植入前遗传学诊断
单倍型
拷贝数变化
单核苷酸多态性
SNP阵列
生物
遗传学
非整倍体
计算生物学
SNP公司
全基因组测序
DNA测序
基因组
染色体
基因
等位基因
基因型
胚胎
作者
Daniel Backenroth,Fouad Zahdeh,Yehuda Kling,Aharon Peretz,Tzvia Rosen,Dina Kort,Sharon Zeligson,Tal Dror,Sophie Kirshberg,Efrat Burak,Reeval Segel,Ephrat Levy‐Lahad,David Zangen,Gheona Altarescu,Shai Carmi,David A. Zeevi
标识
DOI:10.1038/s41436-018-0351-7
摘要
To develop an economical, user-friendly, and accurate all-in-one next-generation sequencing (NGS)-based workflow for single-cell gene variant detection combined with comprehensive chromosome screening in a 24-hour workflow protocol.We subjected single lymphoblast cells or blastomere/blastocyst biopsies from four different families to low coverage (0.3×-1.4×) genome sequencing. We combined copy-number variant (CNV) detection and whole-genome haplotype phase prediction via Haploseek, a novel, user-friendly analysis pipeline. We validated haplotype predictions for each sample by comparing with clinical preimplantation genetic diagnosis (PGD) case results or by single-nucleotide polymorphism (SNP) microarray analysis of bulk DNA from each respective lymphoblast culture donor. CNV predictions were validated by established commercial kits for single-cell CNV prediction.Haplotype phasing of the single lymphoblast/embryo biopsy sequencing data was highly concordant with relevant ground truth haplotypes in all samples/biopsies from all four families. In addition, whole-genome copy-number assessments were concordant with the results of a commercial kit.Our results demonstrate the establishment of a reliable method for all-in-one molecular and chromosomal diagnosis of single cells. Important features of the Haploseek pipeline include rapid sample processing, rapid sequencing, streamlined analysis, and user-friendly reporting, so as to expedite clinical PGD implementation.
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