Multiple displacement amplification as the first step can increase the diagnostic efficiency of preimplantation genetic testing for monogenic disease for β‐thalassemia

2019 ◽  
Vol 45 (8) ◽  
pp. 1515-1521
Author(s):  
Yu Fu ◽  
Xiaoting Shen ◽  
Dongjia Chen ◽  
Zengyan Wang ◽  
Canquan Zhou
Keyword(s):  
Genetic Testing ◽  
Multiple Displacement Amplification ◽  
Monogenic Disease ◽  
Diagnostic Efficiency ◽  
Preimplantation Genetic Testing

scholarly journals Haplotyping by linked-read sequencing (HLRS) of the genetic disease carriers for preimplantation genetic testing without a proband or relatives

2020 ◽  
Author(s):  
Qing Li ◽  
Yan Mao ◽  
Shaoying Li ◽  
Hongzi Du ◽  
Wenzhi He ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Genetic Disease ◽  
De Novo ◽  
Monogenic Disease ◽  
Nucleotide Polymorphisms ◽  
De Novo Mutations ◽  
Preimplantation Genetic Testing ◽  
Linkage Analyses ◽  
Alpha Thalassemia ◽  
Polar Bodies

Abstract Background: In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes.. Typically, haplotype resolution is obtained by genotyping multiple polymorphic markers in both parents and a proband or a relative. Sometimes, single sperm typing, or tests on the polar bodies may also be useful. Nevertheless, this process is time-consuming. At present, there was no simple linkage analysis strategy for patients without affected relatives.Method: To solve this problem, we established a haplotyping by linked-read sequencing (HLRS) method without the requirement for additional relatives. First, the haplotype of the genetic disease carriers in the family was constructed by linked-read sequencing, and then the informative single nucleotide polymorphisms (SNPs) in upstream and downstream mutation region were selected to construct the embryo haplotype and to determine whether the embryo was carrying the mutation. Two families were selected to validate this method; one with alpha thalassemia and the other with NDP gene disorder.Results: The haplotyping by linked-read sequencing (HLRS) method was successfully applied to construct parental haplotypes without recruiting additional family members; the method was also validated for PGT-M. The mutation carriers in these families were sequenced by linked-read sequencing, and their haplotypes were successfully phased. Adjacent SNPs of the mutation gene were identified. The informative SNPs were chosen for linkage analyses to identify the carrier embryos. For the alpha thalassemia family, a normal blastocyst was transferred to the uterus and the accuracy of PGT-M was confirmed by amniocentesis at 16 weeks of gestation. Conclusions: Our results suggest that HLRS can be applied for PGT-M of monogenic disorders or de novo mutations where the mutations haplotype cannot be determined due to absence of affected relatives. Keywords: Preimplantation Genetic Testing for monogenic disease, Linked-read sequencing, Linkage analyses, Haplotype

68. PREIMPLANTATION GENETIC TESTING OF MONOGENIC DISEASE: EXPERIENCE IN RUSSIA

2019 ◽  
Vol 39 ◽  
pp. e68-e69
Author(s):  
S. Zhikrivetskaya Olegovna ◽  
Y. Volkova Leonidovna ◽  
E. Musatova Valerievna ◽  
Y. Sofronova Vladislavovna ◽  
N. Shirokova Anatolievna ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Monogenic Disease ◽  
Preimplantation Genetic Testing ◽  
Disease Experience

scholarly journals Preimplantation genetic testing for a family with usher syndrome through targeted sequencing and haplotype analysis

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Haining Luo ◽  
Chao Chen ◽  
Yun Yang ◽  
Yinfeng Zhang ◽  
Yuan Yuan ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Rare Variant ◽  
Genomic Dna ◽  
Haplotype Analysis ◽  
Multiple Displacement Amplification ◽  
Usher Syndrome ◽  
Nucleotide Polymorphisms ◽  
Preimplantation Genetic Testing ◽  
Targeted Capture ◽  
Capture Sequencing

Abstract Background Preimplantation genetic testing for monogenic defects (PGT-M) has been available in clinical practice. This study aimed to validate the applicability of targeted capture sequencing in developing personalized PGT-M assay. Methods One couple at risk of transmitting Usher Syndrome to their offspring was recruited to this study. Customized capture probe targeted at USH2A gene and 350 kb flanking region were designed for PGT-M. Eleven blastocysts were biopsied and amplified by using multiple displacement amplification (MDA) and capture sequencing. A hidden Markov model (HMM) assisted haplotype analysis was performed to deduce embryo’s genotype by using single nucleotide polymorphisms (SNPs) identified in each sample. The embryo without paternal rare variant was implanted and validated by conventional prenatal or postnatal diagnostic means. Results Four embryos were diagnosed as free of father’s rare variant, two were transferred and one achieved a successful pregnancy. The fetal genotype was confirmed by Sanger sequencing of fetal genomic DNA obtained by amniocentesis. The PGT-M and prenatal diagnosis results were further confirmed by the molecular diagnosis of the baby’s genomic DNA sample. The auditory test showed that the hearing was normal. Conclusions Targeted capture sequencing is an effective and convenient strategy to develop customized PGT-M assay.

scholarly journals PREIMPLANTATION GENETIC TESTING: Preimplantation genetic testing for polygenic disease risk

Reproduction ◽  
2020 ◽  
Vol 160 (5) ◽  
pp. A13-A17 ◽  
Author(s):  
Nathan R Treff ◽  
Diego Marin ◽  
Louis Lello ◽  
Stephen Hsu ◽  
Laurent C A M Tellier
Keyword(s):  
Clinical Practice ◽  
Genetic Testing ◽  
Disease Risk ◽  
Population Level ◽  
Standard Of Care ◽  
Primary Objective ◽  
Monogenic Disease ◽  
Preimplantation Genetic Testing ◽  
Polygenic Disease ◽  
Risk Scoring

Since its introduction to clinical practice, preimplantation genetic testing (PGT) has become a standard of care for couples at risk of having children with monogenic disease and for chromosomal aneuploidy to improve outcomes for patients with infertility. The primary objective of PGT is to reduce the risk of miscarriage and genetic disease and to improve the success of infertility treatment with the delivery of a healthy child. Until recently, the application of PGT to more common but complex polygenic disease was not possible, as the genetic contribution to polygenic disease has been difficult to determine, and the concept of embryo selection across multiple genetic loci has been difficult to comprehend. Several achievements, including the ability to obtain accurate, genome-wide genotypes of the human embryo and the development of population-level biobanks, have now made PGT for polygenic disease risk applicable in clinical practice. With the rapid advances in embryonic polygenic risk scoring, diverse considerations beyond technical capability have been introduced.

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