SMN dosage analysis and risk assessment for spinal muscular atrophy.
SMN dosage analysis and risk assessment for spinal muscular atrophy.
复制标题
脊髓性肌萎缩症的 SMN 剂量分析和风险评估。
DOI：
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发表时间：
2002
影响因子：
9.8
通讯作者：
Robert B. Wilson
中科院分区：
文献类型：
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作者：
S. Ogino;Robert B. Wilson
致编辑：
费尔德科特等人。 (2002) 最近报道了一种基于实时定量 PCR 确定 SMN1 (MIM 600354) 和 SMN2 (MIM 601627) 拷贝数的新方法。他们的方法比其他地方描述的方法具有更高程度的自动化和更快的周转时间（McAndrew et al. 1997; Chen et al. 1999; Wirth et al. 1999; Gerard et al. 2000; Scheffer et al. 2000; Ogino et al. 2001）。他们利用新方法证明，SMN2（SMN1 的着丝粒同源物，脊髓性肌萎缩症的疾病基因（SMA [I 型为 MIM 253300；II 型为 MIM 253550；III 型为 MIM 253400]））的拷贝数影响 SMN1 纯合缺失个体中 SMA 的严重程度。他们发现，SMN2 的拷贝数越多，属于轻度 SMA 类型的可能性就越大。由于这种相关性不是绝对的，因此他们使用贝叶斯类型分析来确定发展每种 SMA 类型的后验概率，其中包括 SMN1 的纯合缺失和 SMN2 的给定拷贝数。我们在下面讨论他们文章中提出的几个重要的伦理、预后和技术问题。
在表 6 中，Feldkotter 等人。报告“根据 SMN2 拷贝数，未受影响的人在出生后接受检测并被发现携带 SMN1 纯合缺失的人将患上 I、II 或 III 型 SMA 的概率”。 SMA 通常是一种儿童期发病的疾病，对未受影响的儿童进行检测存在伦理问题。我们同意美国人类遗传学会和美国医学遗传学会的观点，即“对儿童的及时医疗益处应该是儿童和青少年基因检测的首要理由”（美国人类遗传学会董事会和美国医学遗传学会董事会 1995 年，第 1233 页）。由于目前对于 SMA 没有有效的治疗方法（无论是症状前治疗还是其他治疗），因此对未受影响的儿童进行及时检测的医疗益处尚不清楚。
为了根据缺乏 SMN1 的未受影响儿童的 SMN2 拷贝数预测 SMA 类型，Feldkotter 等人。通过使用比值比而不是传统的条件概率来执行贝叶斯类型的分析。对于先验概率，他们使用 SMA 受影响个体中 SMA 类型的分布：0.51，为 I 型；0.51，为 I 型； .32，对于II型； .17，对于类型 III。即使以这种方式测试未受影响的儿童，出于此目的，这些先验概率也不会是用于贝叶斯或贝叶斯类型分析的正确概率。例如，如果一个孩子在 10 个月大时没有症状，那么他或她患 I 型 SMA 的可能性比患其他类型的可能性要小得多（Zerres 和 Rudnik-Schoneborn 1995）。对于每种 SMA 类型的假设，必须纳入在特定年龄无症状的条件概率。
Feldkotter 等人给出的 SMN2 拷贝数数据。可用于产前检测，预测 SMA 类型。然而，他们使用的先验概率仅适用于 SMA 家族史类型未知的情况。尽管已经描述了患有不止一种 SMA 类型的家庭（而且这种情况并不罕见），但了解受影响家庭成员的 SMA 类型会增加有患 SMA 风险的亲属患该类型 SMA 的先验概率。如果受影响的家庭成员的 SMA 类型未知，则所有 SMA 患者中 SMA 类型的分布将与先验概率的分配相关。
根据所有报告的数据，Feldkotter 等人。指出，由于在 20/834 (2.4%) 健康染色体上发现了两个 SMN1 拷贝，“根据直接 SMN1 测试，4.8% 的正常个体将被误解为非携带者”（第 365 页）。实际上，这些数据意味着约 4.8% 的非携带者将有 3 个 SMN1 拷贝，约 2.4% 的 5 号染色体上有 SMN1 缺失的携带者将在另一条 5 号染色体上有两个 SMN1 拷贝。我们将后者称为“2+0”基因型（Chen 等人，1999）。考虑到大约 1.7% 的携带者具有无法检测到的 SMN1 外显子 7 缺失的基因内突变，Feldkotter 等人。指出这“对于普通人群来说，测试的敏感性降低至 93.5%”（第 365 页）。将约 1.7% 具有基因内突变的携带者与约 2.4%（即 0.024×[1-0.017]）具有 2+0 基因型的携带者相结合，得出 SMN 剂量分析在一般人群中检测 SMA 携带者的总体灵敏度为约 95.9%。如果已知受影响的家庭成员存在 SMN1 纯合缺失，则 SMN 剂量分析在未受影响的家庭成员中检测携带者的灵敏度将为 ∼97.6%（即 0.959/[1-0.017]）。这是因为该家族中基因内突变携带者的概率相对于2+0携带者的概率大大降低（荻野等人，出版中）。
更新我们的综合数据（McAndrew 等人，1997 年；Ogino 等人，2002 年，出版中）给出了 590 条正常 5 号染色体中的 23 条有两个 SMN1 拷贝。将这些数据与 Feldkotter 等人的数据相结合。给出 1,120 条 (3.3%) 正常 5 号染色体中总共有 37 条具有两个 SMN1 拷贝。我们排除了文献中的其他数据（Wirth 等人，1999 年；Gerard 等人，2000 年；Scheffer 等人，2000 年），原因已在别处描述（Ogino 等人，出版中）。根据这些数字，~3.2%（即 0.033×[1–0.017]）的携带者具有 2+0 基因型。因此，用于检测一般人群中携带者的 SMN 剂量分析的灵敏度为 ∼95.1%，而用于检测缺乏 SMN1 的受影响个体的家庭中的携带者的灵敏度为 ∼96.7%（即 0.951/[1-0.017]）。
Feldkotter 等人利用 SMN1 和 SMN2 外显子 7 和内含子 7 中的单核苷酸差异。使用基因特异性引物对仅扩增 SMN1 或仅扩增 SMN2。每个基因的引物对在 3' 端的最后一个或倒数第二个核苷酸处与另一个基因不匹配。这些错配对应于外显子 7（正向引物）和内含子 7（反向引物）的序列差异。 SMN1 和 SMN2 之间的基因转换已在其他地方进行过审查（Burghes 1997），可能会使这种方法变得复杂。如果将 SMN1 外显子 7 序列 (C) 转换为 SMN2 外显子 7 序列 (T)，但 SMN1 内含子 7 序列保持不变，则转换后的基因可能在体内发挥 SMN2 基因的作用。这是因为 SMN2 外显子 7 中的 C→T 转变虽然在翻译上是沉默的，但会降低外显子剪接增强子的活性，从而导致全长蛋白质的表达减少（Lorson 等人，1999 年；Monani 等人，1999 年；Jong 等人，2000 年）。通过使用Feldkotter等人提供的基因特异性引物，转化的基因可能具有与正常SMN1或SMN2基因不同的扩增效率。仅针对外显子 7 中功能重要的多态性而非内含子 7 中的多态性具有等位基因特异性的引物可能会缓解此问题。
To the Editor:
Feldkotter et al. (2002) recently reported a new method to determine, on the basis of real-time, quantitative PCR, copy numbers of SMN1 (MIM 600354) and SMN2 (MIM 601627). Their method allows a greater degree of automation and a faster turnaround time than do methods that have been described elsewhere (McAndrew et al. 1997; Chen et al. 1999; Wirth et al. 1999; Gerard et al. 2000; Scheffer et al. 2000; Ogino et al. 2001). Using their new method, they demonstrated that the copy number of SMN2—which is the centromeric homologue of SMN1, the disease gene for spinal muscular atrophy (SMA [MIM 253300 for type I; MIM 253550 for type II; and MIM 253400 for type III])—influences the severity of SMA in affected individuals with homozygous deletions of SMN1. They found that, the greater the copy number of SMN2 was, the greater the likelihood was of a milder SMA type. Because this correlation is not absolute, they used Bayesian-type analyses to determine the posterior probabilities of developing each SMA type, with both a homozygous deletion of SMN1 and a given copy number of SMN2. We discuss below several important ethical, prognostic, and technical issues raised in their article.
In table 6, Feldkotter et al. report “Probabilities That an Unaffected Who Has Been Tested after Birth and Has Been Found to Carry a Homozygous Absence of SMN1 Will Develop Type I, II, or III SMA, on the Basis of Number of SMN2 Copies.” SMA is usually a childhood-onset disease, and testing of unaffected children is ethically problematic. We agree with the American Society of Human Genetics and the American College of Medical Genetics that “Timely medical benefit to the child should be the primary justification for genetic testing in children and adolescents” (American Society of Human Genetics Board of Directors and American College of Medical Genetics Board of Directors 1995, p. 1233). Since there are currently no effective treatments, presymptomatic or otherwise, for SMA, the timely medical benefit of the testing of unaffected children is unclear.
For the purpose of predicting SMA type from the SMN2 copy number in unaffected children who lack SMN1, Feldkotter et al. perform Bayesian-type analyses by use of odds ratios, rather than conventional conditional probabilities. For the prior probabilities, they use the distribution of types of SMA among individuals affected with SMA: .51, for type I; .32, for type II; and .17, for type III. Even if one were to test unaffected children in this way, for this purpose, these prior probabilities would not be the correct ones to use for Bayesian or Bayesian-type analyses. If a child is asymptomatic at age 10 mo, for example, he or she is much less likely to have type I SMA than to have one of the other types (Zerres and Rudnik-Schoneborn 1995). One would have to incorporate the conditional probabilities of being asymptomatic at a particular age, for the hypothesis of each SMA type.
The data on SMN2 copy number given by Feldkotter et al. could be used in prenatal testing, to predict SMA type. However, the prior probabilities that they use would be applicable only if the family history of SMA is of an unknown type. Although families with more than one type of SMA have been described—and are far from rare—knowing the type of SMA in an affected family member increases the prior probability of that type of SMA in a relative who is at risk of developing SMA. If the type of SMA in that affected family member is unknown, then the distribution of SMA types among all individuals with SMA would be relevant to the assignment of prior probabilities.
On the basis of all reported data, Feldkotter et al. state that, because two SMN1 copies were found on 20/834 (2.4%) healthy chromosomes, “4.8% of normal individuals would be misinterpreted as noncarriers on the basis of the direct SMN1 test” (p. 365). Actually, these data imply that ∼4.8% of noncarriers would have three copies of SMN1 and that ∼2.4% of carriers with an SMN1 deletion on one chromosome 5 would have two SMN1 copies on the other chromosome 5. We have referred to the latter as the “2+0” genotype (Chen et al. 1999). Taking into account the ∼1.7% of carriers who have an intragenic mutation undetectable as an SMN1 exon 7 deletion, Feldkotter et al. state that this “reduces the sensitivity of the test to 93.5% for a person from the general population” (p. 365). Combining the ∼1.7% of carriers who have an intragenic mutation with the ∼2.4% (i.e., 0.024×[1-0.017]) of carriers who have the 2+0 genotype gives the overall sensitivity of SMN dosage analysis for the detection of SMA carriers in the general population as ∼95.9%. If an affected family member were known to have a homozygous deletion of SMN1, then the sensitivity of SMN dosage analysis for the detection of carriers among unaffected family members would be ∼97.6% (i.e., 0.959/[1-0.017]). This is because the probability of an intragenic-mutation carrier in this family is greatly decreased relative to the probability of a 2+0 carrier (Ogino et al., in press).
Updating our combined data (McAndrew et al. 1997; Ogino et al. 2002, in press) gives 23 of 590 normal chromosomes 5 that have two copies of SMN1. Combining these data with those of Feldkotter et al. gives a total of 37 of 1,120 (3.3%) normal chromosomes 5 that have two copies of SMN1. We excluded other data in the literature (Wirth et al. 1999; Gerard et al. 2000; Scheffer et al. 2000), for reasons described elsewhere (Ogino et al., in press). On the basis of these numbers, ∼3.2% (i.e., 0.033×[1–0.017]) of carriers would have the 2+0 genotype. Therefore, the sensitivity of SMN dosage analysis for the detection of carriers in the general population would be ∼95.1%, and that for the detection of carriers in a family with an affected individual lacking SMN1 would be ∼96.7% (i.e., 0.951/[1-0.017]).
Taking advantage of the single nucleotide differences between SMN1 and SMN2 in both exon 7 and intron 7, Feldkotter et al. used gene-specific primer pairs to amplify only SMN1 or only SMN2. The primer pairs for each gene were mismatched for the other gene at either the final or the penultimate nucleotide from the 3′ end. These mismatches corresponded to the sequence differences in exon 7 (forward primers) and intron 7 (reverse primers). Gene conversions between SMN1 and SMN2, which have been reviewed elsewhere (Burghes 1997), could potentially complicate this approach. If the SMN1 exon 7 sequence (C) were converted to the SMN2 exon 7 sequence (T) but the SMN1 intron 7 sequence remained the same, the converted gene would presumably function as an SMN2 gene in vivo. This is because the C→T transition in exon 7 of SMN2, although translationally silent, decreases the activity of an exonic splicing enhancer, so that less full-length protein is expressed (Lorson et al. 1999; Monani et al. 1999; Jong et al. 2000). By use of the gene-specific primers given by Feldkotter et al., the converted gene might have a different amplification efficiency from that of the normal SMN1 or SMN2 gene. Primers that are allele specific only for the functionally important polymorphism in exon 7 but not for the polymorphism in intron 7 might alleviate this problem.
影响因子：
3.5
作者：
Monani, UR;Lorson, CL;McPherson, JD
通讯作者：
McPherson, JD