Translational Genomics Lab, Medical Genetics Institute, Shaare Zedek Medical Center, Jerusalem, Israel.
Braun School of Public Health and Community Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
Genet Med. 2021 Jul;23(7):1334-1340. doi: 10.1038/s41436-021-01145-6. Epub 2021 Mar 26.
We previously developed Haploseek, a method for comprehensive preimplantation genetic testing (PGT). However, some key features were missing, and the method has not yet been systematically validated.
We extended Haploseek to incorporate DNA from embryo grandparents and to allow testing of variants on chromosome X or in regions where parents share common haplotypes. We then validated Haploseek on 151 embryo biopsies from 27 clinical PGT cases. We sequenced all biopsies to low coverage (0.2×), and performed single-nucleotide polymorphism (SNP) microarray genotyping on the embryos' parents and siblings/grandparents. We used the extended Haploseek to predict chromosome copy-number variants (CNVs) and relevant variant-flanking haplotypes in each embryo. We validated haplotype predictions for each clinical sample against polymerase chain reaction (PCR)-based PGT case results, and CNV predictions against established commercial kits.
For each of the 151 embryo biopsies, all Haploseek-derived haplotypes and CNVs were concordant with clinical PGT results. The cases included 17 autosomal dominant, 5 autosomal recessive, and 3 X-linked monogenic disorders. In addition, we evaluated 1 Robertsonian and 2 reciprocal translocations, and 17 cases of chromosome copy-number counting were performed.
Our results demonstrate that Haploseek is clinically accurate and fit for all standard clinical PGT applications.
我们之前开发了 Haploseek 方法，用于综合植入前遗传学检测（PGT）。然而，该方法仍存在一些关键特征缺失，且尚未进行系统验证。
我们扩展了 Haploseek 方法，纳入胚胎祖父母的 DNA，并允许检测 X 染色体或父母共享共同单倍型的区域中的变体。然后，我们在 27 个临床 PGT 案例中的 151 个胚胎活检中验证了 Haploseek 方法。我们对所有活检进行低覆盖率（0.2×）测序，并对胚胎父母和兄弟姐妹/祖父母进行单核苷酸多态性（SNP）微阵列基因分型。我们使用扩展的 Haploseek 方法预测每个胚胎的染色体拷贝数变异（CNV）和相关变体侧翼单倍型。我们针对每个临床样本，通过聚合酶链反应（PCR）为基础的 PGT 案例结果，对基于 Haploseek 的单倍型预测进行验证，针对已建立的商业试剂盒对 CNV 预测进行验证。
对于 151 个胚胎活检中的每一个，Haploseek 衍生的所有单倍型和 CNV 都与临床 PGT 结果一致。这些案例包括 17 种常染色体显性遗传、5 种常染色体隐性遗传和 3 种 X 连锁单基因疾病。此外，我们还评估了 1 例罗伯逊易位和 2 例相互易位，以及 17 例染色体拷贝数计数。
我们的结果表明，Haploseek 具有临床准确性，适用于所有标准的临床 PGT 应用。
