SMA患儿以及38个SMA核心家庭的76名患儿父母的样本,建立荧光定量PCR检测SMN1拷贝数的技术体系,对上海地区1741名无症状孕妇进行SMA携带者筛查,根据Hardy Weinberg平衡定律,计算SMN1等位基因频率.结果 1741名无症状孕妇中共检出SMN1拷贝数为1的SMA携带者45例,0-拷贝、1-拷贝、2拷贝、3-拷贝等位基因频率分别为1.37×10-2、9.45×10-1、2.80×10-2、1.27×10-2,调整后的SMA携带者比率为1∶35,筛查检出率为94.49％.携带者筛查结果阴性的个体,3拷贝的筛查后残留风险相对较高.结论 上海地区SMA携带者发生率与高加索人群相近,携带者筛查具有较高检出率.本研究结果提示,携带者筛查中对于SMN1拷贝数超过2的多拷贝数有必要进一步区分,以获得2-拷贝和3-拷贝等位基因的准确频率,这些数据对于筛查后残留风险的遗传咨询十分重要.     

Pan-ethnic carrier screening and prenatal diagnosis for spinal muscular atrophy: clinical laboratory analysis of >72,400 specimens

Spinal muscular atrophy (SMA) is a leading inherited cause of infant death with a reported incidence of ~1 in 10,000 live births and is second to cystic fibrosis as a common, life-shortening autosomal recessive disorder. The American College of Medical Genetics has recommended population carrier screening for SMA, regardless of race or ethnicity, to facilitate informed reproductive options, although other organizations have cited the need for additional large-scale studies before widespread implementation. We report our data from carrier testing (n = 72,453) and prenatal diagnosis (n = 121) for this condition. Our analysis of large-scale population carrier screening data (n = 68,471) demonstrates the technical feasibility of high throughput testing and provides mutation carrier and allele frequencies at a level of accuracy afforded by large data sets. In our United States pan-ethnic population, the calculated a priori carrier frequency of SMA is 1/54 with a detection rate of 91.2%, and the pan-ethnic disease incidence is calculated to be 1/11,000. Carrier frequency and detection rates provided for six major ethnic groups in the United States range from 1/47 and 94.8% in the Caucasian population to 1/72 and 70.5% in the African American population, respectively. This collective experience can be utilized to facilitate accurate pre- and post-test counseling in the settings of carrier screening and prenatal diagnosis for SMA.     

Population screening for cystic fibrosis in Western Australia: community response

We measured acceptance of carrier testing for cystic fibrosis in the community when offered in a primary care setting, determined variables influencing acceptance, and assessed knowledge of cystic fibrosis 3-6 months later. A total of 5,102 individuals age 18-50 years attending general practices or a family planning clinic in Western Australia completed questionnaires about knowledge of cystic fibrosis and the State Anxiety Inventory. Testing for the delta F508 gene was offered. After 3-6 months, carriers, a sample of consenting participants who were not tested, and a sample of test-negative participants were sent a further questionnaire; 43.5% of participants chose to be tested for cystic fibrosis carrier status. Women, younger people, people with higher education, people without children, and people planning to have children were more likely to be tested. After 3-6 months, carriers gave correct responses to questions about cystic fibrosis more frequently than those who tested negative or were not tested; 82.2% of carriers knew that they were definitely a carrier and 31.1% of test-negative individuals believed they were definitely not carriers. Thus, population carrier screening for cystic fibrosis offered in a community setting in Western Australia was acceptable to almost half of those offered testing, particularly younger people and those planning to have children, for whom knowledge of carrier status could be useful in making reproductive decisions. There was evidence that tested individuals recalled information in a way that minimised their risk of being a carrier.     

Conflicts regarding genetic counseling for fragile X syndrome screening: a survey of clinical geneticists and genetic counselors in Israel

Although fragile X screening has been offered in Israel since 1994, issues related to potential neurological and gynecological symptoms in carriers make counseling for fragile X different from recessive disorders. We evaluated the attitudes of clinical geneticists and genetic counselors regarding genetic counseling given to the women undergoing screening. We performed a self‐administered questionnaire including 13 study questions mailed to all clinical geneticists and genetic counselors in Israel. The questions were related to counseling for women pre‐ and post‐screening regarding themselves and the affected fetuses (including the risk for premature ovarian insufficiency; FXPOI and fragile X‐associated tremor ataxia syndrome; FXTAS). Out of a total of 80 clinical geneticists and genetic counselors, 34 responded with no additional responses on e‐mail re‐call. There was no clear consensus for 11/13 (85%) presented questions. The most striking differences in opinion were observed for issues regarding FXTAS risk in pre‐screening counseling sessions (P < 0.05). This study demonstrates that, there is no consensus on critical variables implying risk for fetus and mother and that counseling practices are dissimilar even in this small cohort of experts. We demonstrated a conflict between the detailed amount of information, which should be given prior to the test in order to allow informed decisions and the overload of information, which may cause confusion. © 2011 Wiley‐Liss, Inc.     

The fragile X syndrome: variability of expression in carrier females

The fra(X) expression in heterozygotes varies considerably from family to family. In family D23, 5 carriers express the fra(X) regardless of age. DNA studies using 3 markers were inconclusive as to whether cytogenetic testing is more reliable in this family than in others. III-2 and III-5 are the critical individuals in the pedigree; further study with closer probes should resolve this question.     

Informed decision making and psychosocial outcomes in pregnant and nonpregnant women offered population fragile X carrier screening

PurposePopulation-based carrier screening for fragile X syndrome (FXS) is still not universally endorsed by professional organizations due to concerns around genetic counseling for complex information and potential for psychosocial harms.MethodsWe determined uptake levels, decision making, and psychosocial impact in a prospective study of pregnant and nonpregnant Australian women offered FXS carrier screening in clinical settings. Women received pretest genetic counseling, and completed questionnaires when deciding and one month later.ResultsOf 1,156 women recruited, 83.1% returned the first questionnaire with 70.6% nonpregnant and 58.8% pregnant women choosing testing (χ²=16.98,P<0.001). Overall, informed choice was high in both nonpregnant (77.4%) and pregnant (72.9%) women (χ²=0.21,P=0.644), and more tested (76.0%) than not-tested (66.7%) women (χ²=6.35,P=0.012) made an informed choice. Measures of depression, stress, and anxiety were similar to population norms for ~85% of women. Decisional conflict and regret were generally low; however, decisional uncertainty and regret were greater in pregnant than nonpregnant women, and not-tested than tested women (uncertainty: χ²=18.51,P<0.001 and χ²=43.11,P<0.001, respectively; regret: χ²=6.61,P<0.037 and χ²=35.54,P<0.001, respectively).ConclusionWe provide evidence to inform guidelines that population FXS carrier screening can be implemented with minimal psychosocial harms following appropriate information and prescreening genetic counseling.     

A clinical and genetic study of spinal muscular atrophy

AIMS: This study evaluates clinical, electromyography (EMG) and genetic analysis of consecutive patients with spinal muscular atrophy (SMA) in a tertiary care adult neurology practice in India. METHODS: Consecutive patients with SMA attending the neurology out patient department during 2001-2003 were included. They were subjected to a detailed clinical examination, nerve conduction and EMG and muscle biopsy. Clinically patients were classified into generalised and segmental SMA. SMN gene deletion study was carried out in all the patients. RESULTS: There were 15 patients with type III and type IV SMA and 15 with segmental SMA (Hirayama disease). The age ranged between 5 and 23 years in type III SMA, 33-50 years in type IV SMA and 16-30 years in Hirayama disease (HD). The latter was found exclusively in males. Family history was observed in 1 patient each in all the groups. In SMA III mother and brother were affected, in SMA IV two siblings and in HD one brother had similar disease. One type III SMA family was associated with deafness and one type IV family had strong association with maturity onset diabetes in young. The EMG was characterised by lack of fibrillations in all type III and IV SMA patients except 1 whereas in HD, 11 out of 15 had fibrillations suggesting ongoing denervation. The EMG was suggestive of reinnervation in generalised SMA in both upper and lower limb muscles where as these abnormalities were restricted to C7-T1 mytomes in HD. Muscle biopsy in 10 patients with generalised SMA revealed group atrophy in all, and loss of fascicular architecture in 3, clumping of nuclei in 7 and hypertrophic fibers in 4. SMN1 gene deletion was present in 3 patients with type III but none in type IV and HD. CONCLUSION: SMN gene deletion was positive in 33% type III SMA whereas it was negative in type IV and HD. Presence of HD only in males may be consistent with X-linked disorder.     

Fragile X syndrome carrier screening in the prenatal genetic counseling setting.

PURPOSE: To document our experience with fragile X carrier screening. METHODS: In this study, 29,103 women with no known or suspected family history of fragile X syndrome were offered fragile X carrier screening during their prenatal genetic counseling visit. Screening acceptance was analyzed by referral indication, carrier frequencies documented, and prenatal outcome data presented. RESULTS: Overall, 7.9% accepted carrier screening. The premutation frequency was 1 in 382, and the intermediate allele frequency was 1 in 143. CONCLUSIONS: Fragile X screening is a desirable option for some women seeking prenatal genetic counseling and should be made available to this population.     

A model for offering carrier screening for fragile X syndrome to nonpregnant women: results from a pilot study

PurposeTo develop a model of offering population carrier screening for fragile X syndrome to nonpregnant women in primary care, using a program evaluation framework.MethodsA three-phase approach included: (I) needs assessment exploring staff and client attitudes, and informing development of educational materials, questionnaires and protocols; (II) offering screening to women, with questionnaires at baseline (Q1) and another (Q2) 1-month later; (III) genetic counseling for test-positive women and interviews with a subgroup of participants.ResultsOf 338 volunteering for Phase II, 94% completed Q1, 59% completed Q2, and 20% (N = 65) chose testing revealing one premutation carrier and three gray zone results; 31 women were interviewed. Tested women had more positive attitudes toward screening (Q1: P < 0.001; Q2: P < 0.001) compared with untested, although there was no significant difference in mean knowledge scores or anxiety. Women generally supported being offered prepregnancy screening; however, reasons against being tested included: not currently planning a family; perceiving benefits of screening as unimportant; and having to return for testing.ConclusionThis is the first prospective study exploring informed decision-making for fragile X syndrome carrier screening, using a thorough process of consultation, with no apparent harms identified. It provides a model for development of future genetic screening programs.     

FMR1 premutation carrier frequency in patients undergoing routine population-based carrier screening: Insights into the prevalence of fragile X syndrome,fragile X-associated tremor/ataxia syndrome,and fragile X-associated primary ovarian insufficiency in the United States

PurposeFragile X syndrome is caused by expansion and methylation of a CGG tract in the 5′ untranslated region of the FMR1 gene. The estimated frequency of expanded alleles (≥55 repeats) in the United States is 1:257–1:382, but these estimates were not calculated from unbiased populations. We sought to determine the frequency of fragile X syndrome premutation (55–200 repeats) and full mutation (>200 repeats) alleles in nonselected, unbiased populations undergoing routine carrier screening for other diseases.MethodsA previously validated laboratory-developed test using triplet-primed polymerase chain reaction was used to detect premutation and full mutation alleles in an unselected series of 11,759 consecutive cystic fibrosis carrier screening samples and 2011 samples submitted for screening for genetic diseases prevalent among the Ashkenazi Jewish population.ResultsPremutations were identified in 48 cystic fibrosis screening samples (1:245) and 15 samples (1:134) from the Ashkenazi Jewish population. Adjusted for the ethnic mix of the US population and self-reported ethnicity in our screening population, the estimated female premutation carrier frequency in the United States was 1:178. The calculated frequency of full mutation alleles was 1:3335 overall, and the calculated premutation frequency in males was 1:400. Based on frequency of larger, ≥70 repeat alleles, and reported penetrance, the calculated fragile X-associated tremor and ataxia syndrome, and fragile X-associated primary ovarian insufficiency frequencies is 1:4848 and 1:3560, respectively.ConclusionOur calculated fragile X syndrome carrier rate is higher than previous estimates for the US population and warrants further consideration of population-based carrier screening.     

Bayesian analysis for cystic fibrosis risks in prenatal and carrier screening.

PURPOSE: Risk assessment is an essential component of genetic counseling and testing, and Bayesian analysis plays a central role in complex risk calculations. We previously developed generalizable Bayesian methods to calculate the autosomal recessive disease risk of a fetus when one or no mutation is detected, and another, independent risk factor is present. Our methods are particularly useful for calculating the CF disease risk for a fetus with echogenic bowel. In genetics practice, however, there are other scenarios for which our previous methods are inadequate. METHODS AND RESULTS: We provide herein methods for calculating genetic risks in a variety of common clinical scenarios. These scenarios include the following: (1) different mutation panels that have been used for the parents and for a fetus; (2) genetic testing results available on the proband or other relatives, in addition to the consultand; (3) fetal ultrasound negative for echogenic bowel with a positive family history; and (4) a consultand with a mixed ethnic background. CONCLUSION: Our Bayesian methods have proven their versatility through application to many different common genetic counseling scenarios. These methods permit autosomal recessive disease and carrier probabilities to be calculated accurately, taking into account all relevant information. Our methods allow accurate genetic risk estimates for patients and their family members for CF or other autosomal recessive disorders.