A precise and cost-efficient whole-genome haplotyping method without probands: preimplantation genetic testing analysis

IF 3.7 2区医学 Q1 OBSTETRICS & GYNECOLOGY

Reproductive biomedicine online Pub Date : 2024-06-21 DOI:10.1016/j.rbmo.2024.104328

Zhiqiang Zhang , Kai Kang , Linan Xu , Xiaolan Li , Shujing He , Ruixia Xu , Lei Jia , Shihui Zhang , Wenlong Su , Peng Sun , Mengnan Gu , Wenqi Shan , Yawen Zhang , Lingyin Kong , Bo Liang , Cong Fang , Zi Ren

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引用次数: 0

Abstract

Research question

Is there a precise and efficient haplotyping method to expand the application of preimplantation genetic testing (PGT)?

Design

In this study, eight cell-line families and 18 clinical families including 99 embryos were used to construct whole-genome haplotyping based on link-read sequencing (Phbol-seq) and optimized analytical workflow with a correction algorithm. The correction algorithm was based on a differentiation of assembly errors and homologous recombination, in which the main feature of parental assembly error was that all embryos (embryo number ≥2) had breakpoints at the same chromosome position.

Results

With Phbol-seq, parental assembly errors and homologous recombination were accurately distinguished and corrected. Using the link-reads (>25% long-reads were ≥30 kilobases [kb]), complete genome-wide parental haplotypes were constructed, and the consistency of the typing results of each chromosome with a conventional method requiring other family members was more than 95%. In addition, the length of N50 contigs was 11.03–16.2 million bases (mb), which was far beyond the N50 contigs from long-read sequencing (148–863 kb). The complete haplotype analysis of all embryos could be performed by Phbol-seq and revealed 100% concordance with the available diagnostic results obtained by the conventional method requiring other family members.

Conclusions

: Phbol-seq has high clinical value as a precise and cost-efficient whole-genome haplotyping method without probands as part of PGT and other genetic research, which could promote the application of PGT to decrease the birth of children with genetic diseases and the development of linkage-related genetic research.

查看原文本刊更多论文

精确且经济高效的无探针全基因组单倍型分析方法：胚胎植入前基因检测分析。

研究问题：是否有一种精确、高效的单倍型分析方法来扩大植入前基因检测（PGT）的应用范围？本研究利用8个细胞系家系和18个临床家系（包括99个胚胎）构建了基于链接读取测序（Phbol-seq）的全基因组单倍型，并利用校正算法优化了分析工作流程。校正算法基于组装错误和同源重组的区分，其中亲本组装错误的主要特征是所有胚胎（胚胎数≥2）都在相同的染色体位置有断点：结果：利用Phbol-seq，亲本组装错误和同源重组得到了准确的区分和校正。利用链接读数（>25%的长读数≥30 千碱基[kb]），构建了完整的全基因组亲本单倍型，每条染色体的分型结果与需要其他家族成员的传统方法的一致性超过 95%。此外，N50 等位基因的长度为 11.03-16.2 百万碱基（mb），远远超过了长线程测序的 N50 等位基因长度（148-863 kb）。通过 Phbol-seq 可以对所有胚胎进行完整的单倍型分析，结果显示，与传统方法获得的需要其他家庭成员参与的诊断结果的一致性达到 100%：结论：Phbol-seq 作为一种精确、低成本的全基因组单倍型分析方法，在 PGT 及其他遗传学研究中具有很高的临床价值，可促进 PGT 的应用，减少遗传病患儿的出生，并推动与关联相关的遗传学研究的发展。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Reproductive biomedicine online 医学-妇产科学

CiteScore

7.20

自引率

7.50%

发文量

391

审稿时长

50 days

期刊介绍： Reproductive BioMedicine Online covers the formation, growth and differentiation of the human embryo. It is intended to bring to public attention new research on biological and clinical research on human reproduction and the human embryo including relevant studies on animals. It is published by a group of scientists and clinicians working in these fields of study. Its audience comprises researchers, clinicians, practitioners, academics and patients. Context: The period of human embryonic growth covered is between the formation of the primordial germ cells in the fetus until mid-pregnancy. High quality research on lower animals is included if it helps to clarify the human situation. Studies progressing to birth and later are published if they have a direct bearing on events in the earlier stages of pregnancy.