Abstract：
Population-wide carrier screening for spinal muscular atrophy (SMA) is recommended by professional organizations to facilitate informed reproductive options. However, genetic screening for SMN1 2 + 0 carriers, accounting for 3%-8% of all SMA carriers, has been challenging due to the large gene size and long distance between the 2 SMN genes.
Here we repurposed a previously developed long-read sequencing-based approach, termed comprehensive analysis of SMA (CASMA), to identify SMN1 2 + 0 carriers through haplotype analysis in family trios (CASMA-trio). Bioinformatics pipelines were developed for accurate haplotype analysis and SMN1 2 + 0 deduction. Seventy-nine subjects from 24 families composed of, at the minimum, 3 were enrolled, and CASMA-trio was employed to determine whether an index subject with 2 SMN1 copies was a 2 + 0 carrier in these families. For the proof-of-principle, SMN2 2 + 0 was also analyzed.
Among the 16 subjects with 2 SMN1 copies, CASMA-trio identified 5 subjects from 4 families as SMN1 2 + 0 carriers, which was consistent with pedigree analysis involving an affected proband. CASMA-trio also identified SMN2 2 + 0 in six out of 43 subjects with 2 SMN2 copies. Additionally, CASMA-trio successfully determined the distribution pattern of SMN1 and SMN2 genes on 2 alleles in all 79 subjects.
CASMA-trio represents an effective and universal approach for SMN1 2 + 0 carriers screening, as it does not reply on the presence of an affected proband, certain single-nucleotide polymorphisms, ethnicity-specific haplotypes, or complicated single-nucleotide polymorphism analysis across 3 generations. Incorporating CASMA-trio into existing SMA carrier screening programs will greatly reduce residual risk ratio.
Here we repurposed a previously developed long-read sequencing-based approach, termed comprehensive analysis of SMA (CASMA), to identify SMN1 2 + 0 carriers through haplotype analysis in family trios (CASMA-trio). Bioinformatics pipelines were developed for accurate haplotype analysis and SMN1 2 + 0 deduction. Seventy-nine subjects from 24 families composed of, at the minimum, 3 were enrolled, and CASMA-trio was employed to determine whether an index subject with 2 SMN1 copies was a 2 + 0 carrier in these families. For the proof-of-principle, SMN2 2 + 0 was also analyzed.
Among the 16 subjects with 2 SMN1 copies, CASMA-trio identified 5 subjects from 4 families as SMN1 2 + 0 carriers, which was consistent with pedigree analysis involving an affected proband. CASMA-trio also identified SMN2 2 + 0 in six out of 43 subjects with 2 SMN2 copies. Additionally, CASMA-trio successfully determined the distribution pattern of SMN1 and SMN2 genes on 2 alleles in all 79 subjects.
CASMA-trio represents an effective and universal approach for SMN1 2 + 0 carriers screening, as it does not reply on the presence of an affected proband, certain single-nucleotide polymorphisms, ethnicity-specific haplotypes, or complicated single-nucleotide polymorphism analysis across 3 generations. Incorporating CASMA-trio into existing SMA carrier screening programs will greatly reduce residual risk ratio.
摘要：
背景：专业组织建议对脊髓性肌萎缩症（SMA）进行全人群携带者筛查，以促进知情的生殖选择。然而,SMN12+0携带者的遗传筛查，占所有SMA载体的3%-8%，由于2个SMN基因之间的大基因大小和长距离，一直具有挑战性。
方法：在这里，我们重新利用了以前开发的基于长读数测序的方法，称为SMA综合分析(CASMA)，通过家族三重奏（CASMA-trio）中的单倍型分析鉴定SMN120携带者。开发了生物信息学管道，用于准确的单倍型分析和SMN120推导。来自24个家庭的79名受试者，至少,3人报名参加,和CASMA-trio用于确定具有2个SMN1拷贝的索引受试者是否是这些家庭中的20携带者。为了原理证明，还分析了SMN22+0。
结果：在16名具有2个SMN1拷贝的受试者中，CASMA-trio将来自4个家庭的5名受试者鉴定为SMN120携带者，这与涉及受影响先证者的谱系分析一致。CASMA-trio还在43名受试者中的6名具有2个SMN2拷贝的受试者中鉴定出SMN22+0。此外,CASMA-trio成功确定了所有79名受试者中2个等位基因上SMN1和SMN2基因的分布模式。
结论：CASMA-trio代表了SMN120携带者筛查的有效且通用的方法，因为它不回答存在受影响的先证者，某些单核苷酸多态性，种族特异性单倍型，或复杂的单核苷酸多态性分析跨3代。将CASMA-trio纳入现有的SMA载体筛查计划将大大降低残余风险率。
方法：在这里，我们重新利用了以前开发的基于长读数测序的方法，称为SMA综合分析(CASMA)，通过家族三重奏（CASMA-trio）中的单倍型分析鉴定SMN120携带者。开发了生物信息学管道，用于准确的单倍型分析和SMN120推导。来自24个家庭的79名受试者，至少,3人报名参加,和CASMA-trio用于确定具有2个SMN1拷贝的索引受试者是否是这些家庭中的20携带者。为了原理证明，还分析了SMN22+0。
结果：在16名具有2个SMN1拷贝的受试者中，CASMA-trio将来自4个家庭的5名受试者鉴定为SMN120携带者，这与涉及受影响先证者的谱系分析一致。CASMA-trio还在43名受试者中的6名具有2个SMN2拷贝的受试者中鉴定出SMN22+0。此外,CASMA-trio成功确定了所有79名受试者中2个等位基因上SMN1和SMN2基因的分布模式。
结论：CASMA-trio代表了SMN120携带者筛查的有效且通用的方法，因为它不回答存在受影响的先证者，某些单核苷酸多态性，种族特异性单倍型，或复杂的单核苷酸多态性分析跨3代。将CASMA-trio纳入现有的SMA载体筛查计划将大大降低残余风险率。
