Bo Gao , Yi Jiang , Mingyu Han , Xiaowen Ji , Dejun Zhang , Lihua Wu , Xue Gao , Shasha Huang , Chaoyue Zhao , Yu Su , Suyan Yang , Xin Zhang , Na Liu , Lu Han , Lihai Wang , Lina Ren , Jinyuan Yang , Jian Wu , Yongyi Yuan , Pu Dai
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Fifty couples carrying pathogenic variants associated with ARNSHL in either <em>GJB2</em> or <em>SLC26A4</em> were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of <em>GJB2</em> and <em>SLC26A4</em>, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. 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引用次数: 0
摘要
常染色体隐性非综合征听力损失(ARNSHL)的无创产前诊断(NIPD)直到近几年才鲜有报道。然而,以前的方法无法对具有挑战性的基因组位点(如拷贝数变异、缺失、倒位或基因重组)或无感知基因型的家庭进行诊断。在此,本研究评估了基于相对单倍型剂量分析(RHDO)的NIPD在确定ARNSHL风险孕妇的胎儿基因分型方面的性能。研究人员招募了50对夫妇,其中一方或双方携带与ARNSHL相关的致病变异。基于 RHDO 的靶向链接读数测序结合全基因覆盖探针,对 49 个符合质量控制标准的家庭的胎儿无细胞 DNA 进行了基因分型。使用侵入性产前诊断(IPD)对胎儿羊水样本进行基因分型,以评估 NIPD 的性能。NIPD结果与IPD结果的一致性为100%(49/49)。此外,还成功鉴定出两个存在拷贝数变异和重组的家系。足够的特异性信息单核苷酸多态性、胎儿无细胞 DNA 浓度和测序深度是基于 RHDO 的 NIPD 的先决条件。这种方法的优点是能覆盖和的整个基因,符合拷贝数变异和重组分析的要求,具有显著的灵敏度和特异性。因此,它在临床上有潜力替代传统的 IPD 方法来治疗 ARNSHL。
Targeted Linked-Read Sequencing for Direct Haplotype Phasing of Parental GJB2/SLC26A4 Alleles
Noninvasive prenatal diagnosis (NIPD) for autosomal recessive nonsyndromic hearing loss (ARNSHL) has been rarely reported until recent years. Additionally, the existing method can not be used for challenging genome loci (eg, copy number variations, deletions, inversions, or gene recombinants) or on families without proband genotype. This study assessed the performance of relative haplotype dosage analysis (RHDO)–based NIPD for identifying fetal genotyping in pregnancies at risk of ARNSHL. Fifty couples carrying pathogenic variants associated with ARNSHL in either GJB2 or SLC26A4 were recruited. The RHDO-based targeted linked-read sequencing combined with whole gene coverage probes was used to genotype the fetal cell-free DNA of 49 families who met the quality control standard. Fetal amniocyte samples were genotyped using invasive prenatal diagnosis (IPD) to assess the performance of NIPD. The NIPD results showed 100% (49/49) concordance with those obtained through IPD. Two families with copy number variation and recombination were also successfully identified. Sufficient specific informative single-nucleotide polymorphisms for haplotyping, as well as the fetal cell-free DNA concentration and sequencing depth, are prerequisites for RHDO-based NIPD. This method has the merits of covering the entire genes of GJB2 and SLC26A4, qualifying for copy number variation and recombination analysis with remarkable sensitivity and specificity. Therefore, it has clinical potential as an alternative to traditional IPD for ARNSHL.
期刊介绍:
The Journal of Molecular Diagnostics, the official publication of the Association for Molecular Pathology (AMP), co-owned by the American Society for Investigative Pathology (ASIP), seeks to publish high quality original papers on scientific advances in the translation and validation of molecular discoveries in medicine into the clinical diagnostic setting, and the description and application of technological advances in the field of molecular diagnostic medicine. The editors welcome for review articles that contain: novel discoveries or clinicopathologic correlations including studies in oncology, infectious diseases, inherited diseases, predisposition to disease, clinical informatics, or the description of polymorphisms linked to disease states or normal variations; the application of diagnostic methodologies in clinical trials; or the development of new or improved molecular methods which may be applied to diagnosis or monitoring of disease or disease predisposition.